Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 40 genes and 12 molecular subtypes across 122 patients, 24 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • TP53 mutation correlated to 'MRNA_CNMF'.

  • NRAS mutation correlated to 'RPPA_CHIERARCHICAL'.

  • FMN2 mutation correlated to 'MRNASEQ_CNMF'.

  • SHROOM4 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • CDH1 mutation correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CTNNB1 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • KRAS mutation correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • VCX2 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • PIK3CA mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • BRAF mutation correlated to 'MRNASEQ_CNMF'.

  • KIAA1804 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • CREBBP mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 40 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, 24 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
CRIPAK 11 (9%) 111 0.643
(1.00) 		0.361
(0.938) 		0.298
(0.839) 		0.0991
(0.547) 		0.00178
(0.0834) 		0.00252
(0.0864) 		0.00224
(0.0834) 		0.00126
(0.0672) 		0.268
(0.799) 		0.761
(1.00)
PIK3CA 36 (30%) 86 0.855
(1.00) 		0.988
(1.00) 		0.162
(0.674) 		0.709
(1.00) 		0.087
(0.491) 		0.265
(0.799) 		1e-05
(0.0012) 		1e-05
(0.0012) 		1e-05
(0.0012) 		1e-05
(0.0012) 		0.113
(0.589) 		0.24
(0.782)
CDH1 12 (10%) 110 0.76
(1.00) 		0.397
(0.962) 		1
(1.00) 		0.195
(0.699) 		0.0135
(0.26) 		0.00492
(0.131) 		0.00396
(0.119) 		0.00887
(0.185) 		0.48
(0.988) 		0.691
(1.00)
SHROOM4 7 (6%) 115 0.47
(0.988) 		0.555
(1.00) 		0.481
(0.988) 		0.758
(1.00) 		0.0159
(0.274) 		0.00226
(0.0834) 		0.0192
(0.289) 		0.00207
(0.0834) 		0.184
(0.699) 		0.128
(0.629)
CTNNB1 19 (16%) 103 0.052
(0.378) 		0.179
(0.699) 		0.9
(1.00) 		0.752
(1.00) 		0.259
(0.799) 		0.0437
(0.345) 		0.0238
(0.332) 		0.00028
(0.0192) 		0.0166
(0.275) 		0.00026
(0.0192) 		1
(1.00) 		0.164
(0.674)
KRAS 63 (52%) 59 0.187
(0.699) 		0.00707
(0.162) 		0.00646
(0.155) 		0.0279
(0.344) 		0.299
(0.839) 		0.0372
(0.344) 		0.457
(0.988) 		0.159
(0.674) 		0.863
(1.00) 		0.0531
(0.38) 		0.686
(1.00) 		0.16
(0.674)
TP53 91 (75%) 31 0.00079
(0.0474) 		0.0292
(0.344) 		0.0292
(0.344) 		0.75
(1.00) 		0.243
(0.782) 		0.187
(0.699) 		0.22
(0.743) 		0.098
(0.547) 		0.116
(0.599) 		0.0242
(0.332) 		0.268
(0.799) 		0.295
(0.838)
NRAS 11 (9%) 111 1
(1.00) 		0.889
(1.00) 		0.521
(1) 		1
(1.00) 		0.615
(1.00) 		0.00329
(0.105) 		0.557
(1.00) 		0.572
(1.00) 		0.491
(0.995) 		0.252
(0.799) 		0.883
(1.00) 		0.0572
(0.392)
FMN2 14 (11%) 108 0.278
(0.809) 		0.86
(1.00) 		0.0365
(0.344) 		0.506
(0.996) 		0.448
(0.988) 		0.104
(0.568) 		0.00989
(0.198) 		0.109
(0.581) 		0.0344
(0.344) 		0.03
(0.344) 		0.496
(0.995) 		1
(1.00)
VCX2 5 (4%) 117 0.734
(1.00) 		0.363
(0.938) 		0.571
(1.00) 		0.146
(0.654) 		0.0366
(0.344) 		0.124
(0.618) 		0.0432
(0.345) 		0.00856
(0.185) 		0.527
(1.00) 		0.32
(0.882)
BRAF 13 (11%) 109 0.769
(1.00) 		0.86
(1.00) 		0.867
(1.00) 		0.313
(0.873) 		0.845
(1.00) 		0.016
(0.274) 		0.00439
(0.124) 		0.121
(0.615) 		0.138
(0.637) 		0.0373
(0.344) 		0.907
(1.00) 		0.0415
(0.345)
KIAA1804 10 (8%) 112 0.513
(0.999) 		0.813
(1.00) 		0.0203
(0.295) 		0.535
(1.00) 		0.455
(0.988) 		0.507
(0.996) 		0.459
(0.988) 		0.0793
(0.485) 		0.0054
(0.136)
CREBBP 10 (8%) 112 0.484
(0.988) 		0.22
(0.743) 		0.168
(0.684) 		0.428
(0.988) 		2e-05
(0.00192) 		0.0382
(0.345) 		0.137
(0.637) 		0.173
(0.688) 		0.893
(1.00) 		0.497
(0.995)
APC 108 (89%) 14 0.615
(1.00) 		0.965
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.48
(0.988) 		0.413
(0.977) 		0.0861
(0.491) 		0.0596
(0.403) 		0.419
(0.985)
RPTN 5 (4%) 117 0.742
(1.00) 		0.852
(1.00) 		0.0364
(0.344) 		0.462
(0.988) 		0.0514
(0.378) 		0.0462
(0.358) 		0.0665
(0.437) 		0.0699
(0.454) 		1
(1.00) 		0.412
(0.977)
ARID1A 11 (9%) 111 0.367
(0.938) 		0.39
(0.956) 		0.469
(0.988) 		0.354
(0.934) 		0.885
(1.00) 		0.148
(0.654) 		0.815
(1.00) 		0.827
(1.00) 		0.492
(0.995) 		0.606
(1.00) 		0.669
(1.00) 		0.163
(0.674)
RBM10 6 (5%) 116 0.723
(1.00) 		0.987
(1.00) 		0.778
(1.00) 		0.409
(0.977) 		0.806
(1.00) 		0.483
(0.988) 		0.922
(1.00) 		0.624
(1.00) 		0.553
(1.00)
HAUS6 5 (4%) 117 0.329
(0.892) 		1
(1.00) 		0.473
(0.988) 		0.367
(0.938) 		0.0813
(0.487) 		0.195
(0.699) 		0.194
(0.699) 		0.192
(0.699) 		0.885
(1.00) 		0.146
(0.654)
GABRP 4 (3%) 118 0.67
(1.00) 		1
(1.00) 		0.346
(0.923) 		0.277
(0.809) 		0.18
(0.699) 		0.824
(1.00)
PON3 4 (3%) 118 0.138
(0.637) 		0.813
(1.00) 		0.0334
(0.344) 		0.071
(0.455) 		0.0565
(0.392) 		0.0336
(0.344) 		0.185
(0.699) 		0.645
(1.00)
RLIM 4 (3%) 118 0.213
(0.736) 		0.0193
(0.289) 		0.47
(0.988) 		0.54
(1.00) 		0.0439
(0.345) 		0.0403
(0.345) 		0.466
(0.988) 		0.519
(1)
SMAD2 6 (5%) 116 1
(1.00) 		0.751
(1.00) 		0.213
(0.736) 		1
(1.00) 		0.137
(0.637) 		0.349
(0.926) 		0.964
(1.00) 		0.989
(1.00) 		0.958
(1.00) 		0.644
(1.00)
TCF7L2 12 (10%) 110 1
(1.00) 		0.436
(0.988) 		0.74
(1.00) 		0.751
(1.00) 		0.572
(1.00) 		0.134
(0.637) 		0.959
(1.00) 		0.671
(1.00) 		0.446
(0.988) 		0.842
(1.00) 		0.34
(0.912) 		0.835
(1.00)
OXSM 4 (3%) 118 0.907
(1.00) 		0.479
(0.988) 		0.371
(0.938) 		0.0798
(0.485) 		0.407
(0.977) 		0.0849
(0.491) 		0.469
(0.988) 		0.385
(0.952)
PCBP1 5 (4%) 117 0.548
(1.00) 		0.619
(1.00) 		0.261
(0.799) 		0.644
(1.00) 		0.337
(0.91) 		0.554
(1.00) 		0.776
(1.00) 		0.589
(1.00)
FLT1 8 (7%) 114 0.836
(1.00) 		0.854
(1.00) 		0.551
(1.00) 		0.329
(0.892) 		0.0284
(0.344) 		0.218
(0.743) 		0.158
(0.674) 		0.384
(0.952) 		0.122
(0.615) 		0.58
(1.00)
SLC12A6 6 (5%) 116 0.454
(0.988) 		0.447
(0.988) 		0.172
(0.687) 		0.87
(1.00) 		0.0416
(0.345) 		0.15
(0.655) 		0.266
(0.799) 		0.326
(0.892)
AKAP9 7 (6%) 115 0.77
(1.00) 		0.714
(1.00) 		0.375
(0.942) 		0.549
(1.00) 		0.247
(0.792) 		0.261
(0.799) 		0.0503
(0.378) 		0.0341
(0.344) 		0.931
(1.00) 		0.676
(1.00)
ELF3 4 (3%) 118 0.498
(0.995) 		0.861
(1.00) 		0.674
(1.00) 		0.368
(0.938) 		0.154
(0.664) 		0.274
(0.809) 		0.148
(0.654) 		1
(1.00) 		0.289
(0.831)
ERBB2 9 (7%) 113 1
(1.00) 		0.849
(1.00) 		0.44
(0.988) 		0.208
(0.736) 		0.107
(0.578) 		0.389
(0.956) 		0.0183
(0.289) 		0.0775
(0.483) 		0.796
(1.00) 		0.382
(0.952) 		0.883
(1.00) 		0.578
(1.00)
CDKL5 4 (3%) 118 0.741
(1.00) 		1
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.035
(0.344) 		0.371
(0.938) 		0.466
(0.988) 		0.516
(0.999)
ZNF354C 5 (4%) 117 0.681
(1.00) 		0.292
(0.834) 		0.042
(0.345) 		0.707
(1.00) 		0.0151
(0.274) 		0.206
(0.734) 		0.243
(0.782) 		0.193
(0.699) 		0.884
(1.00) 		0.147
(0.654)
LIG1 4 (3%) 118 0.818
(1.00) 		0.448
(0.988) 		0.722
(1.00) 		0.539
(1.00) 		0.0261
(0.344) 		0.125
(0.618) 		0.0822
(0.487) 		0.0327
(0.344)
IQCD 3 (2%) 119 0.864
(1.00) 		0.0865
(0.491) 		0.276
(0.809) 		0.508
(0.996) 		0.572
(1.00)
ZBED4 4 (3%) 118 0.213
(0.736) 		0.483
(0.988) 		0.0636
(0.424) 		0.461
(0.988) 		0.0435
(0.345) 		0.571
(1.00) 		0.828
(1.00) 		1
(1.00)
GMCL1 4 (3%) 118 0.906
(1.00) 		0.265
(0.799) 		0.138
(0.637) 		0.462
(0.988) 		0.0759
(0.479) 		0.229
(0.763) 		0.506
(0.996) 		0.516
(0.999) 		0.884
(1.00) 		0.268
(0.799)
CIR1 3 (2%) 119 0.865
(1.00) 		0.359
(0.938) 		0.112
(0.589) 		0.233
(0.765) 		0.17
(0.685) 		0.192
(0.699)
AGL 4 (3%) 118 0.439
(0.988) 		0.263
(0.799) 		0.853
(1.00) 		0.317
(0.881) 		0.697
(1.00) 		0.547
(1.00) 		0.826
(1.00)
FAM123B 10 (8%) 112 0.857
(1.00) 		0.411
(0.977) 		0.225
(0.755) 		0.501
(0.996) 		0.428
(0.988) 		0.426
(0.988) 		0.651
(1.00) 		0.282
(0.816) 		0.61
(1.00) 		0.673
(1.00)
VANGL1 3 (2%) 119 0.396
(0.962) 		1
(1.00) 		1
(1.00) 		0.057
(0.392) 		0.23
(0.763) 		0.0505
(0.378) 		0.195
(0.699)
'APC MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
APC MUTATED 20 16 17
APC WILD-TYPE 5 5 2
'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
APC MUTATED 4 11 9 8 5 7 7 2
APC WILD-TYPE 2 2 3 1 1 2 1 0
'APC MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
APC MUTATED 45 18 17 26
APC WILD-TYPE 6 2 2 4
'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
APC MUTATED 27 17 17 21 3
APC WILD-TYPE 3 2 5 2 0
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.99

