Correlation between gene mutation status and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1Q81BZD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1Q81BZD
Overview
Introduction

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

Summary

Testing the association between mutation status of 37 genes and 12 molecular subtypes across 289 patients, 64 significant findings detected with P value < 0.05 and Q value < 0.25.

  • IDH1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • NOTCH1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • FUBP1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NF1 mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • PIK3CA mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 37 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 64 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
CIC 54 (19%) 235 0.0434
(1.00) 		0.00276
(0.861) 		1e-05
(0.00382) 		1e-05
(0.00382) 		8e-05
(0.0265) 		0.5
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		1e-05
(0.00382) 		2e-05
(0.00678) 		2e-05
(0.00678) 		1e-05
(0.00382)
IDH1 220 (76%) 69 0.272
(1.00) 		0.887
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.00233
(0.736) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.00661
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		1e-05
(0.00382)
NOTCH1 29 (10%) 260 0.463
(1.00) 		0.247
(1.00) 		0.0005
(0.162) 		1e-05
(0.00382) 		0.892
(1.00) 		0.859
(1.00) 		1e-05
(0.00382) 		4e-05
(0.0133) 		9e-05
(0.0296) 		0.00056
(0.181) 		8e-05
(0.0265) 		0.0006
(0.193)
PTEN 13 (4%) 276 1e-05
(0.00382) 		1e-05
(0.00382) 		0.0006
(0.193) 		0.00525
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.0369
(1.00) 		1e-05
(0.00382) 		0.00047
(0.153) 		1e-05
(0.00382)
TP53 146 (51%) 143 0.0628
(1.00) 		0.00459
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.0296
(1.00) 		0.5
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		3e-05
(0.01) 		3e-05
(0.01) 		0.00145
(0.46) 		1e-05
(0.00382)
ATRX 118 (41%) 171 0.0181
(1.00) 		0.126
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.17
(1.00) 		0.778
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.00025
(0.0815) 		2e-05
(0.00678) 		0.0376
(1.00) 		1e-05
(0.00382)
FUBP1 26 (9%) 263 0.0246
(1.00) 		0.0077
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.0181
(1.00) 		0.738
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		6e-05
(0.0199) 		0.0104
(1.00) 		0.513
(1.00) 		0.0002
(0.0654)
EGFR 17 (6%) 272 1e-05
(0.00382) 		1e-05
(0.00382) 		0.00748
(1.00) 		0.0235
(1.00) 		1e-05
(0.00382) 		1e-05
(0.00382) 		0.437
(1.00) 		1e-05
(0.00382) 		0.00607
(1.00) 		1e-05
(0.00382)
PIK3CA 25 (9%) 264 0.00071
(0.227) 		1e-05
(0.00382) 		0.568
(1.00) 		0.733
(1.00) 		0.00546
(1.00) 		0.00072
(0.23) 		0.368
(1.00) 		0.27
(1.00) 		0.287
(1.00) 		0.0438
(1.00)
NF1 19 (7%) 270 0.0664
(1.00) 		2e-05
(0.00678) 		0.0311
(1.00) 		0.222
(1.00) 		0.019
(1.00) 		0.00773
(1.00) 		0.844
(1.00) 		0.00273
(0.854) 		0.163
(1.00) 		0.00012
(0.0394)
IDH2 12 (4%) 277 0.0158
(1.00) 		0.015
(1.00) 		0.518
(1.00) 		0.184
(1.00) 		0.00244
(0.769) 		0.00137
(0.436) 		0.109
(1.00) 		0.0192
(1.00) 		0.00264
(0.829) 		0.0737
(1.00)
PIK3R1 13 (4%) 276 0.603
(1.00) 		0.587
(1.00) 		0.0788
(1.00) 		0.0352
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.786
(1.00) 		0.207
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.72
(1.00)
STK19 8 (3%) 281 0.478
(1.00) 		0.0828
(1.00) 		0.0174
(1.00) 		0.142
(1.00) 		0.616
(1.00) 		0.477
(1.00) 		0.386
(1.00) 		0.899
(1.00) 		0.277
(1.00) 		0.88
(1.00)
ARID1A 12 (4%) 277 0.729
(1.00) 		0.481
(1.00) 		0.457
(1.00) 		0.796
(1.00) 		0.173
(1.00) 		0.156
(1.00) 		0.712
(1.00) 		0.693
(1.00) 		0.197
(1.00) 		0.486
(1.00)
GAGE2B 4 (1%) 285 0.685
(1.00) 		1
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.175
(1.00) 		0.325
(1.00)
CREBZF 5 (2%) 284 0.171
(1.00) 		0.0363
(1.00) 		0.0854
(1.00) 		0.00441
(1.00) 		0.576
(1.00) 		0.411
(1.00) 		0.372
(1.00) 		0.0691
(1.00) 		0.113
(1.00) 		0.315
(1.00)
TCF12 8 (3%) 281 0.597
(1.00) 		0.485
(1.00) 		0.199
(1.00) 		0.448
(1.00) 		0.246
(1.00) 		0.59
(1.00) 		0.344
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SMARCA4 13 (4%) 276 0.129
(1.00) 		0.195
(1.00) 		0.315
(1.00) 		0.848
(1.00) 		0.139
(1.00) 		0.567
(1.00) 		0.0704
(1.00) 		0.119
(1.00) 		0.594
(1.00) 		0.265
(1.00)
VAV3 8 (3%) 281 0.479
(1.00) 		0.506
(1.00) 		0.962
(1.00) 		0.57
(1.00) 		0.0392
(1.00) 		0.478
(1.00) 		0.699
(1.00) 		0.42
(1.00) 		0.545
(1.00) 		0.349
(1.00)
TMEM216 3 (1%) 286 0.338
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.793
(1.00) 		0.895
(1.00) 		0.887
(1.00) 		0.404
(1.00) 		0.599
(1.00) 		0.118
(1.00) 		0.329
(1.00)
ROBO3 4 (1%) 285 0.684
(1.00) 		0.891
(1.00) 		0.642
(1.00) 		0.72
(1.00) 		0.605
(1.00) 		0.539
(1.00) 		1
(1.00) 		1
(1.00)
IRS4 5 (2%) 284 0.212
(1.00) 		0.837
(1.00) 		1
(1.00) 		0.196
(1.00) 		0.858
(1.00) 		0.932
(1.00) 		0.925
(1.00) 		1
(1.00) 		0.0904
(1.00) 		1
(1.00)
HTRA2 4 (1%) 285 0.125
(1.00) 		0.674
(1.00) 		0.414
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.835
(1.00) 		0.269
(1.00) 		0.875
(1.00)
EIF1AX 4 (1%) 285 0.364
(1.00) 		0.318
(1.00) 		0.376
(1.00) 		0.264
(1.00) 		0.868
(1.00) 		0.842
(1.00) 		0.895
(1.00) 		0.255
(1.00) 		0.372
(1.00) 		0.0762
(1.00)
FAM47C 7 (2%) 282 0.385
(1.00) 		0.344
(1.00) 		0.246
(1.00) 		0.315
(1.00) 		0.0592
(1.00) 		0.0291
(1.00) 		0.142
(1.00) 		0.0346
(1.00) 		0.00537
(1.00) 		0.189
(1.00)
PLCG1 4 (1%) 285 0.00331
(1.00) 		0.0156
(1.00) 		0.165
(1.00) 		0.669
(1.00) 		0.348
(1.00) 		0.195
(1.00) 		0.0923
(1.00) 		0.259
(1.00)
DDX5 4 (1%) 285 0.683
(1.00) 		1
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.205
(1.00) 		0.139
(1.00) 		0.439
(1.00) 		0.419
(1.00) 		0.129
(1.00) 		0.754
(1.00)
ZNF709 3 (1%) 286 0.792
(1.00) 		0.818
(1.00) 		0.887
(1.00) 		0.795
(1.00) 		0.0673
(1.00) 		0.194
(1.00) 		0.866
(1.00) 		0.603
(1.00) 		0.787
(1.00) 		1
(1.00)
TRERF1 3 (1%) 286 0.0512
(1.00) 		0.314
(1.00) 		0.441
(1.00) 		0.0685
(1.00) 		0.194
(1.00) 		0.555
(1.00) 		0.864
(1.00) 		0.601
(1.00) 		0.62
(1.00) 		0.769
(1.00)
BCOR 9 (3%) 280 1
(1.00) 		0.867
(1.00) 		0.255
(1.00) 		0.785
(1.00) 		0.916
(1.00) 		0.886
(1.00) 		0.847
(1.00) 		0.391
(1.00) 		0.926
(1.00) 		0.827
(1.00) 		0.394
(1.00) 		0.123
(1.00)
SRPX 3 (1%) 286 0.469
(1.00) 		0.21
(1.00) 		0.337
(1.00) 		1
(1.00) 		0.17
(1.00) 		0.0925
(1.00) 		0.194
(1.00) 		0.42
(1.00) 		0.485
(1.00) 		0.118
(1.00)
DOCK5 6 (2%) 283 0.0776
(1.00) 		0.0897
(1.00) 		0.374
(1.00) 		0.226
(1.00) 		0.134
(1.00) 		0.0726
(1.00) 		0.224
(1.00) 		0.176
(1.00) 		1
(1.00) 		0.716
(1.00)
GIGYF2 4 (1%) 285 0.0341
(1.00) 		0.208
(1.00) 		0.0836
(1.00) 		0.813
(1.00) 		0.541
(1.00) 		0.411
(1.00) 		0.22
(1.00) 		0.0748
(1.00) 		1
(1.00) 		0.255
(1.00)
NIPBL 6 (2%) 283 0.575
(1.00) 		0.0829
(1.00) 		0.841
(1.00) 		0.809
(1.00) 		0.0686
(1.00) 		0.0467
(1.00) 		0.832
(1.00) 		0.504
(1.00) 		0.0838
(1.00) 		0.47
(1.00)
ZBTB20 13 (4%) 276 0.0412
(1.00) 		0.00513
(1.00) 		0.601
(1.00) 		0.356
(1.00) 		0.0741
(1.00) 		0.0807
(1.00) 		0.455
(1.00) 		0.239
(1.00) 		0.116
(1.00) 		0.563
(1.00)
TRIP12 5 (2%) 284 0.307
(1.00) 		0.527
(1.00) 		0.5
(1.00) 		0.282
(1.00) 		0.6
(1.00) 		0.578
(1.00) 		0.856
(1.00) 		0.728
(1.00) 		1
(1.00) 		0.8
(1.00)
KIAA0664 5 (2%) 284 0.729
(1.00) 		0.297
(1.00) 		0.676
(1.00) 		0.26
(1.00) 		0.641
(1.00) 		0.521
(1.00) 		0.278
(1.00) 		0.089
(1.00) 		0.379
(1.00) 		0.22
(1.00)
'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
IDH1 MUTATED 9 7 6
IDH1 WILD-TYPE 0 3 1
'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S2.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
IDH1 MUTATED 6 6 5 5
IDH1 WILD-TYPE 1 1 2 0
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S3.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
IDH1 MUTATED 89 27 102
IDH1 WILD-TYPE 7 42 19

