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 46 genes and 10 molecular subtypes across 223 patients, 23 significant findings detected with P value < 0.05 and Q value < 0.25.

  • APC mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • TP53 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • KRAS mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • FBXW7 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • PIK3CA mutation correlated to 'CN_CNMF'.

  • BRAF mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • CDC27 mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • PCDHA3 mutation correlated to 'MRNA_CHIERARCHICAL'.

  • CASP8 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • PTEN mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • ZFP3 mutation correlated to 'MRNA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • RWDD2B mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 46 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 23 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
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
BRAF 21 (9%) 202 1e-05
(0.00401) 		1e-05
(0.00401) 		5e-05
(0.0196) 		0.401
(1.00) 		1
(1.00) 		0.221
(1.00) 		1e-05
(0.00401) 		1
(1.00) 		0.147
(1.00)
CASP8 10 (4%) 213 0.00029
(0.112) 		1e-05
(0.00401) 		0.00027
(0.105) 		0.043
(1.00) 		0.229
(1.00) 		1
(1.00) 		6e-05
(0.0235) 		1
(1.00) 		0.0572
(1.00)
KRAS 97 (43%) 126 0.00022
(0.0856) 		0.00032
(0.123) 		0.236
(1.00) 		0.107
(1.00) 		0.57
(1.00) 		0.954
(1.00) 		0.00296
(1.00) 		1e-05
(0.00401) 		0.0216
(1.00) 		0.14
(1.00)
TP53 117 (52%) 106 0.00288
(1.00) 		0.00076
(0.287) 		1e-05
(0.00401) 		0.754
(1.00) 		0.955
(1.00) 		0.048
(1.00) 		2e-05
(0.0079) 		0.0323
(1.00) 		0.256
(1.00)
CDC27 13 (6%) 210 0.00037
(0.142) 		0.247
(1.00) 		0.00017
(0.0663) 		0.937
(1.00) 		0.824
(1.00) 		0.495
(1.00) 		0.00381
(1.00) 		0.462
(1.00) 		0.00263
(0.973)
ZFP3 8 (4%) 215 0.00044
(0.168) 		0.0593
(1.00) 		0.00096
(0.361) 		0.291
(1.00) 		0.74
(1.00) 		0.248
(1.00) 		0.00043
(0.165) 		1
(1.00) 		0.00718
(1.00)
APC 163 (73%) 60 0.00566
(1.00) 		0.00092
(0.347) 		0.0429
(1.00) 		0.299
(1.00) 		0.155
(1.00) 		0.788
(1.00) 		3e-05
(0.0118) 		0.644
(1.00) 		0.833
(1.00)
FBXW7 38 (17%) 185 0.0595
(1.00) 		0.0181
(1.00) 		0.00111
(0.415) 		0.011
(1.00) 		0.119
(1.00) 		0.00476
(1.00) 		0.00015
(0.0586) 		0.417
(1.00) 		0.0132
(1.00)
PIK3CA 33 (15%) 190 0.203
(1.00) 		0.409
(1.00) 		0.00045
(0.171) 		0.0615
(1.00) 		0.312
(1.00) 		0.0761
(1.00) 		0.00302
(1.00) 		0.166
(1.00) 		0.744
(1.00)
PCDHA3 12 (5%) 211 0.045
(1.00) 		0.00031
(0.12) 		0.0521
(1.00) 		0.848
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.369
(1.00)
PTEN 7 (3%) 216 0.0274
(1.00) 		0.395
(1.00) 		0.0335
(1.00) 		0.546
(1.00) 		1
(1.00) 		0.0976
(1.00) 		0.00059
(0.224) 		0.347
(1.00) 		0.0251
(1.00)
RWDD2B 7 (3%) 216 0.0266
(1.00) 		0.734
(1.00) 		0.0329
(1.00) 		0.859
(1.00) 		0.486
(1.00) 		1
(1.00) 		0.203
(1.00) 		1
(1.00) 		0.0006
(0.227)
NRAS 20 (9%) 203 0.0466
(1.00) 		0.0325
(1.00) 		0.0812
(1.00) 		0.908
(1.00) 		0.635
(1.00) 		0.313
(1.00) 		0.243
(1.00) 		0.266
(1.00) 		0.628
(1.00)
SMAD4 26 (12%) 197 0.0313
(1.00) 		0.0737
(1.00) 		0.0948
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.114
(1.00) 		1
(1.00) 		0.367
(1.00)
SMAD2 15 (7%) 208 0.131
(1.00) 		0.677
(1.00) 		0.104
(1.00) 		0.591
(1.00) 		0.674
(1.00) 		0.68
(1.00) 		0.00593
(1.00) 		1
(1.00) 		0.731
(1.00)
FAM123B 24 (11%) 199 0.09
(1.00) 		0.303
(1.00) 		0.00876
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.215
(1.00) 		0.337
(1.00) 		1
(1.00) 		0.0612
(1.00)
TCF7L2 18 (8%) 205 1
(1.00) 		0.634
(1.00) 		0.859
(1.00) 		0.838
(1.00) 		0.609
(1.00) 		0.342
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.131
(1.00)
ARID1A 20 (9%) 203 0.0238
(1.00) 		0.195
(1.00) 		0.00425
(1.00) 		0.978
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.364
(1.00) 		1
(1.00) 		0.0134
(1.00)
MGC42105 11 (5%) 212 0.00154
(0.573) 		0.0588
(1.00) 		0.11
(1.00) 		0.135
(1.00) 		1
(1.00) 		1
(1.00) 		0.0259
(1.00) 		1
(1.00) 		0.246
(1.00)
ACVR1B 14 (6%) 209 0.372
(1.00) 		0.027
(1.00) 		0.01
(1.00) 		0.734
(1.00) 		0.192
(1.00) 		1
(1.00) 		0.0827
(1.00) 		0.581
(1.00) 		0.226
(1.00)
KIAA1804 15 (7%) 208 0.268
(1.00) 		0.894
(1.00) 		0.0177
(1.00) 		0.504
(1.00) 		0.75
(1.00) 		0.68
(1.00) 		0.0531
(1.00) 		1
(1.00) 		0.208
(1.00)
PCDHGB1 8 (4%) 215 0.206
(1.00) 		0.197
(1.00) 		0.0977
(1.00) 		0.508
(1.00) 		0.671
(1.00) 		0.69
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.25
(1.00)
PCBP1 5 (2%) 218 0.566
(1.00) 		0.729
(1.00) 		0.739
(1.00) 		1
(1.00) 		0.462
(1.00) 		1
(1.00) 		1
(1.00)
ZHX2 10 (4%) 213 0.118
(1.00) 		0.223
(1.00) 		0.464
(1.00) 		0.237
(1.00) 		0.221
(1.00) 		0.656
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.205
(1.00)
PCDHA2 12 (5%) 211 0.206
(1.00) 		0.784
(1.00) 		0.0514
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.903
(1.00) 		0.541
(1.00) 		0.523
(1.00) 		0.0798
(1.00)
ELF3 8 (4%) 215 0.795
(1.00) 		0.799
(1.00) 		0.0361
(1.00) 		0.879
(1.00) 		0.339
(1.00) 		0.0176
(1.00) 		0.0835
(1.00) 		1
(1.00) 		0.257
(1.00)
CRTC1 4 (2%) 219 0.065
(1.00) 		0.117
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.547
(1.00) 		1
(1.00) 		1
(1.00)
CACNG3 8 (4%) 215 0.0153
(1.00) 		0.203
(1.00) 		0.00263
(0.973) 		0.125
(1.00) 		0.336
(1.00) 		0.163
(1.00) 		0.022
(1.00) 		0.388
(1.00) 		0.0267
(1.00)
PCDHGA7 5 (2%) 218 0.365
(1.00) 		0.492
(1.00) 		0.217
(1.00) 		0.72
(1.00) 		1
(1.00) 		1
(1.00) 		0.647
(1.00)
CCBP2 10 (4%) 213 0.159
(1.00) 		0.0374
(1.00) 		0.387
(1.00) 		0.0707
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.0874
(1.00) 		1
(1.00) 		0.372
(1.00)
MAP2K4 11 (5%) 212 0.461
(1.00) 		0.448
(1.00) 		0.037
(1.00) 		0.101
(1.00) 		0.524
(1.00) 		0.499
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.375
(1.00)
PCDHGA9 6 (3%) 217 0.0684
(1.00) 		0.0768
(1.00) 		0.658
(1.00) 		0.671
(1.00) 		0.592
(1.00) 		0.447
(1.00) 		0.12
(1.00) 		1
(1.00) 		0.734
(1.00)
RBM10 8 (4%) 215 0.279
(1.00) 		0.738
(1.00) 		0.9
(1.00) 		0.238
(1.00) 		0.739
(1.00) 		1
(1.00) 		0.076
(1.00) 		1
(1.00) 		1
(1.00)
DNMT1 17 (8%) 206 0.0238
(1.00) 		0.0652
(1.00) 		0.113
(1.00) 		0.0533
(1.00) 		0.334
(1.00) 		0.407
(1.00) 		0.00432
(1.00) 		1
(1.00) 		0.0699
(1.00)
BCOR 9 (4%) 214 0.0196
(1.00) 		0.281
(1.00) 		0.00537
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.842
(1.00) 		0.027
(1.00) 		1
(1.00) 		0.0252
(1.00)
PCDHGB5 7 (3%) 216 0.0998
(1.00) 		0.0725
(1.00) 		0.0765
(1.00) 		0.88
(1.00) 		0.739
(1.00) 		0.0509
(1.00) 		0.501
(1.00) 		1
(1.00) 		1
(1.00)
TBC1D10C 3 (1%) 220 0.69
(1.00) 		0.238
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.201
(1.00) 		1
(1.00) 		0.596
(1.00)
ERCC6L 5 (2%) 218 0.00503
(1.00) 		0.49
(1.00) 		0.301
(1.00) 		0.726
(1.00) 		1
(1.00) 		1
(1.00) 		0.19
(1.00)
ERBB3 14 (6%) 209 0.135
(1.00) 		0.0415
(1.00) 		0.121
(1.00) 		0.663
(1.00) 		0.728
(1.00) 		1
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.0542
(1.00)
KLK2 3 (1%) 220 0.539
(1.00) 		0.133
(1.00) 		0.467
(1.00) 		1
(1.00) 		0.4
(1.00)
TAPBP 5 (2%) 218 0.102
(1.00) 		0.642
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.361
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.0131
(1.00)
ERBB2 9 (4%) 214 0.379
(1.00) 		0.19
(1.00) 		0.574
(1.00) 		0.0767
(1.00) 		0.288
(1.00) 		0.34
(1.00) 		0.172
(1.00) 		0.385
(1.00) 		0.115
(1.00)
MORC2 5 (2%) 218 0.182
(1.00) 		0.641
(1.00) 		0.146
(1.00) 		0.21
(1.00) 		0.484
(1.00) 		0.72
(1.00) 		0.0196
(1.00) 		1
(1.00) 		0.137
(1.00)
ABCA8 12 (5%) 211 0.00143
(0.533) 		0.0241
(1.00) 		0.0057
(1.00) 		0.0306
(1.00) 		0.288
(1.00) 		0.459
(1.00) 		0.0128
(1.00) 		0.492
(1.00) 		0.367
(1.00)
SETD2 13 (6%) 210 0.0351
(1.00) 		0.182
(1.00) 		0.00096
(0.361) 		0.0929
(1.00) 		0.739
(1.00) 		0.0929
(1.00) 		0.00218
(0.809) 		1
(1.00) 		0.443
(1.00)
ESR1 11 (5%) 212 0.194
(1.00) 		0.0093
(1.00) 		0.0104
(1.00) 		0.718
(1.00) 		0.288
(1.00) 		0.884
(1.00) 		0.169
(1.00) 		1
(1.00) 		0.179
(1.00)
'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00566 (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 CLUS_4
ALL 42 57 67 39
APC MUTATED 21 45 52 31
APC WILD-TYPE 21 12 15 8