Table S5.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
APC MUTATED 15 15 11 12 21 11
APC WILD-TYPE 4 1 3 2 2 0
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 0.98

Table S6.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
APC MUTATED 14 13 20 13 48
APC WILD-TYPE 2 0 2 0 9
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0861 (Fisher's exact test), Q value = 0.49

Table S7.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
APC MUTATED 11 23 6 12 27 15 14
APC WILD-TYPE 0 0 2 0 5 3 3
'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0596 (Fisher's exact test), Q value = 0.4

Table S8.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
APC MUTATED 11 28 14 7 46
APC WILD-TYPE 2 0 0 1 9
'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.419 (Fisher's exact test), Q value = 0.98

Table S9.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
APC MUTATED 19 41 46
APC WILD-TYPE 1 3 8
'CRIPAK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CRIPAK MUTATED 7 1 1 2
CRIPAK WILD-TYPE 44 19 18 28
'CRIPAK MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.94

Table S11.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CRIPAK MUTATED 5 4 2
CRIPAK WILD-TYPE 11 19 16
'CRIPAK MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 0.84

Table S12.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
CRIPAK MUTATED 5 1 0 2 0
CRIPAK WILD-TYPE 25 18 22 21 3
'CRIPAK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0991 (Fisher's exact test), Q value = 0.55

Table S13.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
CRIPAK MUTATED 0 3 2 0 1 2
CRIPAK WILD-TYPE 19 13 12 14 22 9
'CRIPAK MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.083

Table S14.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CRIPAK MUTATED 2 3 4 2 0
CRIPAK WILD-TYPE 14 10 18 11 57

Figure S1.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CRIPAK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.086

Table S15.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CRIPAK MUTATED 2 6 1 2 0 0 0
CRIPAK WILD-TYPE 9 17 7 10 32 18 17

Figure S2.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CRIPAK MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.083

Table S16.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CRIPAK MUTATED 2 5 3 1 0
CRIPAK WILD-TYPE 11 23 11 7 55

Figure S3.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CRIPAK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.067

Table S17.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CRIPAK MUTATED 4 7 0
CRIPAK WILD-TYPE 16 37 54

Figure S4.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CRIPAK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.8

Table S18.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CRIPAK MUTATED 3 1 1 3
CRIPAK WILD-TYPE 5 6 12 5
'CRIPAK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CRIPAK MUTATED 2 1 3 1 1
CRIPAK WILD-TYPE 6 8 9 4 1
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.047

Table S20.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
TP53 MUTATED 9 15 17
TP53 WILD-TYPE 16 6 2

Figure S5.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.34

Table S21.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
TP53 MUTATED 2 9 5 9 5 6 5 0
TP53 WILD-TYPE 4 4 7 0 1 3 3 2

Figure S6.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.34

Table S22.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
TP53 MUTATED 32 17 18 22
TP53 WILD-TYPE 19 3 1 8

Figure S7.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
TP53 MUTATED 14 20 17
TP53 WILD-TYPE 2 3 1
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 0.78

Table S24.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
TP53 MUTATED 18 16 16 19 3
TP53 WILD-TYPE 12 3 6 4 0
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.7

Table S25.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
TP53 MUTATED 12 12 13 11 14 10
TP53 WILD-TYPE 7 4 1 3 9 1
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.74

Table S26.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
TP53 MUTATED 12 12 15 12 39
TP53 WILD-TYPE 4 1 7 1 18
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.098 (Fisher's exact test), Q value = 0.55

Table S27.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
TP53 MUTATED 11 19 7 10 21 10 12
TP53 WILD-TYPE 0 4 1 2 11 8 5
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.6

Table S28.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
TP53 MUTATED 10 25 11 7 35
TP53 WILD-TYPE 3 3 3 1 20
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.33

Table S29.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
TP53 MUTATED 18 36 34
TP53 WILD-TYPE 2 8 20

Figure S8.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.8

Table S30.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
TP53 MUTATED 8 5 10 8
TP53 WILD-TYPE 0 2 3 0
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.84

Table S31.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
TP53 MUTATED 8 7 10 5 1
TP53 WILD-TYPE 0 2 2 0 1
'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S32.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
NRAS MUTATED 2 2 1
NRAS WILD-TYPE 23 19 18
'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
NRAS MUTATED 1 2 1 1 0 0 0 0
NRAS WILD-TYPE 5 11 11 8 6 9 8 2
'NRAS MUTATION STATUS' versus 'CN_CNMF'

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

Table S34.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
NRAS MUTATED 7 2 1 1
NRAS WILD-TYPE 44 18 18 29
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S35.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
NRAS MUTATED 2 2 2
NRAS WILD-TYPE 14 21 16
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S36.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
NRAS MUTATED 2 0 2 3 0
NRAS WILD-TYPE 28 19 20 20 3
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00329 (Fisher's exact test), Q value = 0.11

Table S37.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
NRAS MUTATED 0 1 0 4 0 2
NRAS WILD-TYPE 19 15 14 10 23 9