Figure S1.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S4.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
IDH1 MUTATED 126 1 81 12
IDH1 WILD-TYPE 3 41 7 18

Figure S2.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S5.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
IDH1 MUTATED 42 31 61 57
IDH1 WILD-TYPE 10 30 4 16

Figure S3.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00233 (Fisher's exact test), Q value = 0.74

Table S6.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
IDH1 MUTATED 60 90 41
IDH1 WILD-TYPE 6 38 16

Figure S4.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S7.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
IDH1 MUTATED 74 21 46 65 13
IDH1 WILD-TYPE 1 44 5 18 1

Figure S5.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S8.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
IDH1 MUTATED 77 22 53 67
IDH1 WILD-TYPE 1 43 5 20

Figure S6.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
IDH1 MUTATED 56 41 89 34
IDH1 WILD-TYPE 27 16 24 2

Figure S7.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S10.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
IDH1 MUTATED 115 88 17
IDH1 WILD-TYPE 9 20 40

Figure S8.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S11.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
IDH1 MUTATED 76 68 75
IDH1 WILD-TYPE 42 6 20

Figure S9.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S12.  Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
IDH1 MUTATED 50 60 104 5
IDH1 WILD-TYPE 2 6 18 42

Figure S10.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0628 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
TP53 MUTATED 8 4 3
TP53 WILD-TYPE 1 6 4
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00459 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
TP53 MUTATED 5 7 1 2
TP53 WILD-TYPE 2 0 6 3

Figure S11.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S15.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
TP53 MUTATED 91 28 27
TP53 WILD-TYPE 5 41 94

Figure S12.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S16.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
TP53 MUTATED 125 8 3 10
TP53 WILD-TYPE 4 34 85 20

Figure S13.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TP53 MUTATED 33 30 39 29
TP53 WILD-TYPE 19 31 26 44

Figure S14.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S18.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
TP53 MUTATED 37 68 26
TP53 WILD-TYPE 29 60 31
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S19.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
TP53 MUTATED 74 25 3 37 7
TP53 WILD-TYPE 1 40 48 46 7

Figure S15.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S20.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
TP53 MUTATED 75 27 3 41
TP53 WILD-TYPE 3 38 55 46

Figure S16.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.01

Table S21.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
TP53 MUTATED 51 41 45 9
TP53 WILD-TYPE 32 16 68 27

Figure S17.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.01

Table S22.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
TP53 MUTATED 83 40 23
TP53 WILD-TYPE 41 68 34

Figure S18.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.46

Table S23.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
TP53 MUTATED 66 45 34
TP53 WILD-TYPE 52 29 61

Figure S19.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S24.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
TP53 MUTATED 48 30 56 11
TP53 WILD-TYPE 4 36 66 36

Figure S20.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
ATRX MUTATED 8 3 2
ATRX WILD-TYPE 1 7 5

Figure S21.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
ATRX MUTATED 5 5 1 2
ATRX WILD-TYPE 2 2 6 3
'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S27.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
ATRX MUTATED 75 21 22
ATRX WILD-TYPE 21 48 99

Figure S22.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S28.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
ATRX MUTATED 105 2 2 9
ATRX WILD-TYPE 24 40 86 21

Figure S23.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
ATRX MUTATED 27 23 32 26
ATRX WILD-TYPE 25 38 33 47
'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S30.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
ATRX MUTATED 31 53 24
ATRX WILD-TYPE 35 75 33
'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S31.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
ATRX MUTATED 65 15 1 32 5
ATRX WILD-TYPE 10 50 50 51 9

Figure S24.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S32.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
ATRX MUTATED 65 17 1 35
ATRX WILD-TYPE 13 48 57 52

Figure S25.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.081

Table S33.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
ATRX MUTATED 37 35 39 7
ATRX WILD-TYPE 46 22 74 29

Figure S26.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0068

Table S34.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
ATRX MUTATED 69 37 12
ATRX WILD-TYPE 55 71 45

Figure S27.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
ATRX MUTATED 52 36 29
ATRX WILD-TYPE 66 38 66

Figure S28.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S36.  Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
ATRX MUTATED 38 26 48 5
ATRX WILD-TYPE 14 40 74 42

Figure S29.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
CIC MUTATED 0 5 2
CIC WILD-TYPE 9 5 5

Figure S30.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CIC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.86

Table S38.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
CIC MUTATED 0 0 5 2
CIC WILD-TYPE 7 7 2 3

Figure S31.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S39.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
CIC MUTATED 0 3 51
CIC WILD-TYPE 96 66 70

Figure S32.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S40.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
CIC MUTATED 0 0 54 0
CIC WILD-TYPE 129 42 34 30