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

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
APC MUTATED 26 31 51 41
APC WILD-TYPE 22 6 22 6

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

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0429 (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
ALL 87 79 54
APC MUTATED 55 62 43
APC WILD-TYPE 32 17 11

Figure S3.  Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.299 (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
ALL 40 67 24 26
APC MUTATED 33 45 16 20
APC WILD-TYPE 7 22 8 6
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
APC MUTATED 10 87 17
APC WILD-TYPE 1 39 3
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
APC MUTATED 9 4 22 126
APC WILD-TYPE 5 2 7 45
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.012

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 1 5 1 1 130 35 47
APC MUTATED 1 3 1 0 101 14 41
APC WILD-TYPE 0 2 0 1 29 21 6

Figure S4.  Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
APC MUTATED 3 6 143
APC WILD-TYPE 0 3 51
'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
APC MUTATED 6 45 101
APC WILD-TYPE 1 17 36
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
TP53 MUTATED 17 40 37 14
TP53 WILD-TYPE 25 17 30 25

Figure S5.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.29

Table S11.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
TP53 MUTATED 15 25 36 32
TP53 WILD-TYPE 33 12 37 15

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

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S12.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
TP53 MUTATED 22 60 33
TP53 WILD-TYPE 65 19 21

Figure S7.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
TP53 MUTATED 18 34 14 12
TP53 WILD-TYPE 22 33 10 14
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.955 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
TP53 MUTATED 6 62 10
TP53 WILD-TYPE 5 64 10
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
TP53 MUTATED 8 1 10 96
TP53 WILD-TYPE 6 5 19 75