Figure S9.  Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
NRAS MUTATED 1 1 4 0 5
NRAS WILD-TYPE 15 12 18 13 52
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
NRAS MUTATED 1 5 0 1 2 1 1
NRAS WILD-TYPE 10 18 8 11 30 17 16
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
NRAS MUTATED 1 4 2 1 3
NRAS WILD-TYPE 12 24 12 7 52
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 0.8

Table S41.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
NRAS MUTATED 0 6 5
NRAS WILD-TYPE 20 38 49
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
NRAS MUTATED 1 1 1 0
NRAS WILD-TYPE 7 6 12 8
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0572 (Fisher's exact test), Q value = 0.39

Table S43.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
NRAS MUTATED 1 0 0 1 1
NRAS WILD-TYPE 7 9 12 4 1
'FMN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.81

Table S44.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
FMN2 MUTATED 0 2 1
FMN2 WILD-TYPE 25 19 18
'FMN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
FMN2 MUTATED 0 1 0 1 0 0 1 0
FMN2 WILD-TYPE 6 12 12 8 6 9 7 2
'FMN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.34

Table S46.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
FMN2 MUTATED 4 0 5 5
FMN2 WILD-TYPE 47 20 14 25

Figure S10.  Get High-res Image Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FMN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S47.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
FMN2 MUTATED 4 6 2
FMN2 WILD-TYPE 12 17 16
'FMN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 0.99

Table S48.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
FMN2 MUTATED 2 1 2 5 0
FMN2 WILD-TYPE 28 18 20 18 3
'FMN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.57

Table S49.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
FMN2 MUTATED 0 2 2 4 1 1
FMN2 WILD-TYPE 19 14 12 10 22 10
'FMN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00989 (Fisher's exact test), Q value = 0.2

Table S50.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
FMN2 MUTATED 1 3 2 5 3
FMN2 WILD-TYPE 15 10 20 8 54

Figure S11.  Get High-res Image Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FMN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.58

Table S51.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
FMN2 MUTATED 3 4 1 3 2 1 0
FMN2 WILD-TYPE 8 19 7 9 30 17 17
'FMN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.34

Table S52.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
FMN2 MUTATED 1 8 2 0 3
FMN2 WILD-TYPE 12 20 12 8 52

Figure S12.  Get High-res Image Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FMN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.34

Table S53.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
FMN2 MUTATED 1 10 3
FMN2 WILD-TYPE 19 34 51

Figure S13.  Get High-res Image Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FMN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
FMN2 MUTATED 1 0 4 2
FMN2 WILD-TYPE 7 7 9 6
'FMN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S55.  Gene #5: 'FMN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
FMN2 MUTATED 2 2 2 1 0
FMN2 WILD-TYPE 6 7 10 4 2
'SHROOM4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.99

Table S56.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
SHROOM4 MUTATED 4 0 2 1
SHROOM4 WILD-TYPE 47 20 17 29
'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
SHROOM4 MUTATED 1 4 1
SHROOM4 WILD-TYPE 15 19 17
'SHROOM4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.99

Table S58.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
SHROOM4 MUTATED 3 1 0 3 0
SHROOM4 WILD-TYPE 27 18 22 20 3
'SHROOM4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S59.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
SHROOM4 MUTATED 0 2 1 1 2 1
SHROOM4 WILD-TYPE 19 14 13 13 21 10
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.27

Table S60.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
SHROOM4 MUTATED 1 1 3 2 0
SHROOM4 WILD-TYPE 15 12 19 11 57

Figure S14.  Get High-res Image Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.083

Table S61.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
SHROOM4 MUTATED 1 2 0 4 0 0 0
SHROOM4 WILD-TYPE 10 21 8 8 32 18 17

Figure S15.  Get High-res Image Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.29

Table S62.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
SHROOM4 MUTATED 1 4 2 0 0
SHROOM4 WILD-TYPE 12 24 12 8 55

Figure S16.  Get High-res Image Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.083

Table S63.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
SHROOM4 MUTATED 0 7 0
SHROOM4 WILD-TYPE 20 37 54

Figure S17.  Get High-res Image Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.7

Table S64.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
SHROOM4 MUTATED 1 0 0 2
SHROOM4 WILD-TYPE 7 7 13 6
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.63

Table S65.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
SHROOM4 MUTATED 0 0 1 2 0
SHROOM4 WILD-TYPE 8 9 11 3 2
'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S66.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RPTN MUTATED 1 1 1 1
RPTN WILD-TYPE 50 19 18 29
'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
RPTN MUTATED 2 2 1
RPTN WILD-TYPE 14 21 17
'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.34

Table S68.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
RPTN MUTATED 1 2 0 0 1
RPTN WILD-TYPE 29 17 22 23 2

Figure S18.  Get High-res Image Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 0.99

Table S69.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
RPTN MUTATED 0 2 1 0 1 0
RPTN WILD-TYPE 19 14 13 14 22 11
'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0514 (Fisher's exact test), Q value = 0.38

Table S70.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RPTN MUTATED 2 1 1 1 0
RPTN WILD-TYPE 14 12 21 12 57
'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.36

Table S71.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RPTN MUTATED 1 1 1 2 0 0 0
RPTN WILD-TYPE 10 22 7 10 32 18 17

Figure S19.  Get High-res Image Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0665 (Fisher's exact test), Q value = 0.44

Table S72.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RPTN MUTATED 1 2 1 1 0
RPTN WILD-TYPE 12 26 13 7 55
'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0699 (Fisher's exact test), Q value = 0.45

Table S73.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RPTN MUTATED 1 4 0
RPTN WILD-TYPE 19 40 54
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S74.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
RPTN MUTATED 1 1 1 1
RPTN WILD-TYPE 7 6 12 7
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.98

Table S75.  Gene #7: 'RPTN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
RPTN MUTATED 1 2 0 1 0
RPTN WILD-TYPE 7 7 12 4 2
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.94

Table S76.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
ARID1A MUTATED 3 2 0
ARID1A WILD-TYPE 22 19 19
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.96

Table S77.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
ARID1A MUTATED 1 1 1 0 0 1 0 1
ARID1A WILD-TYPE 5 12 11 9 6 8 8 1
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.99

Table S78.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ARID1A MUTATED 6 3 1 1
ARID1A WILD-TYPE 45 17 18 29
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.93

Table S79.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
ARID1A MUTATED 3 1 2
ARID1A WILD-TYPE 13 22 16
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S80.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
ARID1A MUTATED 1 1 2 1 0
ARID1A WILD-TYPE 29 18 20 22 3
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.65

Table S81.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
ARID1A MUTATED 2 0 2 0 0 1
ARID1A WILD-TYPE 17 16 12 14 23 10
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S82.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ARID1A MUTATED 2 2 1 1 5
ARID1A WILD-TYPE 14 11 21 12 52
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ARID1A MUTATED 2 3 0 1 2 1 2
ARID1A WILD-TYPE 9 20 8 11 30 17 15
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 1

Table S84.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ARID1A MUTATED 1 4 2 0 3
ARID1A WILD-TYPE 12 24 12 8 52
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S85.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ARID1A MUTATED 2 5 3
ARID1A WILD-TYPE 18 39 51
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.669 (Fisher's exact test), Q value = 1

Table S86.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
ARID1A MUTATED 2 0 1 1
ARID1A WILD-TYPE 6 7 12 7
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.67

Table S87.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
ARID1A MUTATED 3 0 1 0 0
ARID1A WILD-TYPE 5 9 11 5 2
'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.76 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CDH1 MUTATED 6 1 1 4
CDH1 WILD-TYPE 45 19 18 26
'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.96

Table S89.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CDH1 MUTATED 5 3 3
CDH1 WILD-TYPE 11 20 15
'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S90.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
CDH1 MUTATED 3 2 2 2 0
CDH1 WILD-TYPE 27 17 20 21 3
'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.7

Table S91.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
CDH1 MUTATED 1 2 0 2 1 3
CDH1 WILD-TYPE 18 14 14 12 22 8
'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.26

Table S92.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CDH1 MUTATED 3 3 3 2 1
CDH1 WILD-TYPE 13 10 19 11 56

Figure S20.  Get High-res Image Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00492 (Fisher's exact test), Q value = 0.13

Table S93.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CDH1 MUTATED 1 6 1 3 0 1 0
CDH1 WILD-TYPE 10 17 7 9 32 17 17

Figure S21.  Get High-res Image Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.12

Table S94.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CDH1 MUTATED 1 6 4 0 1
CDH1 WILD-TYPE 12 22 10 8 54

Figure S22.  Get High-res Image Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00887 (Fisher's exact test), Q value = 0.19

Table S95.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CDH1 MUTATED 4 7 1
CDH1 WILD-TYPE 16 37 53

Figure S23.  Get High-res Image Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.99