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

'CIC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.026

Table S41.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
CIC MUTATED 1 6 20 15
CIC WILD-TYPE 51 55 45 58

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

'CIC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S42.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
CIC MUTATED 8 24 10
CIC WILD-TYPE 58 104 47
'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S43.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
CIC MUTATED 0 1 32 19 2
CIC WILD-TYPE 75 64 19 64 12

Figure S35.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S44.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
CIC MUTATED 0 1 38 15
CIC WILD-TYPE 78 64 20 72

Figure S36.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S45.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
CIC MUTATED 9 2 24 19
CIC WILD-TYPE 74 55 89 17

Figure S37.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0068

Table S46.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
CIC MUTATED 28 26 0
CIC WILD-TYPE 96 82 57

Figure S38.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0068

Table S47.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
CIC MUTATED 7 23 24
CIC WILD-TYPE 111 51 71

Figure S39.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S48.  Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
CIC MUTATED 0 28 26 0
CIC WILD-TYPE 52 38 96 47

Figure S40.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
NOTCH1 MUTATED 0 2 1
NOTCH1 WILD-TYPE 9 8 6
'NOTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S50.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
NOTCH1 MUTATED 0 0 2 1
NOTCH1 WILD-TYPE 7 7 5 4
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.16

Table S51.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
NOTCH1 MUTATED 3 4 22
NOTCH1 WILD-TYPE 93 65 99

Figure S41.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S52.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
NOTCH1 MUTATED 6 0 23 0
NOTCH1 WILD-TYPE 123 42 65 30

Figure S42.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
NOTCH1 MUTATED 4 6 7 9
NOTCH1 WILD-TYPE 48 55 58 64
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
NOTCH1 MUTATED 6 13 7
NOTCH1 WILD-TYPE 60 115 50
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S55.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
NOTCH1 MUTATED 1 2 15 11 0
NOTCH1 WILD-TYPE 74 63 36 72 14

Figure S43.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.013

Table S56.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
NOTCH1 MUTATED 1 2 14 12
NOTCH1 WILD-TYPE 77 63 44 75

Figure S44.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.03

Table S57.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
NOTCH1 MUTATED 1 2 18 8
NOTCH1 WILD-TYPE 82 55 95 28

Figure S45.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.18

Table S58.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
NOTCH1 MUTATED 8 20 1
NOTCH1 WILD-TYPE 116 88 56

Figure S46.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.026

Table S59.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
NOTCH1 MUTATED 3 7 19
NOTCH1 WILD-TYPE 115 67 76

Figure S47.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.19

Table S60.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
NOTCH1 MUTATED 1 8 20 0
NOTCH1 WILD-TYPE 51 58 102 47

Figure S48.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 1

Table S61.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
IDH2 MUTATED 1 1 10
IDH2 WILD-TYPE 95 68 111

Figure S49.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 1

Table S62.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
IDH2 MUTATED 2 0 7 3
IDH2 WILD-TYPE 127 42 81 27

Figure S50.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'IDH2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
IDH2 MUTATED 1 4 2 5
IDH2 WILD-TYPE 51 57 63 68
'IDH2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S64.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
IDH2 MUTATED 1 6 5
IDH2 WILD-TYPE 65 122 52
'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.77

Table S65.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
IDH2 MUTATED 0 0 5 7 0
IDH2 WILD-TYPE 75 65 46 76 14

Figure S51.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.44

Table S66.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
IDH2 MUTATED 0 0 5 7
IDH2 WILD-TYPE 78 65 53 80

Figure S52.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 1

Table S67.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
IDH2 MUTATED 2 0 8 2
IDH2 WILD-TYPE 81 57 105 34
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 1

Table S68.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
IDH2 MUTATED 3 9 0
IDH2 WILD-TYPE 121 99 57

Figure S53.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.83

Table S69.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
IDH2 MUTATED 0 5 7
IDH2 WILD-TYPE 118 69 88

Figure S54.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0737 (Fisher's exact test), Q value = 1

Table S70.  Gene #6: 'IDH2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
IDH2 MUTATED 0 4 8 0
IDH2 WILD-TYPE 52 62 114 47
'FUBP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S71.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
FUBP1 MUTATED 0 4 0
FUBP1 WILD-TYPE 9 6 7

Figure S55.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0077 (Fisher's exact test), Q value = 1

Table S72.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
FUBP1 MUTATED 0 0 4 0
FUBP1 WILD-TYPE 7 7 3 5

Figure S56.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S73.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
FUBP1 MUTATED 0 0 26
FUBP1 WILD-TYPE 96 69 95

Figure S57.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FUBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S74.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
FUBP1 MUTATED 0 0 26 0
FUBP1 WILD-TYPE 129 42 62 30

Figure S58.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FUBP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S75.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
FUBP1 MUTATED 1 2 9 10
FUBP1 WILD-TYPE 51 59 56 63

Figure S59.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FUBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S76.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
FUBP1 MUTATED 7 10 5
FUBP1 WILD-TYPE 59 118 52
'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S77.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
FUBP1 MUTATED 0 1 16 7 2
FUBP1 WILD-TYPE 75 64 35 76 12

Figure S60.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S78.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
FUBP1 MUTATED 0 1 18 7
FUBP1 WILD-TYPE 78 64 40 80

Figure S61.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.02

Table S79.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
FUBP1 MUTATED 4 0 12 10
FUBP1 WILD-TYPE 79 57 101 26

Figure S62.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
FUBP1 MUTATED 14 12 0
FUBP1 WILD-TYPE 110 96 57

Figure S63.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S81.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
FUBP1 MUTATED 8 8 10
FUBP1 WILD-TYPE 110 66 85
'FUBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.065

Table S82.  Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
FUBP1 MUTATED 0 12 14 0
FUBP1 WILD-TYPE 52 54 108 47

Figure S64.  Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0664 (Fisher's exact test), Q value = 1

Table S83.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
NF1 MUTATED 4 9 6
NF1 WILD-TYPE 92 60 115
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0068

Table S84.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
NF1 MUTATED 1 10 5 3
NF1 WILD-TYPE 128 32 83 27

Figure S65.  Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 1

Table S85.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
NF1 MUTATED 1 9 2 4
NF1 WILD-TYPE 51 52 63 69

Figure S66.  Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 1

Table S86.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
NF1 MUTATED 4 11 1
NF1 WILD-TYPE 62 117 56
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 1

Table S87.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
NF1 MUTATED 1 10 3 4 1
NF1 WILD-TYPE 74 55 48 79 13

Figure S67.  Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00773 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
NF1 MUTATED 1 10 4 4
NF1 WILD-TYPE 77 55 54 83

Figure S68.  Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S89.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
NF1 MUTATED 7 4 6 2
NF1 WILD-TYPE 76 53 107 34
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.85

Table S90.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
NF1 MUTATED 5 4 10
NF1 WILD-TYPE 119 104 47

Figure S69.  Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S91.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
NF1 MUTATED 12 3 4
NF1 WILD-TYPE 106 71 91
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.039

Table S92.  Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
NF1 MUTATED 1 2 5 11
NF1 WILD-TYPE 51 64 117 36

Figure S70.  Get High-res Image Gene #8: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S93.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
PIK3R1 MUTATED 2 1 0
PIK3R1 WILD-TYPE 7 9 7
'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S94.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
PIK3R1 MUTATED 2 0 1 0
PIK3R1 WILD-TYPE 5 7 6 5
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0788 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
PIK3R1 MUTATED 1 3 9
PIK3R1 WILD-TYPE 95 66 112
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
PIK3R1 MUTATED 3 1 9 0
PIK3R1 WILD-TYPE 126 41 79 30