Figure S8.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0079

Table S16.  Gene #2: '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 1 5 1 1 130 35 47
TP53 MUTATED 0 4 0 0 83 8 20
TP53 WILD-TYPE 1 1 1 1 47 27 27

Figure S9.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
TP53 MUTATED 3 2 104
TP53 WILD-TYPE 0 7 90

Figure S10.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
TP53 MUTATED 5 28 76
TP53 WILD-TYPE 2 34 61
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.086

Table S19.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
KRAS MUTATED 13 15 31 27
KRAS WILD-TYPE 29 42 36 12

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

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.12

Table S20.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
KRAS MUTATED 20 9 44 13
KRAS WILD-TYPE 28 28 29 34

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

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
KRAS MUTATED 44 30 22
KRAS WILD-TYPE 43 49 32
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 5 2
KRAS MUTATED 0 1 2
KRAS WILD-TYPE 1 4 0
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S23.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
KRAS MUTATED 16 34 9 13
KRAS WILD-TYPE 24 33 15 13
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.954 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
KRAS MUTATED 5 57 10
KRAS WILD-TYPE 6 69 10
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
KRAS MUTATED 2 3 20 69
KRAS WILD-TYPE 12 3 9 102

Figure S13.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S26.  Gene #3: '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 1 5 1 1 130 35 47
KRAS MUTATED 0 3 1 0 43 10 37
KRAS WILD-TYPE 1 2 0 1 87 25 10

Figure S14.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
KRAS MUTATED 0 7 80
KRAS WILD-TYPE 3 2 114

Figure S15.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
KRAS MUTATED 3 20 64
KRAS WILD-TYPE 4 42 73
'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
NRAS MUTATED 0 8 6 5
NRAS WILD-TYPE 42 49 61 34

Figure S16.  Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
NRAS MUTATED 2 4 12 1
NRAS WILD-TYPE 46 33 61 46

Figure S17.  Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0812 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
NRAS MUTATED 10 9 1
NRAS WILD-TYPE 77 70 53
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
NRAS MUTATED 3 7 1 2
NRAS WILD-TYPE 37 60 23 24
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
NRAS MUTATED 0 11 2
NRAS WILD-TYPE 11 115 18
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
NRAS MUTATED 1 0 5 13
NRAS WILD-TYPE 13 6 24 158
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S35.  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 1 5 1 1 130 35 47
NRAS MUTATED 0 0 0 0 12 0 7
NRAS WILD-TYPE 1 5 1 1 118 35 40
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
NRAS MUTATED 1 0 17
NRAS WILD-TYPE 2 9 177
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
NRAS MUTATED 1 5 12
NRAS WILD-TYPE 6 57 125
'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
SMAD4 MUTATED 7 4 4 9
SMAD4 WILD-TYPE 35 53 63 30

Figure S18.  Get High-res Image Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S39.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
SMAD4 MUTATED 9 2 11 2
SMAD4 WILD-TYPE 39 35 62 45
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0948 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
SMAD4 MUTATED 15 5 6
SMAD4 WILD-TYPE 72 74 48
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S41.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
SMAD4 MUTATED 4 10 4 3
SMAD4 WILD-TYPE 36 57 20 23
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S42.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
SMAD4 MUTATED 1 18 2
SMAD4 WILD-TYPE 10 108 18
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
SMAD4 MUTATED 0 1 4 20
SMAD4 WILD-TYPE 14 5 25 151
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
SMAD4 MUTATED 0 0 0 0 9 6 10
SMAD4 WILD-TYPE 1 5 1 1 121 29 37
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
SMAD4 MUTATED 0 1 24
SMAD4 WILD-TYPE 3 8 170
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
SMAD4 MUTATED 0 5 20
SMAD4 WILD-TYPE 7 57 117
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
FBXW7 MUTATED 11 6 7 9
FBXW7 WILD-TYPE 31 51 60 30
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S48.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
FBXW7 MUTATED 15 4 10 4
FBXW7 WILD-TYPE 33 33 63 43

Figure S19.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.42

Table S49.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
FBXW7 MUTATED 24 5 9
FBXW7 WILD-TYPE 63 74 45

Figure S20.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 1

Table S50.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
FBXW7 MUTATED 7 9 2 11
FBXW7 WILD-TYPE 33 58 22 15

Figure S21.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S51.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
FBXW7 MUTATED 1 21 7
FBXW7 WILD-TYPE 10 105 13
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
FBXW7 MUTATED 1 0 12 25
FBXW7 WILD-TYPE 13 6 17 146

Figure S22.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.059

Table S53.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
FBXW7 MUTATED 1 1 0 0 12 15 9
FBXW7 WILD-TYPE 0 4 1 1 118 20 38

Figure S23.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
FBXW7 MUTATED 0 0 36
FBXW7 WILD-TYPE 3 9 158
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
FBXW7 MUTATED 3 5 28
FBXW7 WILD-TYPE 4 57 109

Figure S24.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
SMAD2 MUTATED 4 2 2 5
SMAD2 WILD-TYPE 38 55 65 34
'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S57.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
SMAD2 MUTATED 5 2 4 2
SMAD2 WILD-TYPE 43 35 69 45
'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 1

Table S58.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
SMAD2 MUTATED 10 3 2
SMAD2 WILD-TYPE 77 76 52
'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S59.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
SMAD2 MUTATED 2 3 2 3
SMAD2 WILD-TYPE 38 64 22 23
'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S60.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
SMAD2 MUTATED 0 8 2
SMAD2 WILD-TYPE 11 118 18
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
SMAD2 MUTATED 0 0 3 12
SMAD2 WILD-TYPE 14 6 26 159
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: '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 1 5 1 1 130 35 47
SMAD2 MUTATED 1 0 0 0 6 0 8
SMAD2 WILD-TYPE 0 5 1 1 124 35 39

Figure S25.  Get High-res Image Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S63.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
SMAD2 MUTATED 0 0 14
SMAD2 WILD-TYPE 3 9 180
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S64.  Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
SMAD2 MUTATED 0 3 11
SMAD2 WILD-TYPE 7 59 126
'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.09 (Fisher's exact test), Q value = 1

Table S65.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
FAM123B MUTATED 9 5 4 5
FAM123B WILD-TYPE 33 52 63 34
'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S66.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
FAM123B MUTATED 9 4 7 3
FAM123B WILD-TYPE 39 33 66 44
'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00876 (Fisher's exact test), Q value = 1

Table S67.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
FAM123B MUTATED 16 5 2
FAM123B WILD-TYPE 71 74 52

Figure S26.  Get High-res Image Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S68.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
FAM123B MUTATED 2 7 2 4
FAM123B WILD-TYPE 38 60 22 22
'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S69.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
FAM123B MUTATED 1 12 2
FAM123B WILD-TYPE 10 114 18
'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 1