Table S96.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CDH1 MUTATED 3 1 2 3
CDH1 WILD-TYPE 5 6 11 5
'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S97.  Gene #9: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CDH1 MUTATED 2 1 4 1 1
CDH1 WILD-TYPE 6 8 8 4 1
'RBM10 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S98.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
RBM10 MUTATED 3 1 1
RBM10 WILD-TYPE 22 20 18
'RBM10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S99.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
RBM10 MUTATED 1 1 1 1 0 1 0 0
RBM10 WILD-TYPE 5 12 11 8 6 8 8 2
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S100.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RBM10 MUTATED 4 1 0 1
RBM10 WILD-TYPE 47 19 19 29
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 0.98

Table S101.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
RBM10 MUTATED 3 0 0 2 0
RBM10 WILD-TYPE 27 19 22 21 3
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S102.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
RBM10 MUTATED 1 0 0 1 2 1
RBM10 WILD-TYPE 18 16 14 13 21 10
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.99

Table S103.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RBM10 MUTATED 0 1 2 0 2
RBM10 WILD-TYPE 16 12 20 13 55
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.922 (Fisher's exact test), Q value = 1

Table S104.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RBM10 MUTATED 0 2 0 0 2 1 0
RBM10 WILD-TYPE 11 21 8 12 30 17 17
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S105.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RBM10 MUTATED 0 1 0 1 4
RBM10 WILD-TYPE 13 27 14 7 51
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S106.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RBM10 MUTATED 1 1 4
RBM10 WILD-TYPE 19 43 50
'HAUS6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.89

Table S107.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
HAUS6 MUTATED 4 0 1 0
HAUS6 WILD-TYPE 47 20 18 30
'HAUS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S108.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
HAUS6 MUTATED 1 2 1
HAUS6 WILD-TYPE 15 21 17
'HAUS6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 0.99

Table S109.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
HAUS6 MUTATED 0 1 1 2 0
HAUS6 WILD-TYPE 30 18 21 21 3
'HAUS6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.94

Table S110.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
HAUS6 MUTATED 1 2 0 1 0 0
HAUS6 WILD-TYPE 18 14 14 13 23 11
'HAUS6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0813 (Fisher's exact test), Q value = 0.49

Table S111.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
HAUS6 MUTATED 1 2 0 1 1
HAUS6 WILD-TYPE 15 11 22 12 56
'HAUS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.7

Table S112.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
HAUS6 MUTATED 0 3 0 1 0 1 0
HAUS6 WILD-TYPE 11 20 8 11 32 17 17
'HAUS6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.7

Table S113.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
HAUS6 MUTATED 0 2 2 0 1
HAUS6 WILD-TYPE 13 26 12 8 54
'HAUS6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.7

Table S114.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
HAUS6 MUTATED 0 4 1
HAUS6 WILD-TYPE 20 40 53
'HAUS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S115.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
HAUS6 MUTATED 0 1 1 1
HAUS6 WILD-TYPE 8 6 12 7
'HAUS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.65

Table S116.  Gene #11: 'HAUS6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
HAUS6 MUTATED 0 0 2 0 1
HAUS6 WILD-TYPE 8 9 10 5 1
'CTNNB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.052 (Fisher's exact test), Q value = 0.38

Table S117.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
CTNNB1 MUTATED 0 3 0
CTNNB1 WILD-TYPE 25 18 19
'CTNNB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 0.7

Table S118.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
CTNNB1 MUTATED 0 3 0 0 0 0 0 0
CTNNB1 WILD-TYPE 6 10 12 9 6 9 8 2
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.9 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CTNNB1 MUTATED 7 3 3 6
CTNNB1 WILD-TYPE 44 17 16 24
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S120.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CTNNB1 MUTATED 4 8 4
CTNNB1 WILD-TYPE 12 15 14
'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.8

Table S121.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
CTNNB1 MUTATED 2 5 2 5 0
CTNNB1 WILD-TYPE 28 14 20 18 3
'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.35

Table S122.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
CTNNB1 MUTATED 0 4 3 3 1 3
CTNNB1 WILD-TYPE 19 12 11 11 22 8

Figure S24.  Get High-res Image Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.33

Table S123.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CTNNB1 MUTATED 6 3 3 3 4
CTNNB1 WILD-TYPE 10 10 19 10 53

Figure S25.  Get High-res Image Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.019

Table S124.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CTNNB1 MUTATED 5 5 1 4 0 4 0
CTNNB1 WILD-TYPE 6 18 7 8 32 14 17

Figure S26.  Get High-res Image Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.27

Table S125.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CTNNB1 MUTATED 2 9 4 0 4
CTNNB1 WILD-TYPE 11 19 10 8 51

Figure S27.  Get High-res Image Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.019

Table S126.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CTNNB1 MUTATED 0 15 4
CTNNB1 WILD-TYPE 20 29 50

Figure S28.  Get High-res Image Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S127.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CTNNB1 MUTATED 2 2 3 2
CTNNB1 WILD-TYPE 6 5 10 6
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.67

Table S128.  Gene #12: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CTNNB1 MUTATED 1 3 2 1 2
CTNNB1 WILD-TYPE 7 6 10 4 0
'GABRP MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
GABRP MUTATED 2 0 0 2
GABRP WILD-TYPE 49 20 19 28
'GABRP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
GABRP MUTATED 1 1 1
GABRP WILD-TYPE 15 22 17
'GABRP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.92

Table S131.  Gene #13: 'GABRP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
GABRP MUTATED 0 1 1 1 1
GABRP WILD-TYPE 16 12 21 12 56
'GABRP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.81

Table S132.  Gene #13: 'GABRP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
GABRP MUTATED 0 1 0 1 0 2 0
GABRP WILD-TYPE 11 22 8 11 32 16 17
'GABRP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 0.7

Table S133.  Gene #13: 'GABRP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
GABRP MUTATED 0 0 2 0 2
GABRP WILD-TYPE 13 28 12 8 53
'GABRP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S134.  Gene #13: 'GABRP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
GABRP MUTATED 1 1 2
GABRP WILD-TYPE 19 43 52
'PON3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.64

Table S135.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
PON3 MUTATED 1 1 2 0
PON3 WILD-TYPE 50 19 17 30
'PON3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S136.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
PON3 MUTATED 1 1 2
PON3 WILD-TYPE 15 22 16
'PON3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.34

Table S137.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
PON3 MUTATED 0 1 1 2 0
PON3 WILD-TYPE 16 12 21 11 57

Figure S29.  Get High-res Image Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PON3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.071 (Fisher's exact test), Q value = 0.45

Table S138.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
PON3 MUTATED 0 2 0 2 0 0 0
PON3 WILD-TYPE 11 21 8 10 32 18 17
'PON3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0565 (Fisher's exact test), Q value = 0.39

Table S139.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
PON3 MUTATED 0 2 2 0 0
PON3 WILD-TYPE 13 26 12 8 55
'PON3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.34

Table S140.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
PON3 MUTATED 0 4 0
PON3 WILD-TYPE 20 40 54

Figure S30.  Get High-res Image Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PON3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.7

Table S141.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
PON3 MUTATED 1 0 0 2
PON3 WILD-TYPE 7 7 13 6
'PON3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S142.  Gene #14: 'PON3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
PON3 MUTATED 1 0 1 1 0
PON3 WILD-TYPE 7 9 11 4 2
'RLIM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.74

Table S143.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RLIM MUTATED 2 0 2 0
RLIM WILD-TYPE 49 20 17 30
'RLIM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.29

Table S144.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
RLIM MUTATED 3 0 0
RLIM WILD-TYPE 13 23 18

Figure S31.  Get High-res Image Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'RLIM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.99

Table S145.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
RLIM MUTATED 1 0 0 2 0
RLIM WILD-TYPE 29 19 22 21 3
'RLIM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
RLIM MUTATED 0 0 1 0 1 1
RLIM WILD-TYPE 19 16 13 14 22 10
'RLIM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.35

Table S147.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RLIM MUTATED 1 0 1 2 0
RLIM WILD-TYPE 15 13 21 11 57

Figure S32.  Get High-res Image Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RLIM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.35

Table S148.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RLIM MUTATED 2 0 0 1 0 1 0
RLIM WILD-TYPE 9 23 8 11 32 17 17

Figure S33.  Get High-res Image Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RLIM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.99

Table S149.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RLIM MUTATED 1 1 1 0 1
RLIM WILD-TYPE 12 27 13 8 54
'RLIM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S150.  Gene #15: 'RLIM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RLIM MUTATED 1 2 1
RLIM WILD-TYPE 19 42 53
'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S151.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
SMAD2 MUTATED 1 1 1
SMAD2 WILD-TYPE 24 20 18
'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S152.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
SMAD2 MUTATED 0 0 1 0 0 1 1 0
SMAD2 WILD-TYPE 6 13 11 9 6 8 7 2
'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.74