Figure S71.  Get High-res Image Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S97.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
PIK3R1 MUTATED 3 2 4 4
PIK3R1 WILD-TYPE 49 59 61 69
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S98.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
PIK3R1 MUTATED 3 7 3
PIK3R1 WILD-TYPE 63 121 54
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S99.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
PIK3R1 MUTATED 2 3 4 4 0
PIK3R1 WILD-TYPE 73 62 47 79 14
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S100.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
PIK3R1 MUTATED 3 2 4 4
PIK3R1 WILD-TYPE 75 63 54 83
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S101.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
PIK3R1 MUTATED 4 1 4 4
PIK3R1 WILD-TYPE 79 56 109 32
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S102.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
PIK3R1 MUTATED 7 5 1
PIK3R1 WILD-TYPE 117 103 56
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S103.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
PIK3R1 MUTATED 6 3 4
PIK3R1 WILD-TYPE 112 71 91
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S104.  Gene #9: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
PIK3R1 MUTATED 3 2 7 1
PIK3R1 WILD-TYPE 49 64 115 46
'STK19 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 1

Table S105.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
STK19 MUTATED 3 3 2
STK19 WILD-TYPE 93 66 119
'STK19 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0828 (Fisher's exact test), Q value = 1

Table S106.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
STK19 MUTATED 4 2 0 2
STK19 WILD-TYPE 125 40 88 28
'STK19 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 1

Table S107.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
STK19 MUTATED 4 0 0 2
STK19 WILD-TYPE 48 61 65 71

Figure S72.  Get High-res Image Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'STK19 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S108.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
STK19 MUTATED 3 1 2
STK19 WILD-TYPE 63 127 55
'STK19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S109.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
STK19 MUTATED 2 2 0 4 0
STK19 WILD-TYPE 73 63 51 79 14
'STK19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
STK19 MUTATED 2 2 0 4
STK19 WILD-TYPE 76 63 58 83
'STK19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S111.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
STK19 MUTATED 1 3 4 0
STK19 WILD-TYPE 82 54 109 36
'STK19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S112.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
STK19 MUTATED 3 3 2
STK19 WILD-TYPE 121 105 55
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S113.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
STK19 MUTATED 3 4 1
STK19 WILD-TYPE 115 70 94
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S114.  Gene #10: 'STK19 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
STK19 MUTATED 1 2 3 2
STK19 WILD-TYPE 51 64 119 45
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S115.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
PTEN MUTATED 0 13 0
PTEN WILD-TYPE 96 56 121

Figure S73.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S116.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
PTEN MUTATED 0 13 0 0
PTEN WILD-TYPE 129 29 88 30

Figure S74.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.19

Table S117.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
PTEN MUTATED 1 8 1 0
PTEN WILD-TYPE 51 53 64 73

Figure S75.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00525 (Fisher's exact test), Q value = 1

Table S118.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
PTEN MUTATED 0 10 0
PTEN WILD-TYPE 66 118 57

Figure S76.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S119.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
PTEN MUTATED 0 13 0 0 0
PTEN WILD-TYPE 75 52 51 83 14

Figure S77.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S120.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
PTEN MUTATED 0 12 0 1
PTEN WILD-TYPE 78 53 58 86

Figure S78.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 1

Table S121.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
PTEN MUTATED 8 3 2 0
PTEN WILD-TYPE 75 54 111 36

Figure S79.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S122.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
PTEN MUTATED 0 0 13
PTEN WILD-TYPE 124 108 44

Figure S80.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.15

Table S123.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
PTEN MUTATED 12 0 1
PTEN WILD-TYPE 106 74 94

Figure S81.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S124.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
PTEN MUTATED 0 0 0 13
PTEN WILD-TYPE 52 66 122 34

Figure S82.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.23

Table S125.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
PIK3CA MUTATED 1 7 17
PIK3CA WILD-TYPE 95 62 104

Figure S83.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S126.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
PIK3CA MUTATED 1 5 17 2
PIK3CA WILD-TYPE 128 37 71 28

Figure S84.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S127.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
PIK3CA MUTATED 3 7 4 8
PIK3CA WILD-TYPE 49 54 61 65
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S128.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
PIK3CA MUTATED 7 10 5
PIK3CA WILD-TYPE 59 118 52
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 1

Table S129.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
PIK3CA MUTATED 1 5 9 7 3
PIK3CA WILD-TYPE 74 60 42 76 11

Figure S85.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.23

Table S130.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
PIK3CA MUTATED 0 6 10 9
PIK3CA WILD-TYPE 78 59 48 78

Figure S86.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S131.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
PIK3CA MUTATED 4 5 11 5
PIK3CA WILD-TYPE 79 52 102 31
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 1

Table S132.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
PIK3CA MUTATED 7 12 6
PIK3CA WILD-TYPE 117 96 51
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S133.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
PIK3CA MUTATED 8 5 12
PIK3CA WILD-TYPE 110 69 83
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
PIK3CA MUTATED 0 7 13 5
PIK3CA WILD-TYPE 52 59 109 42

Figure S87.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S135.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
ARID1A MUTATED 5 2 4
ARID1A WILD-TYPE 91 67 117
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S136.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
ARID1A MUTATED 5 1 6 0
ARID1A WILD-TYPE 124 41 82 30
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S137.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
ARID1A MUTATED 2 1 5 4
ARID1A WILD-TYPE 50 60 60 69
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S138.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
ARID1A MUTATED 2 7 3
ARID1A WILD-TYPE 64 121 54
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S139.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
ARID1A MUTATED 3 0 4 5 0
ARID1A WILD-TYPE 72 65 47 78 14
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S140.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
ARID1A MUTATED 3 0 4 5
ARID1A WILD-TYPE 75 65 54 82
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S141.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
ARID1A MUTATED 3 1 6 2
ARID1A WILD-TYPE 80 56 107 34
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S142.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
ARID1A MUTATED 6 5 1
ARID1A WILD-TYPE 118 103 56
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S143.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
ARID1A MUTATED 2 4 6
ARID1A WILD-TYPE 116 70 89
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S144.  Gene #13: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
ARID1A MUTATED 1 5 5 1
ARID1A WILD-TYPE 51 61 117 46
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S145.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
EGFR MUTATED 0 16 1
EGFR WILD-TYPE 96 53 120

Figure S88.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S146.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
EGFR MUTATED 0 14 1 2
EGFR WILD-TYPE 129 28 87 28

Figure S89.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00748 (Fisher's exact test), Q value = 1

Table S147.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
EGFR MUTATED 1 9 1 3
EGFR WILD-TYPE 51 52 64 70

Figure S90.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 1

Table S148.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
EGFR MUTATED 0 11 3
EGFR WILD-TYPE 66 117 54

Figure S91.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S149.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
EGFR MUTATED 0 13 1 3 0
EGFR WILD-TYPE 75 52 50 80 14

Figure S92.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S150.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
EGFR MUTATED 0 13 1 3
EGFR WILD-TYPE 78 52 57 84

Figure S93.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 1

Table S151.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
EGFR MUTATED 6 4 7 0
EGFR WILD-TYPE 77 53 106 36
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S152.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
EGFR MUTATED 0 4 13
EGFR WILD-TYPE 124 104 44

Figure S94.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00607 (Fisher's exact test), Q value = 1

Table S153.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
EGFR MUTATED 12 0 5
EGFR WILD-TYPE 106 74 90

Figure S95.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S154.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
EGFR MUTATED 0 0 3 14
EGFR WILD-TYPE 52 66 119 33

Figure S96.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GAGE2B MUTATION STATUS' versus 'CN_CNMF'