Table S70.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
FAM123B MUTATED 1 1 6 16
FAM123B WILD-TYPE 13 5 23 155
'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: '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 1 5 1 1 130 35 47
FAM123B MUTATED 0 0 0 0 10 5 9
FAM123B WILD-TYPE 1 5 1 1 120 30 38
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S72.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
FAM123B MUTATED 0 1 22
FAM123B WILD-TYPE 3 8 172
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0612 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
FAM123B MUTATED 2 3 18
FAM123B WILD-TYPE 5 59 119
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S74.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PIK3CA MUTATED 8 4 7 7
PIK3CA WILD-TYPE 34 53 60 32
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S75.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PIK3CA MUTATED 9 3 10 4
PIK3CA WILD-TYPE 39 34 63 43
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S76.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PIK3CA MUTATED 23 5 4
PIK3CA WILD-TYPE 64 74 50

Figure S27.  Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0615 (Fisher's exact test), Q value = 1

Table S77.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PIK3CA MUTATED 11 9 1 6
PIK3CA WILD-TYPE 29 58 23 20
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S78.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
PIK3CA MUTATED 3 19 5
PIK3CA WILD-TYPE 8 107 15
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0761 (Fisher's exact test), Q value = 1

Table S79.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PIK3CA MUTATED 0 2 7 24
PIK3CA WILD-TYPE 14 4 22 147
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 1

Table S80.  Gene #9: '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 1 5 1 1 130 35 47
PIK3CA MUTATED 0 1 0 0 11 5 16
PIK3CA WILD-TYPE 1 4 1 1 119 30 31

Figure S28.  Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PIK3CA MUTATED 0 3 26
PIK3CA WILD-TYPE 3 6 168
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S82.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PIK3CA MUTATED 1 7 21
PIK3CA WILD-TYPE 6 55 116
'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S83.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
TCF7L2 MUTATED 3 4 5 3
TCF7L2 WILD-TYPE 39 53 62 36
'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S84.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
TCF7L2 MUTATED 2 4 5 4
TCF7L2 WILD-TYPE 46 33 68 43
'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S85.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
TCF7L2 MUTATED 6 7 5
TCF7L2 WILD-TYPE 81 72 49
'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S86.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
TCF7L2 MUTATED 3 5 1 3
TCF7L2 WILD-TYPE 37 62 23 23
'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S87.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
TCF7L2 MUTATED 1 9 2
TCF7L2 WILD-TYPE 10 117 18
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S88.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
TCF7L2 MUTATED 1 0 0 16
TCF7L2 WILD-TYPE 13 6 29 155
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S89.  Gene #10: '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 1 5 1 1 130 35 47
TCF7L2 MUTATED 0 0 0 0 12 2 3
TCF7L2 WILD-TYPE 1 5 1 1 118 33 44
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S90.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
TCF7L2 MUTATED 0 0 15
TCF7L2 WILD-TYPE 3 9 179
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
TCF7L2 MUTATED 2 4 9
TCF7L2 WILD-TYPE 5 58 128
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 1

Table S92.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ARID1A MUTATED 9 3 3 4
ARID1A WILD-TYPE 33 54 64 35

Figure S29.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S93.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ARID1A MUTATED 8 4 4 3
ARID1A WILD-TYPE 40 33 69 44
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 1

Table S94.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ARID1A MUTATED 15 3 2
ARID1A WILD-TYPE 72 76 52

Figure S30.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S95.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ARID1A MUTATED 4 6 2 3
ARID1A WILD-TYPE 36 61 22 23
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S96.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ARID1A MUTATED 0 12 3
ARID1A WILD-TYPE 11 114 17
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S97.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ARID1A MUTATED 1 0 2 17
ARID1A WILD-TYPE 13 6 27 154
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S98.  Gene #11: '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 1 5 1 1 130 35 47
ARID1A MUTATED 0 0 0 0 10 7 3
ARID1A WILD-TYPE 1 5 1 1 120 28 44
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S99.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ARID1A MUTATED 0 0 16
ARID1A WILD-TYPE 3 9 178
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 1

Table S100.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ARID1A MUTATED 2 8 6
ARID1A WILD-TYPE 5 54 131

Figure S31.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S101.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
BRAF MUTATED 13 1 1 4
BRAF WILD-TYPE 29 56 66 35

Figure S32.  Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S102.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
BRAF MUTATED 15 1 3 0
BRAF WILD-TYPE 33 36 70 47

Figure S33.  Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.02

Table S103.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
BRAF MUTATED 17 0 4
BRAF WILD-TYPE 70 79 50

Figure S34.  Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S104.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
BRAF MUTATED 3 4 4 1
BRAF WILD-TYPE 37 63 20 25
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S105.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
BRAF MUTATED 1 10 1
BRAF WILD-TYPE 10 116 19
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S106.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
BRAF MUTATED 0 1 5 15
BRAF WILD-TYPE 14 5 24 156
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S107.  Gene #12: '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 1 5 1 1 130 35 47
BRAF MUTATED 0 0 0 1 4 15 1
BRAF WILD-TYPE 1 5 1 0 126 20 46

Figure S35.  Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S108.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
BRAF MUTATED 0 1 20
BRAF WILD-TYPE 3 8 174
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S109.  Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
BRAF MUTATED 0 3 18
BRAF WILD-TYPE 7 59 119
'MGC42105 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.57

Table S110.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
MGC42105 MUTATED 6 0 1 4
MGC42105 WILD-TYPE 36 57 66 35

Figure S36.  Get High-res Image Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MGC42105 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0588 (Fisher's exact test), Q value = 1

Table S111.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
MGC42105 MUTATED 6 0 4 1
MGC42105 WILD-TYPE 42 37 69 46
'MGC42105 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 1

Table S112.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
MGC42105 MUTATED 8 2 1
MGC42105 WILD-TYPE 79 77 53
'MGC42105 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S113.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
MGC42105 MUTATED 0 3 1 3
MGC42105 WILD-TYPE 40 64 23 23
'MGC42105 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S114.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
MGC42105 MUTATED 0 6 1
MGC42105 WILD-TYPE 11 120 19
'MGC42105 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
MGC42105 MUTATED 0 0 1 9
MGC42105 WILD-TYPE 14 6 28 162
'MGC42105 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 1

Table S116.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
MGC42105 MUTATED 1 0 0 0 3 4 2
MGC42105 WILD-TYPE 0 5 1 1 127 31 45

Figure S37.  Get High-res Image Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MGC42105 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
MGC42105 MUTATED 0 0 11
MGC42105 WILD-TYPE 3 9 183
'MGC42105 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
MGC42105 MUTATED 0 1 10
MGC42105 WILD-TYPE 7 61 127
'ACVR1B MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S119.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ACVR1B MUTATED 3 2 2 4
ACVR1B WILD-TYPE 39 55 65 35
'ACVR1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 1