Table S153.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
SMAD2 MUTATED 5 0 1 0
SMAD2 WILD-TYPE 46 20 18 30
'SMAD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S154.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
SMAD2 MUTATED 1 1 1
SMAD2 WILD-TYPE 15 22 17
'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.64

Table S155.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
SMAD2 MUTATED 0 1 0 3 0
SMAD2 WILD-TYPE 30 18 22 20 3
'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 0.93

Table S156.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
SMAD2 MUTATED 0 2 0 0 2 0
SMAD2 WILD-TYPE 19 14 14 14 21 11
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S157.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
SMAD2 MUTATED 1 1 1 0 3
SMAD2 WILD-TYPE 15 12 21 13 54
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.989 (Fisher's exact test), Q value = 1

Table S158.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
SMAD2 MUTATED 0 2 0 0 2 1 1
SMAD2 WILD-TYPE 11 21 8 12 30 17 16
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S159.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
SMAD2 MUTATED 0 1 1 0 4
SMAD2 WILD-TYPE 13 27 13 8 51
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S160.  Gene #16: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
SMAD2 MUTATED 0 2 4
SMAD2 WILD-TYPE 20 42 50
'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S161.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
TCF7L2 MUTATED 2 2 2
TCF7L2 WILD-TYPE 23 19 17
'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 0.99

Table S162.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
TCF7L2 MUTATED 1 0 1 1 1 0 2 0
TCF7L2 WILD-TYPE 5 13 11 8 5 9 6 2
'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S163.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
TCF7L2 MUTATED 4 2 3 3
TCF7L2 WILD-TYPE 47 18 16 27
'TCF7L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S164.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
TCF7L2 MUTATED 2 3 1
TCF7L2 WILD-TYPE 14 20 17
'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
TCF7L2 MUTATED 1 3 1 2 0
TCF7L2 WILD-TYPE 29 16 21 21 3
'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.64

Table S166.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
TCF7L2 MUTATED 0 2 0 3 1 1
TCF7L2 WILD-TYPE 19 14 14 11 22 10
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.959 (Fisher's exact test), Q value = 1

Table S167.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
TCF7L2 MUTATED 1 1 2 2 6
TCF7L2 WILD-TYPE 15 12 20 11 51
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S168.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
TCF7L2 MUTATED 1 3 1 1 5 0 1
TCF7L2 WILD-TYPE 10 20 7 11 27 18 16
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.99

Table S169.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
TCF7L2 MUTATED 1 5 0 0 5
TCF7L2 WILD-TYPE 12 23 14 8 50
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S170.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
TCF7L2 MUTATED 1 5 5
TCF7L2 WILD-TYPE 19 39 49
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.91

Table S171.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
TCF7L2 MUTATED 0 1 4 1
TCF7L2 WILD-TYPE 8 6 9 7
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S172.  Gene #17: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
TCF7L2 MUTATED 1 2 3 0 0
TCF7L2 WILD-TYPE 7 7 9 5 2
'OXSM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S173.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
OXSM MUTATED 2 0 1 1
OXSM WILD-TYPE 49 20 18 29
'OXSM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.99

Table S174.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
OXSM MUTATED 0 1 2
OXSM WILD-TYPE 16 22 16
'OXSM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.94

Table S175.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
OXSM MUTATED 0 0 1 2 0
OXSM WILD-TYPE 30 19 21 21 3
'OXSM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0798 (Fisher's exact test), Q value = 0.49

Table S176.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
OXSM MUTATED 0 0 1 2 0 0
OXSM WILD-TYPE 19 16 13 12 23 11
'OXSM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.98

Table S177.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
OXSM MUTATED 1 0 1 1 1
OXSM WILD-TYPE 15 13 21 12 56
'OXSM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0849 (Fisher's exact test), Q value = 0.49

Table S178.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
OXSM MUTATED 1 0 1 1 0 1 0
OXSM WILD-TYPE 10 23 7 11 32 17 17
'OXSM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.99

Table S179.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
OXSM MUTATED 1 1 1 0 1
OXSM WILD-TYPE 12 27 13 8 54
'OXSM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.95

Table S180.  Gene #18: 'OXSM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
OXSM MUTATED 0 3 1
OXSM WILD-TYPE 20 41 53
'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
PCBP1 MUTATED 4 0 0 1
PCBP1 WILD-TYPE 47 20 19 29
'PCBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S182.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
PCBP1 MUTATED 1 2 0
PCBP1 WILD-TYPE 15 21 18
'PCBP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.8

Table S183.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
PCBP1 MUTATED 0 1 0 2 0
PCBP1 WILD-TYPE 30 18 22 21 3
'PCBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
PCBP1 MUTATED 0 1 0 0 2 0
PCBP1 WILD-TYPE 19 15 14 14 21 11
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.91

Table S185.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
PCBP1 MUTATED 1 1 2 0 1
PCBP1 WILD-TYPE 15 12 20 13 56
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
PCBP1 MUTATED 0 3 0 0 1 1 0
PCBP1 WILD-TYPE 11 20 8 12 31 17 17
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
PCBP1 MUTATED 0 2 1 0 2
PCBP1 WILD-TYPE 13 26 13 8 53
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188.  Gene #19: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
PCBP1 MUTATED 0 3 2
PCBP1 WILD-TYPE 20 41 52
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.7

Table S189.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
KRAS MUTATED 17 10 8
KRAS WILD-TYPE 8 11 11
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.16

Table S190.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
KRAS MUTATED 3 10 9 3 3 5 0 2
KRAS WILD-TYPE 3 3 3 6 3 4 8 0

Figure S34.  Get High-res Image Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.16

Table S191.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
KRAS MUTATED 31 14 4 13
KRAS WILD-TYPE 20 6 15 17

Figure S35.  Get High-res Image Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.34

Table S192.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
KRAS MUTATED 3 14 10
KRAS WILD-TYPE 13 9 8

Figure S36.  Get High-res Image Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.84

Table S193.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
KRAS MUTATED 16 13 9 9 1
KRAS WILD-TYPE 14 6 13 14 2
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.34

Table S194.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
KRAS MUTATED 10 10 3 4 16 5
KRAS WILD-TYPE 9 6 11 10 7 6

Figure S37.  Get High-res Image Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.99

Table S195.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
KRAS MUTATED 8 6 15 5 28
KRAS WILD-TYPE 8 7 7 8 29
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.67

Table S196.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
KRAS MUTATED 4 12 4 7 11 13 11
KRAS WILD-TYPE 7 11 4 5 21 5 6
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S197.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
KRAS MUTATED 6 14 6 3 30
KRAS WILD-TYPE 7 14 8 5 25
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0531 (Fisher's exact test), Q value = 0.38

Table S198.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
KRAS MUTATED 5 24 30
KRAS WILD-TYPE 15 20 24
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S199.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
KRAS MUTATED 2 4 6 3
KRAS WILD-TYPE 6 3 7 5
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.67

Table S200.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
KRAS MUTATED 4 4 7 0 0
KRAS WILD-TYPE 4 5 5 5 2
'FLT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S201.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
FLT1 MUTATED 4 2 1 1
FLT1 WILD-TYPE 47 18 18 29
'FLT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
FLT1 MUTATED 2 2 1
FLT1 WILD-TYPE 14 21 17
'FLT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S203.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
FLT1 MUTATED 3 0 1 3 0
FLT1 WILD-TYPE 27 19 21 20 3
'FLT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 0.89

Table S204.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
FLT1 MUTATED 1 0 2 0 2 2
FLT1 WILD-TYPE 18 16 12 14 21 9
'FLT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.34

Table S205.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
FLT1 MUTATED 0 2 3 2 1
FLT1 WILD-TYPE 16 11 19 11 56

Figure S38.  Get High-res Image Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FLT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.74

Table S206.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
FLT1 MUTATED 2 2 1 1 0 1 1
FLT1 WILD-TYPE 9 21 7 11 32 17 16
'FLT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.67

Table S207.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
FLT1 MUTATED 2 1 2 1 2
FLT1 WILD-TYPE 11 27 12 7 53
'FLT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.95

Table S208.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
FLT1 MUTATED 1 5 2
FLT1 WILD-TYPE 19 39 52
'FLT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.61

Table S209.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
FLT1 MUTATED 0 1 0 2
FLT1 WILD-TYPE 8 6 13 6
'FLT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S210.  Gene #21: 'FLT1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
FLT1 MUTATED 0 2 1 0 0
FLT1 WILD-TYPE 8 7 11 5 2
'SLC12A6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.99

Table S211.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
SLC12A6 MUTATED 4 1 1 0
SLC12A6 WILD-TYPE 47 19 18 30
'SLC12A6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.99

Table S212.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
SLC12A6 MUTATED 0 3 1
SLC12A6 WILD-TYPE 16 20 17
'SLC12A6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.69