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

Table S155.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
GAGE2B MUTATED 2 0 2
GAGE2B WILD-TYPE 94 69 119
'GAGE2B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S156.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
GAGE2B MUTATED 2 0 2 0
GAGE2B WILD-TYPE 127 42 86 30
'GAGE2B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S157.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
GAGE2B MUTATED 0 0 2 2
GAGE2B WILD-TYPE 52 61 63 71
'GAGE2B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S158.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
GAGE2B MUTATED 1 2 1
GAGE2B WILD-TYPE 65 126 56
'GAGE2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S159.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
GAGE2B MUTATED 2 0 1 1 0
GAGE2B WILD-TYPE 73 65 50 82 14
'GAGE2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S160.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
GAGE2B MUTATED 2 0 0 2
GAGE2B WILD-TYPE 76 65 58 85
'GAGE2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S161.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
GAGE2B MUTATED 1 1 2 0
GAGE2B WILD-TYPE 82 56 111 36
'GAGE2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S162.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
GAGE2B MUTATED 2 2 0
GAGE2B WILD-TYPE 122 106 57
'GAGE2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S163.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
GAGE2B MUTATED 0 2 2
GAGE2B WILD-TYPE 118 72 93
'GAGE2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.325 (Fisher's exact test), Q value = 1

Table S164.  Gene #15: 'GAGE2B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
GAGE2B MUTATED 2 0 2 0
GAGE2B WILD-TYPE 50 66 120 47
'CREBZF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S165.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
CREBZF MUTATED 0 1 4
CREBZF WILD-TYPE 96 68 117
'CREBZF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 1

Table S166.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
CREBZF MUTATED 0 0 4 1
CREBZF WILD-TYPE 129 42 84 29

Figure S97.  Get High-res Image Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CREBZF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0854 (Fisher's exact test), Q value = 1

Table S167.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
CREBZF MUTATED 0 1 0 4
CREBZF WILD-TYPE 52 60 65 69
'CREBZF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00441 (Fisher's exact test), Q value = 1

Table S168.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
CREBZF MUTATED 1 0 4
CREBZF WILD-TYPE 65 128 53

Figure S98.  Get High-res Image Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CREBZF MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S169.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
CREBZF MUTATED 0 1 1 3 0
CREBZF WILD-TYPE 75 64 50 80 14
'CREBZF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S170.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
CREBZF MUTATED 0 1 1 3
CREBZF WILD-TYPE 78 64 57 84
'CREBZF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S171.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
CREBZF MUTATED 0 1 3 1
CREBZF WILD-TYPE 83 56 110 35
'CREBZF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0691 (Fisher's exact test), Q value = 1

Table S172.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
CREBZF MUTATED 0 4 1
CREBZF WILD-TYPE 124 104 56
'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 1

Table S173.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
CREBZF MUTATED 1 0 4
CREBZF WILD-TYPE 117 74 91
'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S174.  Gene #16: 'CREBZF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
CREBZF MUTATED 0 0 4 1
CREBZF WILD-TYPE 52 66 118 46
'TCF12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S175.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
TCF12 MUTATED 2 1 5
TCF12 WILD-TYPE 94 68 116
'TCF12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 1

Table S176.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
TCF12 MUTATED 2 1 4 1
TCF12 WILD-TYPE 127 41 84 29
'TCF12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S177.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TCF12 MUTATED 1 1 5 1
TCF12 WILD-TYPE 51 60 60 72
'TCF12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 1

Table S178.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
TCF12 MUTATED 1 6 1
TCF12 WILD-TYPE 65 122 56
'TCF12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 1

Table S179.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
TCF12 MUTATED 1 2 4 1 0
TCF12 WILD-TYPE 74 63 47 82 14
'TCF12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
TCF12 MUTATED 1 2 3 2
TCF12 WILD-TYPE 77 63 55 85
'TCF12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 1

Table S181.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
TCF12 MUTATED 3 0 3 2
TCF12 WILD-TYPE 80 57 110 34
'TCF12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S182.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
TCF12 MUTATED 4 3 1
TCF12 WILD-TYPE 120 105 56
'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S183.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
TCF12 MUTATED 3 2 3
TCF12 WILD-TYPE 115 72 92
'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S184.  Gene #17: 'TCF12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
TCF12 MUTATED 1 2 4 1
TCF12 WILD-TYPE 51 64 118 46
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S185.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
SMARCA4 MUTATED 8 2 3
SMARCA4 WILD-TYPE 88 67 118
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S186.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
SMARCA4 MUTATED 9 0 4 0
SMARCA4 WILD-TYPE 120 42 84 30
'SMARCA4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S187.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
SMARCA4 MUTATED 0 3 4 4
SMARCA4 WILD-TYPE 52 58 61 69
'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S188.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
SMARCA4 MUTATED 2 6 3
SMARCA4 WILD-TYPE 64 122 54
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S189.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
SMARCA4 MUTATED 3 0 4 5 1
SMARCA4 WILD-TYPE 72 65 47 78 13
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S190.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
SMARCA4 MUTATED 5 1 3 4
SMARCA4 WILD-TYPE 73 64 55 83
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0704 (Fisher's exact test), Q value = 1

Table S191.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
SMARCA4 MUTATED 3 0 6 4
SMARCA4 WILD-TYPE 80 57 107 32
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S192.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
SMARCA4 MUTATED 8 5 0
SMARCA4 WILD-TYPE 116 103 57
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S193.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
SMARCA4 MUTATED 4 3 6
SMARCA4 WILD-TYPE 114 71 89
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S194.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
SMARCA4 MUTATED 3 2 8 0
SMARCA4 WILD-TYPE 49 64 114 47
'VAV3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S195.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
VAV3 MUTATED 3 3 2
VAV3 WILD-TYPE 93 66 119
'VAV3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S196.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
VAV3 MUTATED 3 1 2 2
VAV3 WILD-TYPE 126 41 86 28
'VAV3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S197.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
VAV3 MUTATED 1 2 2 3
VAV3 WILD-TYPE 51 59 63 70
'VAV3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S198.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
VAV3 MUTATED 2 3 3
VAV3 WILD-TYPE 64 125 54
'VAV3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 1

Table S199.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
VAV3 MUTATED 0 3 1 2 2
VAV3 WILD-TYPE 75 62 50 81 12

Figure S99.  Get High-res Image Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VAV3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.478 (Fisher's exact test), Q value = 1

Table S200.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
VAV3 MUTATED 2 2 0 4
VAV3 WILD-TYPE 76 63 58 83
'VAV3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S201.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
VAV3 MUTATED 2 1 5 0
VAV3 WILD-TYPE 81 56 108 36
'VAV3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 1

Table S202.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
VAV3 MUTATED 2 5 1
VAV3 WILD-TYPE 122 103 56
'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 1

Table S203.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
VAV3 MUTATED 2 2 4
VAV3 WILD-TYPE 116 72 91
'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S204.  Gene #19: 'VAV3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
VAV3 MUTATED 2 0 4 2
VAV3 WILD-TYPE 50 66 118 45
'TMEM216 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S205.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
TMEM216 MUTATED 2 1 0
TMEM216 WILD-TYPE 94 68 121
'TMEM216 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S206.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
TMEM216 MUTATED 2 0 1 0
TMEM216 WILD-TYPE 127 42 87 30
'TMEM216 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S207.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TMEM216 MUTATED 1 1 0 1
TMEM216 WILD-TYPE 51 60 65 72
'TMEM216 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S208.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
TMEM216 MUTATED 1 1 1
TMEM216 WILD-TYPE 65 127 56
'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S209.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
TMEM216 MUTATED 1 0 1 1 0
TMEM216 WILD-TYPE 74 65 50 82 14
'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S210.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
TMEM216 MUTATED 1 0 1 1
TMEM216 WILD-TYPE 77 65 57 86
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.404 (Fisher's exact test), Q value = 1

Table S211.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
TMEM216 MUTATED 0 1 1 1
TMEM216 WILD-TYPE 83 56 112 35
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S212.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
TMEM216 MUTATED 1 2 0
TMEM216 WILD-TYPE 123 106 57
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 1