Table S120.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ACVR1B MUTATED 5 4 2 0
ACVR1B WILD-TYPE 43 33 71 47

Figure S38.  Get High-res Image Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ACVR1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 1

Table S121.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ACVR1B MUTATED 11 2 1
ACVR1B WILD-TYPE 76 77 53

Figure S39.  Get High-res Image Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACVR1B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S122.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ACVR1B MUTATED 2 5 1 3
ACVR1B WILD-TYPE 38 62 23 23
'ACVR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S123.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ACVR1B MUTATED 1 7 3
ACVR1B WILD-TYPE 10 119 17
'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S124.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ACVR1B MUTATED 1 0 2 11
ACVR1B WILD-TYPE 13 6 27 160
'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0827 (Fisher's exact test), Q value = 1

Table S125.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
ACVR1B MUTATED 0 0 0 0 4 6 4
ACVR1B WILD-TYPE 1 5 1 1 126 29 43
'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S126.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ACVR1B MUTATED 0 1 13
ACVR1B WILD-TYPE 3 8 181
'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S127.  Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ACVR1B MUTATED 1 2 11
ACVR1B WILD-TYPE 6 60 126
'CDC27 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.14

Table S128.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
CDC27 MUTATED 4 0 1 7
CDC27 WILD-TYPE 38 57 66 32

Figure S40.  Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDC27 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S129.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
CDC27 MUTATED 6 1 3 2
CDC27 WILD-TYPE 42 36 70 45
'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.066

Table S130.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
CDC27 MUTATED 12 0 1
CDC27 WILD-TYPE 75 79 53

Figure S41.  Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S131.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
CDC27 MUTATED 2 5 1 2
CDC27 WILD-TYPE 38 62 23 24
'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S132.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
CDC27 MUTATED 1 8 1
CDC27 WILD-TYPE 10 118 19
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S133.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
CDC27 MUTATED 0 1 1 11
CDC27 WILD-TYPE 14 5 28 160
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 1

Table S134.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
CDC27 MUTATED 1 0 0 1 4 4 3
CDC27 WILD-TYPE 0 5 1 0 126 31 44

Figure S42.  Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S135.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
CDC27 MUTATED 0 1 9
CDC27 WILD-TYPE 3 8 185
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.97

Table S136.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
CDC27 MUTATED 3 3 4
CDC27 WILD-TYPE 4 59 133

Figure S43.  Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S137.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
KIAA1804 MUTATED 3 1 6 4
KIAA1804 WILD-TYPE 39 56 61 35
'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S138.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
KIAA1804 MUTATED 4 2 4 4
KIAA1804 WILD-TYPE 44 35 69 43
'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 1

Table S139.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
KIAA1804 MUTATED 10 5 0
KIAA1804 WILD-TYPE 77 74 54

Figure S44.  Get High-res Image Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S140.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
KIAA1804 MUTATED 2 6 1 4
KIAA1804 WILD-TYPE 38 61 23 22
'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S141.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
KIAA1804 MUTATED 0 12 1
KIAA1804 WILD-TYPE 11 114 19
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S142.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
KIAA1804 MUTATED 0 0 3 12
KIAA1804 WILD-TYPE 14 6 26 159
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0531 (Fisher's exact test), Q value = 1

Table S143.  Gene #16: '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 1 5 1 1 130 35 47
KIAA1804 MUTATED 1 0 0 0 5 4 5
KIAA1804 WILD-TYPE 0 5 1 1 125 31 42
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S144.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
KIAA1804 MUTATED 0 0 15
KIAA1804 WILD-TYPE 3 9 179
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S145.  Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
KIAA1804 MUTATED 1 2 12
KIAA1804 WILD-TYPE 6 60 125
'PCDHGB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 1

Table S146.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCDHGB1 MUTATED 3 1 1 3
PCDHGB1 WILD-TYPE 39 56 66 36
'PCDHGB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S147.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PCDHGB1 MUTATED 4 2 1 1
PCDHGB1 WILD-TYPE 44 35 72 46
'PCDHGB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0977 (Fisher's exact test), Q value = 1

Table S148.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PCDHGB1 MUTATED 6 2 0
PCDHGB1 WILD-TYPE 81 77 54
'PCDHGB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S149.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PCDHGB1 MUTATED 1 2 0 2
PCDHGB1 WILD-TYPE 39 65 24 24
'PCDHGB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S150.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
PCDHGB1 MUTATED 0 4 1
PCDHGB1 WILD-TYPE 11 122 19
'PCDHGB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S151.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PCDHGB1 MUTATED 0 0 2 6
PCDHGB1 WILD-TYPE 14 6 27 165
'PCDHGB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S152.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
PCDHGB1 MUTATED 0 0 0 0 3 2 3
PCDHGB1 WILD-TYPE 1 5 1 1 127 33 44
'PCDHGB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S153.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCDHGB1 MUTATED 0 0 6
PCDHGB1 WILD-TYPE 3 9 188
'PCDHGB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S154.  Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PCDHGB1 MUTATED 1 1 4
PCDHGB1 WILD-TYPE 6 61 133
'PCBP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S155.  Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCBP1 MUTATED 0 1 2 2
PCBP1 WILD-TYPE 42 56 65 37
'PCBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S156.  Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PCBP1 MUTATED 1 0 2 2
PCBP1 WILD-TYPE 47 37 71 45
'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S157.  Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PCBP1 MUTATED 2 1 2
PCBP1 WILD-TYPE 85 78 52
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S158.  Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PCBP1 MUTATED 0 0 0 5
PCBP1 WILD-TYPE 14 6 29 166
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S159.  Gene #18: '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 1 5 1 1 130 35 47
PCBP1 MUTATED 0 0 0 0 5 0 0
PCBP1 WILD-TYPE 1 5 1 1 125 35 47
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S160.  Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCBP1 MUTATED 0 0 4
PCBP1 WILD-TYPE 3 9 190
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S161.  Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PCBP1 MUTATED 0 1 3
PCBP1 WILD-TYPE 7 61 134
'ZHX2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S162.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ZHX2 MUTATED 5 1 2 1
ZHX2 WILD-TYPE 37 56 65 38
'ZHX2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S163.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ZHX2 MUTATED 4 1 1 3
ZHX2 WILD-TYPE 44 36 72 44
'ZHX2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S164.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ZHX2 MUTATED 6 2 2
ZHX2 WILD-TYPE 81 77 52
'ZHX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 1

Table S165.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ZHX2 MUTATED 0 4 0 2
ZHX2 WILD-TYPE 40 63 24 24
'ZHX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S166.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ZHX2 MUTATED 0 4 2
ZHX2 WILD-TYPE 11 122 18
'ZHX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S167.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ZHX2 MUTATED 0 0 0 10
ZHX2 WILD-TYPE 14 6 29 161
'ZHX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S168.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
ZHX2 MUTATED 0 0 0 0 3 3 4
ZHX2 WILD-TYPE 1 5 1 1 127 32 43
'ZHX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S169.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ZHX2 MUTATED 0 0 8
ZHX2 WILD-TYPE 3 9 186
'ZHX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 1