Table S213.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
SLC12A6 MUTATED 0 2 0 1 0
SLC12A6 WILD-TYPE 30 17 22 22 3
'SLC12A6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S214.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
SLC12A6 MUTATED 0 1 1 0 1 0
SLC12A6 WILD-TYPE 19 15 13 14 22 11
'SLC12A6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.35

Table S215.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
SLC12A6 MUTATED 1 3 1 0 1
SLC12A6 WILD-TYPE 15 10 21 13 56

Figure S39.  Get High-res Image Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SLC12A6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.65

Table S216.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
SLC12A6 MUTATED 0 3 0 1 0 2 0
SLC12A6 WILD-TYPE 11 20 8 11 32 16 17
'SLC12A6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.8

Table S217.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
SLC12A6 MUTATED 0 4 0 0 2
SLC12A6 WILD-TYPE 13 24 14 8 53
'SLC12A6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.89

Table S218.  Gene #22: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
SLC12A6 MUTATED 0 4 2
SLC12A6 WILD-TYPE 20 40 52
'AKAP9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S219.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
AKAP9 MUTATED 2 1 0
AKAP9 WILD-TYPE 23 20 19
'AKAP9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S220.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
AKAP9 MUTATED 0 1 2 0 0 0 0 0
AKAP9 WILD-TYPE 6 12 10 9 6 9 8 2
'AKAP9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.94

Table S221.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
AKAP9 MUTATED 4 2 1 0
AKAP9 WILD-TYPE 47 18 18 30
'AKAP9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S222.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
AKAP9 MUTATED 0 2 2
AKAP9 WILD-TYPE 16 21 16
'AKAP9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.79

Table S223.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
AKAP9 MUTATED 1 0 0 3 0
AKAP9 WILD-TYPE 29 19 22 20 3
'AKAP9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.8

Table S224.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
AKAP9 MUTATED 0 0 1 0 3 0
AKAP9 WILD-TYPE 19 16 13 14 20 11
'AKAP9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0503 (Fisher's exact test), Q value = 0.38

Table S225.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
AKAP9 MUTATED 0 2 3 1 1
AKAP9 WILD-TYPE 16 11 19 12 56
'AKAP9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.34

Table S226.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
AKAP9 MUTATED 0 2 0 1 0 4 0
AKAP9 WILD-TYPE 11 21 8 11 32 14 17

Figure S40.  Get High-res Image Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'AKAP9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S227.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
AKAP9 MUTATED 1 1 1 0 4
AKAP9 WILD-TYPE 12 27 13 8 51
'AKAP9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S228.  Gene #23: 'AKAP9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
AKAP9 MUTATED 0 3 4
AKAP9 WILD-TYPE 20 41 50
'VCX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S229.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
VCX2 MUTATED 2 0 1 2
VCX2 WILD-TYPE 49 20 18 28
'VCX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.94

Table S230.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
VCX2 MUTATED 3 1 1
VCX2 WILD-TYPE 13 22 17
'VCX2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S231.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
VCX2 MUTATED 1 2 0 1 0
VCX2 WILD-TYPE 29 17 22 22 3
'VCX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.65

Table S232.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
VCX2 MUTATED 0 2 1 0 0 1
VCX2 WILD-TYPE 19 14 13 14 23 10
'VCX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.34

Table S233.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
VCX2 MUTATED 1 1 1 2 0
VCX2 WILD-TYPE 15 12 21 11 57

Figure S41.  Get High-res Image Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VCX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.62

Table S234.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
VCX2 MUTATED 1 2 1 1 0 0 0
VCX2 WILD-TYPE 10 21 7 11 32 18 17
'VCX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.35

Table S235.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
VCX2 MUTATED 2 2 1 0 0
VCX2 WILD-TYPE 11 26 13 8 55

Figure S42.  Get High-res Image Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VCX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00856 (Fisher's exact test), Q value = 0.19

Table S236.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
VCX2 MUTATED 3 2 0
VCX2 WILD-TYPE 17 42 54

Figure S43.  Get High-res Image Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'VCX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S237.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
VCX2 MUTATED 0 1 2 2
VCX2 WILD-TYPE 8 6 11 6
'VCX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.88

Table S238.  Gene #24: 'VCX2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
VCX2 MUTATED 2 2 0 1 0
VCX2 WILD-TYPE 6 7 12 4 2
'ELF3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S239.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
ELF3 MUTATED 1 2 0
ELF3 WILD-TYPE 24 19 19
'ELF3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S240.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
ELF3 MUTATED 0 2 1 0 0 0 0 0
ELF3 WILD-TYPE 6 11 11 9 6 9 8 2
'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S241.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ELF3 MUTATED 2 0 0 2
ELF3 WILD-TYPE 49 20 19 28
'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.94

Table S242.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
ELF3 MUTATED 0 0 1 2 0
ELF3 WILD-TYPE 30 19 21 21 3
'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.66

Table S243.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
ELF3 MUTATED 1 0 0 2 0 0
ELF3 WILD-TYPE 18 16 14 12 23 11
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.81

Table S244.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ELF3 MUTATED 0 1 2 0 1
ELF3 WILD-TYPE 16 12 20 13 56
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.65

Table S245.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ELF3 MUTATED 0 1 1 0 0 2 0
ELF3 WILD-TYPE 11 22 7 12 32 16 17
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S246.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ELF3 MUTATED 0 1 0 0 3
ELF3 WILD-TYPE 13 27 14 8 52
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.83

Table S247.  Gene #25: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ELF3 MUTATED 1 0 3
ELF3 WILD-TYPE 19 44 51
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S248.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
PIK3CA MUTATED 2 1 2
PIK3CA WILD-TYPE 23 20 17
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.988 (Fisher's exact test), Q value = 1

Table S249.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
PIK3CA MUTATED 0 2 1 1 0 1 0 0
PIK3CA WILD-TYPE 6 11 11 8 6 8 8 2
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.67

Table S250.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
PIK3CA MUTATED 12 4 9 11
PIK3CA WILD-TYPE 39 16 10 19
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S251.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
PIK3CA MUTATED 9 11 11
PIK3CA WILD-TYPE 7 12 7
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.087 (Fisher's exact test), Q value = 0.49

Table S252.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
PIK3CA MUTATED 7 6 4 12 0
PIK3CA WILD-TYPE 23 13 18 11 3
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.8

Table S253.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
PIK3CA MUTATED 3 5 7 4 5 5
PIK3CA WILD-TYPE 16 11 7 10 18 6
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S254.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
PIK3CA MUTATED 9 5 8 10 4
PIK3CA WILD-TYPE 7 8 14 3 53

Figure S44.  Get High-res Image Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S255.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
PIK3CA MUTATED 8 9 5 7 2 4 1
PIK3CA WILD-TYPE 3 14 3 5 30 14 16

Figure S45.  Get High-res Image Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S256.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
PIK3CA MUTATED 6 18 5 1 5
PIK3CA WILD-TYPE 7 10 9 7 50

Figure S46.  Get High-res Image Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S257.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
PIK3CA MUTATED 7 24 4
PIK3CA WILD-TYPE 13 20 50

Figure S47.  Get High-res Image Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.59

Table S258.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
PIK3CA MUTATED 6 1 7 5
PIK3CA WILD-TYPE 2 6 6 3
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 0.78

Table S259.  Gene #26: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
PIK3CA MUTATED 5 2 7 4 1
PIK3CA WILD-TYPE 3 7 5 1 1
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S260.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
BRAF MUTATED 2 1 0
BRAF WILD-TYPE 23 20 19
'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S261.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
BRAF MUTATED 0 1 1 0 1 0 0 0
BRAF WILD-TYPE 6 12 11 9 5 9 8 2
'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S262.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
BRAF MUTATED 6 1 2 4
BRAF WILD-TYPE 45 19 17 26
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.87

Table S263.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
BRAF MUTATED 3 2 5
BRAF WILD-TYPE 13 21 13
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S264.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
BRAF MUTATED 4 4 2 3 0
BRAF WILD-TYPE 26 15 20 20 3
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.27

Table S265.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
BRAF MUTATED 0 2 4 2 1 4
BRAF WILD-TYPE 19 14 10 12 22 7

Figure S48.  Get High-res Image Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.12

Table S266.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
BRAF MUTATED 4 1 4 3 1
BRAF WILD-TYPE 12 12 18 10 56

Figure S49.  Get High-res Image Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.61

Table S267.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
BRAF MUTATED 2 4 2 2 1 2 0
BRAF WILD-TYPE 9 19 6 10 31 16 17
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.64

Table S268.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
BRAF MUTATED 3 5 2 0 3
BRAF WILD-TYPE 10 23 12 8 52
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.34

Table S269.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
BRAF MUTATED 4 7 2
BRAF WILD-TYPE 16 37 52

Figure S50.  Get High-res Image Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S270.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
BRAF MUTATED 2 1 1 1
BRAF WILD-TYPE 6 6 12 7
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.35

Table S271.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
BRAF MUTATED 0 3 0 1 1
BRAF WILD-TYPE 8 6 12 4 1