Table S213.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
TMEM216 MUTATED 0 2 1
TMEM216 WILD-TYPE 118 72 94
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S214.  Gene #20: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
TMEM216 MUTATED 0 2 1 0
TMEM216 WILD-TYPE 52 64 121 47
'ROBO3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S215.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
ROBO3 MUTATED 2 0 2
ROBO3 WILD-TYPE 94 69 119
'ROBO3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S216.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
ROBO3 MUTATED 3 0 1 0
ROBO3 WILD-TYPE 126 42 87 30
'ROBO3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S217.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
ROBO3 MUTATED 2 0 0 2 0
ROBO3 WILD-TYPE 73 65 51 81 14
'ROBO3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S218.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
ROBO3 MUTATED 2 0 1 1
ROBO3 WILD-TYPE 76 65 57 86
'ROBO3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 1

Table S219.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
ROBO3 MUTATED 1 0 2 1
ROBO3 WILD-TYPE 82 57 111 35
'ROBO3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S220.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
ROBO3 MUTATED 3 1 0
ROBO3 WILD-TYPE 121 107 57
'ROBO3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S221.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
ROBO3 MUTATED 2 1 1
ROBO3 WILD-TYPE 116 73 94
'ROBO3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S222.  Gene #21: 'ROBO3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
ROBO3 MUTATED 1 1 2 0
ROBO3 WILD-TYPE 51 65 120 47
'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S223.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
IRS4 MUTATED 1 3 1
IRS4 WILD-TYPE 95 66 120
'IRS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S224.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
IRS4 MUTATED 3 1 1 0
IRS4 WILD-TYPE 126 41 87 30
'IRS4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S225.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
IRS4 MUTATED 0 1 1 1
IRS4 WILD-TYPE 52 60 64 72
'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 1

Table S226.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
IRS4 MUTATED 0 1 2
IRS4 WILD-TYPE 66 127 55
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S227.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
IRS4 MUTATED 2 1 0 2 0
IRS4 WILD-TYPE 73 64 51 81 14
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S228.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
IRS4 MUTATED 2 1 1 1
IRS4 WILD-TYPE 76 64 57 86
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.925 (Fisher's exact test), Q value = 1

Table S229.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
IRS4 MUTATED 1 1 3 0
IRS4 WILD-TYPE 82 56 110 36
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S230.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
IRS4 MUTATED 2 2 1
IRS4 WILD-TYPE 122 106 56
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0904 (Fisher's exact test), Q value = 1

Table S231.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
IRS4 MUTATED 0 2 3
IRS4 WILD-TYPE 118 72 92
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S232.  Gene #22: 'IRS4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
IRS4 MUTATED 1 1 2 1
IRS4 WILD-TYPE 51 65 120 46
'HTRA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S233.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
HTRA2 MUTATED 3 1 0
HTRA2 WILD-TYPE 93 68 121
'HTRA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S234.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
HTRA2 MUTATED 2 0 1 1
HTRA2 WILD-TYPE 127 42 87 29
'HTRA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S235.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
HTRA2 MUTATED 2 1 0 1
HTRA2 WILD-TYPE 50 60 65 72
'HTRA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S236.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
HTRA2 MUTATED 1 2 1
HTRA2 WILD-TYPE 65 126 56
'HTRA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S237.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
HTRA2 MUTATED 1 1 1 1 0
HTRA2 WILD-TYPE 74 64 50 82 14
'HTRA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S238.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
HTRA2 MUTATED 1 1 1 1
HTRA2 WILD-TYPE 77 64 57 86
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S239.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
HTRA2 MUTATED 2 0 1 1
HTRA2 WILD-TYPE 81 57 112 35
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S240.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
HTRA2 MUTATED 2 2 0
HTRA2 WILD-TYPE 122 106 57
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S241.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
HTRA2 MUTATED 1 2 0
HTRA2 WILD-TYPE 117 72 95
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S242.  Gene #23: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
HTRA2 MUTATED 1 1 1 0
HTRA2 WILD-TYPE 51 65 121 47
'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S243.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
EIF1AX MUTATED 0 1 3
EIF1AX WILD-TYPE 96 68 118
'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S244.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
EIF1AX MUTATED 4 0 0 0
EIF1AX WILD-TYPE 125 42 88 30
'EIF1AX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S245.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
EIF1AX MUTATED 0 0 2 2
EIF1AX WILD-TYPE 52 61 63 71
'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S246.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
EIF1AX MUTATED 0 2 2
EIF1AX WILD-TYPE 66 126 55
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S247.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
EIF1AX MUTATED 2 1 0 1 0
EIF1AX WILD-TYPE 73 64 51 82 14
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S248.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
EIF1AX MUTATED 2 1 0 1
EIF1AX WILD-TYPE 76 64 58 86
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S249.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
EIF1AX MUTATED 2 1 1 0
EIF1AX WILD-TYPE 81 56 112 36
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S250.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
EIF1AX MUTATED 3 0 1
EIF1AX WILD-TYPE 121 108 56
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S251.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
EIF1AX MUTATED 3 1 0
EIF1AX WILD-TYPE 115 73 95
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0762 (Fisher's exact test), Q value = 1

Table S252.  Gene #24: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
EIF1AX MUTATED 2 2 0 0
EIF1AX WILD-TYPE 50 64 122 47
'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S253.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
FAM47C MUTATED 1 1 5
FAM47C WILD-TYPE 95 68 116
'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 1

Table S254.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
FAM47C MUTATED 2 0 4 1
FAM47C WILD-TYPE 127 42 84 29
'FAM47C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 1

Table S255.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
FAM47C MUTATED 1 0 1 4
FAM47C WILD-TYPE 51 61 64 69
'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S256.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
FAM47C MUTATED 1 2 3
FAM47C WILD-TYPE 65 126 54
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0592 (Fisher's exact test), Q value = 1

Table S257.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
FAM47C MUTATED 0 0 2 5 0
FAM47C WILD-TYPE 75 65 49 78 14
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 1

Table S258.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
FAM47C MUTATED 0 0 2 5
FAM47C WILD-TYPE 78 65 56 82

Figure S100.  Get High-res Image Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S259.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
FAM47C MUTATED 1 0 6 0
FAM47C WILD-TYPE 82 57 107 36
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 1

Table S260.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
FAM47C MUTATED 1 6 0
FAM47C WILD-TYPE 123 102 57

Figure S101.  Get High-res Image Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00537 (Fisher's exact test), Q value = 1

Table S261.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
FAM47C MUTATED 0 1 6
FAM47C WILD-TYPE 118 73 89

Figure S102.  Get High-res Image Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 1

Table S262.  Gene #25: 'FAM47C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
FAM47C MUTATED 0 1 6 0
FAM47C WILD-TYPE 52 65 116 47
'PLCG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 1

Table S263.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
PLCG1 MUTATED 0 4 0
PLCG1 WILD-TYPE 96 65 121

Figure S103.  Get High-res Image Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PLCG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 1

Table S264.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
PLCG1 MUTATED 1 3 0 0
PLCG1 WILD-TYPE 128 39 88 30

Figure S104.  Get High-res Image Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PLCG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S265.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
PLCG1 MUTATED 1 3 0 0 0
PLCG1 WILD-TYPE 74 62 51 83 14
'PLCG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.669 (Fisher's exact test), Q value = 1

Table S266.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
PLCG1 MUTATED 1 2 0 1
PLCG1 WILD-TYPE 77 63 58 86
'PLCG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S267.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
PLCG1 MUTATED 3 0 1 0
PLCG1 WILD-TYPE 80 57 112 36
'PLCG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S268.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
PLCG1 MUTATED 2 0 2
PLCG1 WILD-TYPE 122 108 55
'PLCG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0923 (Fisher's exact test), Q value = 1

Table S269.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
PLCG1 MUTATED 4 0 0
PLCG1 WILD-TYPE 114 74 95
'PLCG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 1

Table S270.  Gene #26: 'PLCG1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
PLCG1 MUTATED 0 1 1 2
PLCG1 WILD-TYPE 52 65 121 45
'DDX5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S271.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
DDX5 MUTATED 2 0 2
DDX5 WILD-TYPE 94 69 119
'DDX5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S272.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
DDX5 MUTATED 2 0 2 0
DDX5 WILD-TYPE 127 42 86 30
'DDX5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S273.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
DDX5 MUTATED 1 1 1 1
DDX5 WILD-TYPE 51 60 64 72
'DDX5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S274.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
DDX5 MUTATED 2 1 1
DDX5 WILD-TYPE 64 127 56
'DDX5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 1