Table S170.  Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ZHX2 MUTATED 1 1 6
ZHX2 WILD-TYPE 6 61 131
'PCDHA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 1

Table S171.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCDHA3 MUTATED 4 3 0 3
PCDHA3 WILD-TYPE 38 54 67 36

Figure S45.  Get High-res Image Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PCDHA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.12

Table S172.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PCDHA3 MUTATED 6 4 0 0
PCDHA3 WILD-TYPE 42 33 73 47

Figure S46.  Get High-res Image Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PCDHA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0521 (Fisher's exact test), Q value = 1

Table S173.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PCDHA3 MUTATED 9 2 1
PCDHA3 WILD-TYPE 78 77 53
'PCDHA3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S174.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PCDHA3 MUTATED 2 4 2 2
PCDHA3 WILD-TYPE 38 63 22 24
'PCDHA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S175.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
PCDHA3 MUTATED 0 9 1
PCDHA3 WILD-TYPE 11 117 19
'PCDHA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S176.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PCDHA3 MUTATED 1 0 3 8
PCDHA3 WILD-TYPE 13 6 26 163
'PCDHA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S177.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
PCDHA3 MUTATED 0 0 0 0 3 3 6
PCDHA3 WILD-TYPE 1 5 1 1 127 32 41
'PCDHA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S178.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCDHA3 MUTATED 0 0 11
PCDHA3 WILD-TYPE 3 9 183
'PCDHA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S179.  Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PCDHA3 MUTATED 1 2 8
PCDHA3 WILD-TYPE 6 60 129
'PCDHA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 1

Table S180.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCDHA2 MUTATED 3 3 1 4
PCDHA2 WILD-TYPE 39 54 66 35
'PCDHA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S181.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PCDHA2 MUTATED 4 2 3 2
PCDHA2 WILD-TYPE 44 35 70 45
'PCDHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0514 (Fisher's exact test), Q value = 1

Table S182.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PCDHA2 MUTATED 9 2 1
PCDHA2 WILD-TYPE 78 77 53
'PCDHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S183.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PCDHA2 MUTATED 1 2 1 0
PCDHA2 WILD-TYPE 39 65 23 26
'PCDHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S184.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
PCDHA2 MUTATED 0 4 0
PCDHA2 WILD-TYPE 11 122 20
'PCDHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S185.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PCDHA2 MUTATED 0 0 2 10
PCDHA2 WILD-TYPE 14 6 27 161
'PCDHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S186.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
PCDHA2 MUTATED 0 0 0 0 5 3 4
PCDHA2 WILD-TYPE 1 5 1 1 125 32 43
'PCDHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCDHA2 MUTATED 0 1 11
PCDHA2 WILD-TYPE 3 8 183
'PCDHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0798 (Fisher's exact test), Q value = 1

Table S188.  Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PCDHA2 MUTATED 2 3 7
PCDHA2 WILD-TYPE 5 59 130
'ELF3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S189.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ELF3 MUTATED 1 1 3 2
ELF3 WILD-TYPE 41 56 64 37
'ELF3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S190.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ELF3 MUTATED 1 1 4 1
ELF3 WILD-TYPE 47 36 69 46
'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 1

Table S191.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ELF3 MUTATED 4 0 4
ELF3 WILD-TYPE 83 79 50

Figure S47.  Get High-res Image Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S192.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ELF3 MUTATED 2 3 0 1
ELF3 WILD-TYPE 38 64 24 25
'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S193.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ELF3 MUTATED 1 4 1
ELF3 WILD-TYPE 10 122 19
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 1

Table S194.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ELF3 MUTATED 1 1 3 3
ELF3 WILD-TYPE 13 5 26 168

Figure S48.  Get High-res Image Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0835 (Fisher's exact test), Q value = 1

Table S195.  Gene #22: '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 1 5 1 1 130 35 47
ELF3 MUTATED 0 1 0 0 2 1 4
ELF3 WILD-TYPE 1 4 1 1 128 34 43
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S196.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ELF3 MUTATED 0 0 8
ELF3 WILD-TYPE 3 9 186
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S197.  Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ELF3 MUTATED 1 3 4
ELF3 WILD-TYPE 6 59 133
'CRTC1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.065 (Fisher's exact test), Q value = 1

Table S198.  Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
CRTC1 MUTATED 0 0 4 0
CRTC1 WILD-TYPE 42 57 63 39
'CRTC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S199.  Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
CRTC1 MUTATED 0 0 1 3
CRTC1 WILD-TYPE 48 37 72 44
'CRTC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S200.  Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
CRTC1 MUTATED 1 2 1
CRTC1 WILD-TYPE 86 77 53
'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S201.  Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
CRTC1 MUTATED 0 0 0 4
CRTC1 WILD-TYPE 14 6 29 167
'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.547 (Fisher's exact test), Q value = 1

Table S202.  Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
CRTC1 MUTATED 0 0 0 0 4 0 0
CRTC1 WILD-TYPE 1 5 1 1 126 35 47
'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S203.  Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
CRTC1 MUTATED 0 0 4
CRTC1 WILD-TYPE 3 9 190
'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S204.  Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
CRTC1 MUTATED 0 1 3
CRTC1 WILD-TYPE 7 61 134
'CASP8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S205.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
CASP8 MUTATED 6 0 0 3
CASP8 WILD-TYPE 36 57 67 36

Figure S49.  Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S206.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
CASP8 MUTATED 9 0 0 0
CASP8 WILD-TYPE 39 37 73 47

Figure S50.  Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.1

Table S207.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
CASP8 MUTATED 10 0 0
CASP8 WILD-TYPE 77 79 54

Figure S51.  Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 1

Table S208.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
CASP8 MUTATED 4 1 0 3
CASP8 WILD-TYPE 36 66 24 23

Figure S52.  Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S209.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
CASP8 MUTATED 1 5 2
CASP8 WILD-TYPE 10 121 18
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S210.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
CASP8 MUTATED 0 0 1 9
CASP8 WILD-TYPE 14 6 28 162
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.024

Table S211.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
CASP8 MUTATED 0 0 0 0 0 8 2
CASP8 WILD-TYPE 1 5 1 1 130 27 45

Figure S53.  Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S212.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
CASP8 MUTATED 0 0 8
CASP8 WILD-TYPE 3 9 186
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0572 (Fisher's exact test), Q value = 1

Table S213.  Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
CASP8 MUTATED 1 0 7
CASP8 WILD-TYPE 6 62 130
'CACNG3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 1