Figure S51.  Get High-res Image Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S272.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
KIAA1804 MUTATED 3 4 1
KIAA1804 WILD-TYPE 22 17 18
'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S273.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
KIAA1804 MUTATED 0 1 3 1 0 2 1 0
KIAA1804 WILD-TYPE 6 12 9 8 6 7 7 2
'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.3

Table S274.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
KIAA1804 MUTATED 9 0 0 1
KIAA1804 WILD-TYPE 42 20 19 29

Figure S52.  Get High-res Image Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S275.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
KIAA1804 MUTATED 4 0 2 3 0
KIAA1804 WILD-TYPE 26 19 20 20 3
'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.99

Table S276.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
KIAA1804 MUTATED 2 0 1 2 4 0
KIAA1804 WILD-TYPE 17 16 13 12 19 11
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S277.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
KIAA1804 MUTATED 0 1 3 0 6
KIAA1804 WILD-TYPE 16 12 19 13 51
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.99

Table S278.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
KIAA1804 MUTATED 0 2 0 0 3 4 1
KIAA1804 WILD-TYPE 11 21 8 12 29 14 16
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0793 (Fisher's exact test), Q value = 0.49

Table S279.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
KIAA1804 MUTATED 0 0 1 0 9
KIAA1804 WILD-TYPE 13 28 13 8 46
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0054 (Fisher's exact test), Q value = 0.14

Table S280.  Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
KIAA1804 MUTATED 1 0 9
KIAA1804 WILD-TYPE 19 44 45

Figure S53.  Get High-res Image Gene #28: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S281.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
ERBB2 MUTATED 2 1 1
ERBB2 WILD-TYPE 23 20 18
'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S282.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
ERBB2 MUTATED 0 1 2 1 0 0 0 0
ERBB2 WILD-TYPE 6 12 10 8 6 9 8 2
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.99

Table S283.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ERBB2 MUTATED 4 1 0 4
ERBB2 WILD-TYPE 47 19 19 26
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.74

Table S284.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
ERBB2 MUTATED 0 4 1
ERBB2 WILD-TYPE 16 19 17
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.58

Table S285.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
ERBB2 MUTATED 0 2 1 4 0
ERBB2 WILD-TYPE 30 17 21 19 3
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.96

Table S286.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
ERBB2 MUTATED 1 1 0 3 2 0
ERBB2 WILD-TYPE 18 15 14 11 21 11
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.29

Table S287.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ERBB2 MUTATED 2 3 3 0 1
ERBB2 WILD-TYPE 14 10 19 13 56

Figure S54.  Get High-res Image Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0775 (Fisher's exact test), Q value = 0.48

Table S288.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ERBB2 MUTATED 0 4 2 0 1 2 0
ERBB2 WILD-TYPE 11 19 6 12 31 16 17
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S289.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ERBB2 MUTATED 2 2 1 0 4
ERBB2 WILD-TYPE 11 26 13 8 51
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.95

Table S290.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ERBB2 MUTATED 0 5 4
ERBB2 WILD-TYPE 20 39 50
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S291.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
ERBB2 MUTATED 0 1 1 1
ERBB2 WILD-TYPE 8 6 12 7
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S292.  Gene #29: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
ERBB2 MUTATED 0 2 1 0 0
ERBB2 WILD-TYPE 8 7 11 5 2
'CDKL5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S293.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CDKL5 MUTATED 1 1 1 1
CDKL5 WILD-TYPE 50 19 18 29
'CDKL5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S294.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CDKL5 MUTATED 1 1 1
CDKL5 WILD-TYPE 15 22 17
'CDKL5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S295.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
CDKL5 MUTATED 1 0 1 1 0
CDKL5 WILD-TYPE 29 19 21 22 3
'CDKL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S296.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
CDKL5 MUTATED 1 0 0 0 1 1
CDKL5 WILD-TYPE 18 16 14 14 22 10
'CDKL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.34

Table S297.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CDKL5 MUTATED 0 1 1 2 0
CDKL5 WILD-TYPE 16 12 21 11 57

Figure S55.  Get High-res Image Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDKL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 0.94

Table S298.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CDKL5 MUTATED 1 1 0 1 0 1 0
CDKL5 WILD-TYPE 10 22 8 11 32 17 17
'CDKL5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.99

Table S299.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CDKL5 MUTATED 1 1 1 0 1
CDKL5 WILD-TYPE 12 27 13 8 54
'CDKL5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.516 (Fisher's exact test), Q value = 1

Table S300.  Gene #30: 'CDKL5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CDKL5 MUTATED 1 2 1
CDKL5 WILD-TYPE 19 42 53
'ZNF354C MUTATION STATUS' versus 'CN_CNMF'

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

Table S301.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ZNF354C MUTATED 3 0 0 2
ZNF354C WILD-TYPE 48 20 19 28
'ZNF354C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.83

Table S302.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
ZNF354C MUTATED 1 3 0
ZNF354C WILD-TYPE 15 20 18
'ZNF354C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.35

Table S303.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
ZNF354C MUTATED 0 1 0 4 0
ZNF354C WILD-TYPE 30 18 22 19 3

Figure S56.  Get High-res Image Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ZNF354C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S304.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
ZNF354C MUTATED 0 1 1 0 2 1
ZNF354C WILD-TYPE 19 15 13 14 21 10
'ZNF354C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.27

Table S305.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ZNF354C MUTATED 2 0 3 0 0
ZNF354C WILD-TYPE 14 13 19 13 57

Figure S57.  Get High-res Image Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ZNF354C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.73

Table S306.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ZNF354C MUTATED 1 2 1 0 0 1 0
ZNF354C WILD-TYPE 10 21 7 12 32 17 17
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 0.78

Table S307.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ZNF354C MUTATED 1 1 1 1 1
ZNF354C WILD-TYPE 12 27 13 7 54
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.7

Table S308.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ZNF354C MUTATED 0 4 1
ZNF354C WILD-TYPE 20 40 53
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S309.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
ZNF354C MUTATED 0 1 1 1
ZNF354C WILD-TYPE 8 6 12 7
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 0.65

Table S310.  Gene #31: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
ZNF354C MUTATED 0 0 2 0 1
ZNF354C WILD-TYPE 8 9 10 5 1
'LIG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S311.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
LIG1 MUTATED 3 0 0 1
LIG1 WILD-TYPE 48 20 19 29
'LIG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 0.99

Table S312.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
LIG1 MUTATED 0 3 1
LIG1 WILD-TYPE 16 20 17
'LIG1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S313.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
LIG1 MUTATED 2 0 0 1 0
LIG1 WILD-TYPE 28 19 22 22 3
'LIG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S314.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
LIG1 MUTATED 0 0 1 0 1 1
LIG1 WILD-TYPE 19 16 13 14 22 10
'LIG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.34

Table S315.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
LIG1 MUTATED 0 1 3 0 0
LIG1 WILD-TYPE 16 12 19 13 57

Figure S58.  Get High-res Image Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'LIG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.62

Table S316.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
LIG1 MUTATED 0 2 1 1 0 0 0
LIG1 WILD-TYPE 11 21 7 11 32 18 17
'LIG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0822 (Fisher's exact test), Q value = 0.49

Table S317.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
LIG1 MUTATED 0 2 1 1 0
LIG1 WILD-TYPE 13 26 13 7 55
'LIG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.34

Table S318.  Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
LIG1 MUTATED 0 4 0
LIG1 WILD-TYPE 20 40 54

Figure S59.  Get High-res Image Gene #32: 'LIG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'IQCD MUTATION STATUS' versus 'CN_CNMF'

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

Table S319.  Gene #33: 'IQCD MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
IQCD MUTATED 1 1 0 1
IQCD WILD-TYPE 50 19 19 29
'IQCD MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0865 (Fisher's exact test), Q value = 0.49

Table S320.  Gene #33: 'IQCD MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
IQCD MUTATED 0 1 2 0 0
IQCD WILD-TYPE 16 12 20 13 57
'IQCD MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.81

Table S321.  Gene #33: 'IQCD MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
IQCD MUTATED 0 1 1 0 0 1 0
IQCD WILD-TYPE 11 22 7 12 32 17 17
'IQCD MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S322.  Gene #33: 'IQCD MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
IQCD MUTATED 1 1 0 0 1
IQCD WILD-TYPE 12 27 14 8 54
'IQCD MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S323.  Gene #33: 'IQCD MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
IQCD MUTATED 1 1 1
IQCD WILD-TYPE 19 43 53
'ZBED4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.74

Table S324.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ZBED4 MUTATED 2 0 2 0
ZBED4 WILD-TYPE 49 20 17 30
'ZBED4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.99

Table S325.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
ZBED4 MUTATED 0 1 2
ZBED4 WILD-TYPE 16 22 16
'ZBED4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0636 (Fisher's exact test), Q value = 0.42