Table S275.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
DDX5 MUTATED 2 0 2 0 0
DDX5 WILD-TYPE 73 65 49 83 14
'DDX5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S276.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
DDX5 MUTATED 2 0 2 0
DDX5 WILD-TYPE 76 65 56 87
'DDX5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S277.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
DDX5 MUTATED 0 1 3 0
DDX5 WILD-TYPE 83 56 110 36
'DDX5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S278.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
DDX5 MUTATED 1 3 0
DDX5 WILD-TYPE 123 105 57
'DDX5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S279.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
DDX5 MUTATED 0 1 3
DDX5 WILD-TYPE 118 73 92
'DDX5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S280.  Gene #27: 'DDX5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
DDX5 MUTATED 0 1 3 0
DDX5 WILD-TYPE 52 65 119 47
'ZNF709 MUTATION STATUS' versus 'CN_CNMF'

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

Table S281.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
ZNF709 MUTATED 1 0 2
ZNF709 WILD-TYPE 95 69 119
'ZNF709 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S282.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
ZNF709 MUTATED 1 0 2 0
ZNF709 WILD-TYPE 128 42 86 30
'ZNF709 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S283.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
ZNF709 MUTATED 1 0 1 1
ZNF709 WILD-TYPE 51 61 64 72
'ZNF709 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S284.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
ZNF709 MUTATED 1 1 1
ZNF709 WILD-TYPE 65 127 56
'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 1

Table S285.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
ZNF709 MUTATED 0 0 0 2 1
ZNF709 WILD-TYPE 75 65 51 81 13
'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S286.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
ZNF709 MUTATED 0 0 2 1
ZNF709 WILD-TYPE 78 65 56 86
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S287.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
ZNF709 MUTATED 1 0 2 0
ZNF709 WILD-TYPE 82 57 111 36
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S288.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
ZNF709 MUTATED 1 2 0
ZNF709 WILD-TYPE 123 106 57
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S289.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
ZNF709 MUTATED 2 0 1
ZNF709 WILD-TYPE 116 74 94
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S290.  Gene #28: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
ZNF709 MUTATED 0 1 2 0
ZNF709 WILD-TYPE 52 65 120 47
'TRERF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0512 (Fisher's exact test), Q value = 1

Table S291.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
TRERF1 MUTATED 3 0 0
TRERF1 WILD-TYPE 93 69 121
'TRERF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S292.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
TRERF1 MUTATED 2 0 0 1
TRERF1 WILD-TYPE 127 42 88 29
'TRERF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S293.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TRERF1 MUTATED 1 0 0 2
TRERF1 WILD-TYPE 51 61 65 71
'TRERF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0685 (Fisher's exact test), Q value = 1

Table S294.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
TRERF1 MUTATED 1 0 2
TRERF1 WILD-TYPE 65 128 55
'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S295.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
TRERF1 MUTATED 1 0 0 1 1
TRERF1 WILD-TYPE 74 65 51 82 13
'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S296.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
TRERF1 MUTATED 2 0 0 1
TRERF1 WILD-TYPE 76 65 58 86
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S297.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
TRERF1 MUTATED 1 0 2 0
TRERF1 WILD-TYPE 82 57 111 36
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S298.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
TRERF1 MUTATED 1 2 0
TRERF1 WILD-TYPE 123 106 57
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S299.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
TRERF1 MUTATED 1 0 2
TRERF1 WILD-TYPE 117 74 93
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S300.  Gene #29: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
TRERF1 MUTATED 1 0 2 0
TRERF1 WILD-TYPE 51 66 120 47
'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S301.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
BCOR MUTATED 1 1 1
BCOR WILD-TYPE 8 9 6
'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S302.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 5
BCOR MUTATED 1 0 1 1
BCOR WILD-TYPE 6 7 6 4
'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S303.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
BCOR MUTATED 1 2 6
BCOR WILD-TYPE 95 67 115
'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S304.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
BCOR MUTATED 3 1 4 1
BCOR WILD-TYPE 126 41 84 29
'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S305.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
BCOR MUTATED 2 2 1 2
BCOR WILD-TYPE 50 59 64 71
'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S306.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
BCOR MUTATED 2 3 2
BCOR WILD-TYPE 64 125 55
'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S307.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
BCOR MUTATED 2 1 2 4 0
BCOR WILD-TYPE 73 64 49 79 14
'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S308.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
BCOR MUTATED 1 1 2 5
BCOR WILD-TYPE 77 64 56 82
'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S309.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
BCOR MUTATED 3 1 4 1
BCOR WILD-TYPE 80 56 109 35
'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S310.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
BCOR MUTATED 3 4 2
BCOR WILD-TYPE 121 104 55
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S311.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
BCOR MUTATED 2 4 3
BCOR WILD-TYPE 116 70 92
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S312.  Gene #30: 'BCOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
BCOR MUTATED 0 5 3 1
BCOR WILD-TYPE 52 61 119 46
'SRPX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S313.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
SRPX MUTATED 0 1 2
SRPX WILD-TYPE 96 68 119
'SRPX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S314.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
SRPX MUTATED 0 1 2 0
SRPX WILD-TYPE 129 41 86 30
'SRPX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S315.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
SRPX MUTATED 0 1 2 0
SRPX WILD-TYPE 52 60 63 73
'SRPX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S316.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
SRPX MUTATED 1 2 0
SRPX WILD-TYPE 65 126 57
'SRPX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S317.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
SRPX MUTATED 0 1 2 0 0
SRPX WILD-TYPE 75 64 49 83 14
'SRPX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0925 (Fisher's exact test), Q value = 1

Table S318.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
SRPX MUTATED 0 1 2 0
SRPX WILD-TYPE 78 64 56 87
'SRPX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S319.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
SRPX MUTATED 1 1 0 1
SRPX WILD-TYPE 82 56 113 35
'SRPX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 1

Table S320.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
SRPX MUTATED 2 0 1
SRPX WILD-TYPE 122 108 56
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 1

Table S321.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
SRPX MUTATED 2 1 0
SRPX WILD-TYPE 116 73 95
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 1

Table S322.  Gene #31: 'SRPX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
SRPX MUTATED 0 2 0 1
SRPX WILD-TYPE 52 64 122 46
'DOCK5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0776 (Fisher's exact test), Q value = 1

Table S323.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
DOCK5 MUTATED 1 4 1
DOCK5 WILD-TYPE 95 65 120
'DOCK5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 1

Table S324.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
DOCK5 MUTATED 1 3 2 0
DOCK5 WILD-TYPE 128 39 86 30
'DOCK5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S325.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
DOCK5 MUTATED 2 2 0 1
DOCK5 WILD-TYPE 50 59 65 72
'DOCK5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S326.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
DOCK5 MUTATED 3 2 0
DOCK5 WILD-TYPE 63 126 57
'DOCK5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S327.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
DOCK5 MUTATED 0 4 1 1 0
DOCK5 WILD-TYPE 75 61 50 82 14
'DOCK5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0726 (Fisher's exact test), Q value = 1

Table S328.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
DOCK5 MUTATED 0 4 1 1
DOCK5 WILD-TYPE 78 61 57 86
'DOCK5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S329.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
DOCK5 MUTATED 2 3 1 0
DOCK5 WILD-TYPE 81 54 112 36
'DOCK5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S330.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
DOCK5 MUTATED 2 1 3
DOCK5 WILD-TYPE 122 107 54
'DOCK5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S331.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
DOCK5 MUTATED 3 1 2
DOCK5 WILD-TYPE 115 73 93
'DOCK5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S332.  Gene #32: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
DOCK5 MUTATED 1 1 2 2
DOCK5 WILD-TYPE 51 65 120 45
'GIGYF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 1