Table S214.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
CACNG3 MUTATED 4 1 0 3
CACNG3 WILD-TYPE 38 56 67 36

Figure S54.  Get High-res Image Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CACNG3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S215.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
CACNG3 MUTATED 4 1 3 0
CACNG3 WILD-TYPE 44 36 70 47
'CACNG3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.97

Table S216.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
CACNG3 MUTATED 7 0 0
CACNG3 WILD-TYPE 80 79 54

Figure S55.  Get High-res Image Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CACNG3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S217.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
CACNG3 MUTATED 1 1 1 3
CACNG3 WILD-TYPE 39 66 23 23
'CACNG3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.336 (Fisher's exact test), Q value = 1

Table S218.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
CACNG3 MUTATED 1 4 1
CACNG3 WILD-TYPE 10 122 19
'CACNG3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S219.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
CACNG3 MUTATED 0 1 2 5
CACNG3 WILD-TYPE 14 5 27 166
'CACNG3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 1

Table S220.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
CACNG3 MUTATED 1 0 0 0 2 3 2
CACNG3 WILD-TYPE 0 5 1 1 128 32 45

Figure S56.  Get High-res Image Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CACNG3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S221.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
CACNG3 MUTATED 0 1 7
CACNG3 WILD-TYPE 3 8 187
'CACNG3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 1

Table S222.  Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
CACNG3 MUTATED 2 1 5
CACNG3 WILD-TYPE 5 61 132

Figure S57.  Get High-res Image Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PCDHGA7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S223.  Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCDHGA7 MUTATED 2 0 2 1
PCDHGA7 WILD-TYPE 40 57 65 38
'PCDHGA7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S224.  Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PCDHGA7 MUTATED 2 0 1 2
PCDHGA7 WILD-TYPE 46 37 72 45
'PCDHGA7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 1

Table S225.  Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PCDHGA7 MUTATED 3 0 2
PCDHGA7 WILD-TYPE 84 79 52
'PCDHGA7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S226.  Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PCDHGA7 MUTATED 0 0 1 4
PCDHGA7 WILD-TYPE 14 6 28 167
'PCDHGA7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S227.  Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
PCDHGA7 MUTATED 0 0 0 0 3 1 1
PCDHGA7 WILD-TYPE 1 5 1 1 127 34 46
'PCDHGA7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S228.  Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCDHGA7 MUTATED 0 0 4
PCDHGA7 WILD-TYPE 3 9 190
'PCDHGA7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S229.  Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PCDHGA7 MUTATED 0 2 2
PCDHGA7 WILD-TYPE 7 60 135
'CCBP2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S230.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
CCBP2 MUTATED 3 2 1 4
CCBP2 WILD-TYPE 39 55 66 35
'CCBP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 1

Table S231.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
CCBP2 MUTATED 3 0 7 0
CCBP2 WILD-TYPE 45 37 66 47

Figure S58.  Get High-res Image Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CCBP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S232.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
CCBP2 MUTATED 6 3 1
CCBP2 WILD-TYPE 81 76 53
'CCBP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0707 (Fisher's exact test), Q value = 1

Table S233.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
CCBP2 MUTATED 2 2 0 4
CCBP2 WILD-TYPE 38 65 24 22
'CCBP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S234.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
CCBP2 MUTATED 0 7 1
CCBP2 WILD-TYPE 11 119 19
'CCBP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S235.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
CCBP2 MUTATED 0 0 3 7
CCBP2 WILD-TYPE 14 6 26 164
'CCBP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0874 (Fisher's exact test), Q value = 1

Table S236.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
CCBP2 MUTATED 1 0 0 0 4 3 2
CCBP2 WILD-TYPE 0 5 1 1 126 32 45
'CCBP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
CCBP2 MUTATED 0 0 9
CCBP2 WILD-TYPE 3 9 185
'CCBP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S238.  Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
CCBP2 MUTATED 1 2 6
CCBP2 WILD-TYPE 6 60 131
'MAP2K4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 1

Table S239.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
MAP2K4 MUTATED 3 1 4 3
MAP2K4 WILD-TYPE 39 56 63 36
'MAP2K4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S240.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
MAP2K4 MUTATED 5 1 3 2
MAP2K4 WILD-TYPE 43 36 70 45
'MAP2K4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 1

Table S241.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
MAP2K4 MUTATED 8 3 0
MAP2K4 WILD-TYPE 79 76 54

Figure S59.  Get High-res Image Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S242.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
MAP2K4 MUTATED 1 4 0 4
MAP2K4 WILD-TYPE 39 63 24 22
'MAP2K4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 1

Table S243.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
MAP2K4 MUTATED 0 7 2
MAP2K4 WILD-TYPE 11 119 18
'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S244.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
MAP2K4 MUTATED 0 0 3 8
MAP2K4 WILD-TYPE 14 6 26 163
'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S245.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
MAP2K4 MUTATED 0 0 0 0 5 3 3
MAP2K4 WILD-TYPE 1 5 1 1 125 32 44
'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S246.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
MAP2K4 MUTATED 0 0 9
MAP2K4 WILD-TYPE 3 9 185
'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 1

Table S247.  Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
MAP2K4 MUTATED 1 2 6
MAP2K4 WILD-TYPE 6 60 131
'PCDHGA9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0684 (Fisher's exact test), Q value = 1

Table S248.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCDHGA9 MUTATED 2 1 0 3
PCDHGA9 WILD-TYPE 40 56 67 36
'PCDHGA9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0768 (Fisher's exact test), Q value = 1

Table S249.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PCDHGA9 MUTATED 4 1 1 0
PCDHGA9 WILD-TYPE 44 36 72 47
'PCDHGA9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S250.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PCDHGA9 MUTATED 3 1 2
PCDHGA9 WILD-TYPE 84 78 52
'PCDHGA9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S251.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PCDHGA9 MUTATED 1 1 1 1
PCDHGA9 WILD-TYPE 39 66 23 25
'PCDHGA9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S252.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
PCDHGA9 MUTATED 0 3 1
PCDHGA9 WILD-TYPE 11 123 19
'PCDHGA9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S253.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PCDHGA9 MUTATED 0 0 2 4
PCDHGA9 WILD-TYPE 14 6 27 167
'PCDHGA9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S254.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
PCDHGA9 MUTATED 0 0 0 0 1 3 2
PCDHGA9 WILD-TYPE 1 5 1 1 129 32 45
'PCDHGA9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S255.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCDHGA9 MUTATED 0 0 6
PCDHGA9 WILD-TYPE 3 9 188
'PCDHGA9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S256.  Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PCDHGA9 MUTATED 0 1 5
PCDHGA9 WILD-TYPE 7 61 132
'RBM10 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S257.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
RBM10 MUTATED 2 1 1 3
RBM10 WILD-TYPE 40 56 66 36
'RBM10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S258.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
RBM10 MUTATED 3 1 2 1
RBM10 WILD-TYPE 45 36 71 46
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S259.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
RBM10 MUTATED 4 2 2
RBM10 WILD-TYPE 83 77 52
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S260.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
RBM10 MUTATED 0 4 0 2
RBM10 WILD-TYPE 40 63 24 24
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S261.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
RBM10 MUTATED 0 5 1
RBM10 WILD-TYPE 11 121 19
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S262.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
RBM10 MUTATED 0 0 1 6
RBM10 WILD-TYPE 14 6 28 165
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.076 (Fisher's exact test), Q value = 1