Table S326.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
ZBED4 MUTATED 0 3 0 1 0
ZBED4 WILD-TYPE 30 16 22 22 3
'ZBED4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 0.99

Table S327.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
ZBED4 MUTATED 0 2 1 0 1 0
ZBED4 WILD-TYPE 19 14 13 14 22 11
'ZBED4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.35

Table S328.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ZBED4 MUTATED 1 2 1 0 0
ZBED4 WILD-TYPE 15 11 21 13 57

Figure S60.  Get High-res Image Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ZBED4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S329.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ZBED4 MUTATED 0 1 0 1 0 1 1
ZBED4 WILD-TYPE 11 22 8 11 32 17 16
'ZBED4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S330.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ZBED4 MUTATED 0 2 0 0 2
ZBED4 WILD-TYPE 13 26 14 8 53
'ZBED4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S331.  Gene #34: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ZBED4 MUTATED 0 2 2
ZBED4 WILD-TYPE 20 42 52
'GMCL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S332.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
GMCL1 MUTATED 2 0 1 1
GMCL1 WILD-TYPE 49 20 18 29
'GMCL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.8

Table S333.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
GMCL1 MUTATED 1 0 2
GMCL1 WILD-TYPE 15 23 16
'GMCL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.64

Table S334.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
GMCL1 MUTATED 0 1 0 3 0
GMCL1 WILD-TYPE 30 18 22 20 3
'GMCL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 0.99

Table S335.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
GMCL1 MUTATED 0 2 0 1 1 0
GMCL1 WILD-TYPE 19 14 14 13 22 11
'GMCL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0759 (Fisher's exact test), Q value = 0.48

Table S336.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
GMCL1 MUTATED 1 0 2 1 0
GMCL1 WILD-TYPE 15 13 20 12 57
'GMCL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.76

Table S337.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
GMCL1 MUTATED 1 1 1 0 0 1 0
GMCL1 WILD-TYPE 10 22 7 12 32 17 17
'GMCL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S338.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
GMCL1 MUTATED 0 2 1 0 1
GMCL1 WILD-TYPE 13 26 13 8 54
'GMCL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.516 (Fisher's exact test), Q value = 1

Table S339.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
GMCL1 MUTATED 1 2 1
GMCL1 WILD-TYPE 19 42 53
'GMCL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S340.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
GMCL1 MUTATED 0 1 1 1
GMCL1 WILD-TYPE 8 6 12 7
'GMCL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.8

Table S341.  Gene #35: 'GMCL1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
GMCL1 MUTATED 0 1 1 0 1
GMCL1 WILD-TYPE 8 8 11 5 1
'CIR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S342.  Gene #36: 'CIR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CIR1 MUTATED 1 1 0 1
CIR1 WILD-TYPE 50 19 19 29
'CIR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 0.94

Table S343.  Gene #36: 'CIR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CIR1 MUTATED 2 1 0
CIR1 WILD-TYPE 14 22 18
'CIR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.59

Table S344.  Gene #36: 'CIR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CIR1 MUTATED 0 1 1 1 0
CIR1 WILD-TYPE 16 12 21 12 57
'CIR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.76

Table S345.  Gene #36: 'CIR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CIR1 MUTATED 1 1 0 1 0 0 0
CIR1 WILD-TYPE 10 22 8 11 32 18 17
'CIR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.69

Table S346.  Gene #36: 'CIR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CIR1 MUTATED 1 1 1 0 0
CIR1 WILD-TYPE 12 27 13 8 55
'CIR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.7

Table S347.  Gene #36: 'CIR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CIR1 MUTATED 1 2 0
CIR1 WILD-TYPE 19 42 54
'AGL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 0.99

Table S348.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
AGL MUTATED 3 1 0 0
AGL WILD-TYPE 48 19 19 30
'AGL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 0.8

Table S349.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
AGL MUTATED 0 0 2 2 0
AGL WILD-TYPE 30 19 20 21 3
'AGL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S350.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
AGL MUTATED 1 0 1 0 1 1
AGL WILD-TYPE 18 16 13 14 22 10
'AGL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.88

Table S351.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
AGL MUTATED 1 0 2 0 1
AGL WILD-TYPE 15 13 20 13 56
'AGL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S352.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
AGL MUTATED 0 1 1 0 1 1 0
AGL WILD-TYPE 11 22 7 12 31 17 17
'AGL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 1

Table S353.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
AGL MUTATED 0 1 0 1 2
AGL WILD-TYPE 13 27 14 7 53
'AGL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S354.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
AGL MUTATED 1 1 2
AGL WILD-TYPE 19 43 52
'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S355.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
FAM123B MUTATED 2 1 2
FAM123B WILD-TYPE 23 20 17
'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 0.98

Table S356.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
FAM123B MUTATED 0 1 1 0 2 0 1 0
FAM123B WILD-TYPE 6 12 11 9 4 9 7 2
'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.76

Table S357.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
FAM123B MUTATED 3 3 0 4
FAM123B WILD-TYPE 48 17 19 26
'FAM123B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S358.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
FAM123B MUTATED 1 1 3
FAM123B WILD-TYPE 15 22 15
'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.99

Table S359.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
FAM123B MUTATED 4 2 0 3 0
FAM123B WILD-TYPE 26 17 22 20 3
'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 0.99

Table S360.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
FAM123B MUTATED 1 0 1 1 4 2
FAM123B WILD-TYPE 18 16 13 13 19 9
'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S361.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
FAM123B MUTATED 2 0 3 1 4
FAM123B WILD-TYPE 14 13 19 12 53
'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.82

Table S362.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
FAM123B MUTATED 2 1 1 0 1 3 2
FAM123B WILD-TYPE 9 22 7 12 31 15 15
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S363.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
FAM123B MUTATED 2 2 0 0 6
FAM123B WILD-TYPE 11 26 14 8 49
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S364.  Gene #38: 'FAM123B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
FAM123B MUTATED 1 3 6
FAM123B WILD-TYPE 19 41 48
'VANGL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.96

Table S365.  Gene #39: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
VANGL1 MUTATED 3 0 0 0
VANGL1 WILD-TYPE 48 20 19 30
'VANGL1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S366.  Gene #39: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
VANGL1 MUTATED 1 0 1 1 0
VANGL1 WILD-TYPE 29 19 21 22 3
'VANGL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S367.  Gene #39: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
VANGL1 MUTATED 1 1 0 0 1 0
VANGL1 WILD-TYPE 18 15 14 14 22 11
'VANGL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.057 (Fisher's exact test), Q value = 0.39

Table S368.  Gene #39: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
VANGL1 MUTATED 2 0 1 0 0
VANGL1 WILD-TYPE 14 13 21 13 57
'VANGL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.76

Table S369.  Gene #39: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
VANGL1 MUTATED 0 2 0 1 0 0 0
VANGL1 WILD-TYPE 11 21 8 11 32 18 17
'VANGL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0505 (Fisher's exact test), Q value = 0.38

Table S370.  Gene #39: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
VANGL1 MUTATED 0 1 2 0 0
VANGL1 WILD-TYPE 13 27 12 8 55
'VANGL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.7

Table S371.  Gene #39: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
VANGL1 MUTATED 1 2 0
VANGL1 WILD-TYPE 19 42 54
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.99

Table S372.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CREBBP MUTATED 6 1 0 2
CREBBP WILD-TYPE 45 19 19 28
'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.74

Table S373.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CREBBP MUTATED 1 3 5
CREBBP WILD-TYPE 15 20 13
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.68

Table S374.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 19 22 23 3
CREBBP MUTATED 1 2 1 4 1
CREBBP WILD-TYPE 29 17 21 19 2
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.99

Table S375.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 19 16 14 14 23 11
CREBBP MUTATED 1 0 1 1 4 2
CREBBP WILD-TYPE 18 16 13 13 19 9
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0019

Table S376.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CREBBP MUTATED 2 0 8 0 0
CREBBP WILD-TYPE 14 13 14 13 57

Figure S61.  Get High-res Image Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.35

Table S377.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CREBBP MUTATED 1 4 2 1 0 2 0
CREBBP WILD-TYPE 10 19 6 11 32 16 17

Figure S62.  Get High-res Image Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.64

Table S378.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CREBBP MUTATED 1 4 1 2 2
CREBBP WILD-TYPE 12 24 13 6 53
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.69

Table S379.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CREBBP MUTATED 3 5 2
CREBBP WILD-TYPE 17 39 52
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S380.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CREBBP MUTATED 2 1 2 2
CREBBP WILD-TYPE 6 6 11 6
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S381.  Gene #40: 'CREBBP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CREBBP MUTATED 3 1 3 0 0
CREBBP WILD-TYPE 5 8 9 5 2
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/20018501/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/20140629/READ-TP.transferedmergedcluster.txt

  • Number of patients = 122

  • Number of significantly mutated genes = 40

  • Number of Molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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