Table S333.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
GIGYF2 MUTATED 1 3 0
GIGYF2 WILD-TYPE 95 66 121

Figure S105.  Get High-res Image Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'GIGYF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S334.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
GIGYF2 MUTATED 1 2 1 0
GIGYF2 WILD-TYPE 128 40 87 30
'GIGYF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0836 (Fisher's exact test), Q value = 1

Table S335.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
GIGYF2 MUTATED 0 3 1 0
GIGYF2 WILD-TYPE 52 58 64 73
'GIGYF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S336.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
GIGYF2 MUTATED 1 3 0
GIGYF2 WILD-TYPE 65 125 57
'GIGYF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S337.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
GIGYF2 MUTATED 1 2 1 0 0
GIGYF2 WILD-TYPE 74 63 50 83 14
'GIGYF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S338.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
GIGYF2 MUTATED 1 2 1 0
GIGYF2 WILD-TYPE 77 63 57 87
'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 1

Table S339.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
GIGYF2 MUTATED 0 2 1 1
GIGYF2 WILD-TYPE 83 55 112 35
'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0748 (Fisher's exact test), Q value = 1

Table S340.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
GIGYF2 MUTATED 0 2 2
GIGYF2 WILD-TYPE 124 106 55
'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S341.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
GIGYF2 MUTATED 2 1 1
GIGYF2 WILD-TYPE 116 73 94
'GIGYF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S342.  Gene #33: 'GIGYF2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
GIGYF2 MUTATED 0 1 1 2
GIGYF2 WILD-TYPE 52 65 121 45
'NIPBL MUTATION STATUS' versus 'CN_CNMF'

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

Table S343.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
NIPBL MUTATED 1 1 4
NIPBL WILD-TYPE 95 68 117
'NIPBL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0829 (Fisher's exact test), Q value = 1

Table S344.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
NIPBL MUTATED 1 0 5 0
NIPBL WILD-TYPE 128 42 83 30
'NIPBL MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S345.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
NIPBL MUTATED 0 1 2 1
NIPBL WILD-TYPE 52 60 63 72
'NIPBL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S346.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
NIPBL MUTATED 1 3 0
NIPBL WILD-TYPE 65 125 57
'NIPBL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0686 (Fisher's exact test), Q value = 1

Table S347.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
NIPBL MUTATED 1 0 4 1 0
NIPBL WILD-TYPE 74 65 47 82 14
'NIPBL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 1

Table S348.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
NIPBL MUTATED 1 0 4 1
NIPBL WILD-TYPE 77 65 54 86

Figure S106.  Get High-res Image Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NIPBL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S349.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
NIPBL MUTATED 2 2 2 0
NIPBL WILD-TYPE 81 55 111 36
'NIPBL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S350.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
NIPBL MUTATED 4 2 0
NIPBL WILD-TYPE 120 106 57
'NIPBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0838 (Fisher's exact test), Q value = 1

Table S351.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
NIPBL MUTATED 1 4 1
NIPBL WILD-TYPE 117 70 94
'NIPBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S352.  Gene #34: 'NIPBL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
NIPBL MUTATED 1 3 2 0
NIPBL WILD-TYPE 51 63 120 47
'ZBTB20 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 1

Table S353.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
ZBTB20 MUTATED 2 1 10
ZBTB20 WILD-TYPE 94 68 111

Figure S107.  Get High-res Image Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZBTB20 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 1

Table S354.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
ZBTB20 MUTATED 2 1 10 0
ZBTB20 WILD-TYPE 127 41 78 30

Figure S108.  Get High-res Image Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZBTB20 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S355.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
ZBTB20 MUTATED 3 1 2 4
ZBTB20 WILD-TYPE 49 60 63 69
'ZBTB20 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 1

Table S356.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
ZBTB20 MUTATED 4 3 3
ZBTB20 WILD-TYPE 62 125 54
'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0741 (Fisher's exact test), Q value = 1

Table S357.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
ZBTB20 MUTATED 1 1 3 6 2
ZBTB20 WILD-TYPE 74 64 48 77 12
'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0807 (Fisher's exact test), Q value = 1

Table S358.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
ZBTB20 MUTATED 1 1 5 6
ZBTB20 WILD-TYPE 77 64 53 81
'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 1

Table S359.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
ZBTB20 MUTATED 3 1 8 1
ZBTB20 WILD-TYPE 80 56 105 35
'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S360.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
ZBTB20 MUTATED 4 8 1
ZBTB20 WILD-TYPE 120 100 56
'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S361.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
ZBTB20 MUTATED 3 2 8
ZBTB20 WILD-TYPE 115 72 87
'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S362.  Gene #35: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
ZBTB20 MUTATED 1 3 8 1
ZBTB20 WILD-TYPE 51 63 114 46
'TRIP12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S363.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
TRIP12 MUTATED 1 0 4
TRIP12 WILD-TYPE 95 69 117
'TRIP12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S364.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
TRIP12 MUTATED 2 0 3 0
TRIP12 WILD-TYPE 127 42 85 30
'TRIP12 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S365.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TRIP12 MUTATED 1 0 1 3
TRIP12 WILD-TYPE 51 61 64 70
'TRIP12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S366.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
TRIP12 MUTATED 2 1 2
TRIP12 WILD-TYPE 64 127 55
'TRIP12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S367.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
TRIP12 MUTATED 1 0 2 2 0
TRIP12 WILD-TYPE 74 65 49 81 14
'TRIP12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S368.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
TRIP12 MUTATED 1 0 2 2
TRIP12 WILD-TYPE 77 65 56 85
'TRIP12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S369.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
TRIP12 MUTATED 1 1 2 1
TRIP12 WILD-TYPE 82 56 111 35
'TRIP12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S370.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
TRIP12 MUTATED 3 2 0
TRIP12 WILD-TYPE 121 106 57
'TRIP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S371.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
TRIP12 MUTATED 2 1 2
TRIP12 WILD-TYPE 116 73 93
'TRIP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S372.  Gene #36: 'TRIP12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
TRIP12 MUTATED 1 2 2 0
TRIP12 WILD-TYPE 51 64 120 47
'KIAA0664 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S373.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 69 121
KIAA0664 MUTATED 1 2 2
KIAA0664 WILD-TYPE 95 67 119
'KIAA0664 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S374.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 42 88 30
KIAA0664 MUTATED 1 2 2 0
KIAA0664 WILD-TYPE 128 40 86 30
'KIAA0664 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S375.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
KIAA0664 MUTATED 1 1 0 2
KIAA0664 WILD-TYPE 51 60 65 71
'KIAA0664 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S376.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 128 57
KIAA0664 MUTATED 0 2 2
KIAA0664 WILD-TYPE 66 126 55
'KIAA0664 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S377.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 65 51 83 14
KIAA0664 MUTATED 0 2 1 2 0
KIAA0664 WILD-TYPE 75 63 50 81 14
'KIAA0664 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S378.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 65 58 87
KIAA0664 MUTATED 0 2 1 2
KIAA0664 WILD-TYPE 78 63 57 85
'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S379.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 83 57 113 36
KIAA0664 MUTATED 0 2 2 1
KIAA0664 WILD-TYPE 83 55 111 35
'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.089 (Fisher's exact test), Q value = 1

Table S380.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 108 57
KIAA0664 MUTATED 0 3 2
KIAA0664 WILD-TYPE 124 105 55
'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S381.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 74 95
KIAA0664 MUTATED 2 0 3
KIAA0664 WILD-TYPE 116 74 92
'KIAA0664 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 1

Table S382.  Gene #37: 'KIAA0664 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 66 122 47
KIAA0664 MUTATED 0 0 3 2
KIAA0664 WILD-TYPE 52 66 119 45
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = LGG-TP.transferedmergedcluster.txt

  • Number of patients = 289

  • Number of significantly mutated genes = 37

  • Number of Molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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