Table S263.  Gene #30: '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 1 5 1 1 130 35 47
RBM10 MUTATED 0 1 0 0 3 3 0
RBM10 WILD-TYPE 1 4 1 1 127 32 47
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S264.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
RBM10 MUTATED 0 0 8
RBM10 WILD-TYPE 3 9 186
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S265.  Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
RBM10 MUTATED 0 2 6
RBM10 WILD-TYPE 7 60 131
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 1

Table S266.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PTEN MUTATED 2 0 1 4
PTEN WILD-TYPE 40 57 66 35

Figure S60.  Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 1

Table S267.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PTEN MUTATED 3 1 3 0
PTEN WILD-TYPE 45 36 70 47
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 1

Table S268.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PTEN MUTATED 6 0 1
PTEN WILD-TYPE 81 79 53

Figure S61.  Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S269.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PTEN MUTATED 2 1 0 1
PTEN WILD-TYPE 38 66 24 25
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S270.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
PTEN MUTATED 0 4 0
PTEN WILD-TYPE 11 122 20
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0976 (Fisher's exact test), Q value = 1

Table S271.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PTEN MUTATED 0 1 2 4
PTEN WILD-TYPE 14 5 27 167
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.22

Table S272.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
PTEN MUTATED 1 0 0 0 0 1 5
PTEN WILD-TYPE 0 5 1 1 130 34 42

Figure S62.  Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S273.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PTEN MUTATED 0 1 6
PTEN WILD-TYPE 3 8 188
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 1

Table S274.  Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PTEN MUTATED 2 1 4
PTEN WILD-TYPE 5 61 133

Figure S63.  Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'DNMT1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 1

Table S275.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
DNMT1 MUTATED 4 2 2 7
DNMT1 WILD-TYPE 38 55 65 32

Figure S64.  Get High-res Image Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'DNMT1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0652 (Fisher's exact test), Q value = 1

Table S276.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
DNMT1 MUTATED 8 1 3 3
DNMT1 WILD-TYPE 40 36 70 44
'DNMT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S277.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
DNMT1 MUTATED 11 4 2
DNMT1 WILD-TYPE 76 75 52
'DNMT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0533 (Fisher's exact test), Q value = 1

Table S278.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
DNMT1 MUTATED 2 4 1 6
DNMT1 WILD-TYPE 38 63 23 20
'DNMT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 1

Table S279.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
DNMT1 MUTATED 1 9 3
DNMT1 WILD-TYPE 10 117 17
'DNMT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 1

Table S280.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
DNMT1 MUTATED 0 0 4 12
DNMT1 WILD-TYPE 14 6 25 159
'DNMT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00432 (Fisher's exact test), Q value = 1

Table S281.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
DNMT1 MUTATED 1 1 0 0 4 6 4
DNMT1 WILD-TYPE 0 4 1 1 126 29 43

Figure S65.  Get High-res Image Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'DNMT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S282.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
DNMT1 MUTATED 0 0 15
DNMT1 WILD-TYPE 3 9 179
'DNMT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0699 (Fisher's exact test), Q value = 1

Table S283.  Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
DNMT1 MUTATED 1 1 13
DNMT1 WILD-TYPE 6 61 124
'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 1

Table S284.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
BCOR MUTATED 3 0 1 4
BCOR WILD-TYPE 39 57 66 35

Figure S66.  Get High-res Image Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S285.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
BCOR MUTATED 4 1 1 2
BCOR WILD-TYPE 44 36 72 45
'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00537 (Fisher's exact test), Q value = 1

Table S286.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
BCOR MUTATED 8 0 1
BCOR WILD-TYPE 79 79 53

Figure S67.  Get High-res Image Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 1

Table S287.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
BCOR MUTATED 1 5 0 2
BCOR WILD-TYPE 39 62 24 24
'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S288.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
BCOR MUTATED 0 7 1
BCOR WILD-TYPE 11 119 19
'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S289.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
BCOR MUTATED 0 0 2 7
BCOR WILD-TYPE 14 6 27 164
'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 1

Table S290.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
BCOR MUTATED 0 0 0 0 1 3 5
BCOR WILD-TYPE 1 5 1 1 129 32 42

Figure S68.  Get High-res Image Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S291.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
BCOR MUTATED 0 0 8
BCOR WILD-TYPE 3 9 186
'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 1

Table S292.  Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
BCOR MUTATED 2 1 5
BCOR WILD-TYPE 5 61 132

Figure S69.  Get High-res Image Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PCDHGB5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0998 (Fisher's exact test), Q value = 1

Table S293.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCDHGB5 MUTATED 2 2 0 3
PCDHGB5 WILD-TYPE 40 55 67 36
'PCDHGB5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0725 (Fisher's exact test), Q value = 1

Table S294.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
PCDHGB5 MUTATED 4 2 1 0
PCDHGB5 WILD-TYPE 44 35 72 47
'PCDHGB5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0765 (Fisher's exact test), Q value = 1

Table S295.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
PCDHGB5 MUTATED 5 0 2
PCDHGB5 WILD-TYPE 82 79 52
'PCDHGB5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S296.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PCDHGB5 MUTATED 2 3 0 1
PCDHGB5 WILD-TYPE 38 64 24 25
'PCDHGB5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S297.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
PCDHGB5 MUTATED 0 5 1
PCDHGB5 WILD-TYPE 11 121 19
'PCDHGB5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0509 (Fisher's exact test), Q value = 1

Table S298.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
PCDHGB5 MUTATED 2 0 2 3
PCDHGB5 WILD-TYPE 12 6 27 168
'PCDHGB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S299.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
PCDHGB5 MUTATED 0 0 0 0 3 1 3
PCDHGB5 WILD-TYPE 1 5 1 1 127 34 44
'PCDHGB5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S300.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCDHGB5 MUTATED 0 0 5
PCDHGB5 WILD-TYPE 3 9 189
'PCDHGB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S301.  Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
PCDHGB5 MUTATED 0 1 4
PCDHGB5 WILD-TYPE 7 61 133
'ZFP3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.17

Table S302.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ZFP3 MUTATED 3 0 0 5
ZFP3 WILD-TYPE 39 57 67 34

Figure S70.  Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ZFP3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0593 (Fisher's exact test), Q value = 1

Table S303.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ZFP3 MUTATED 5 1 2 0
ZFP3 WILD-TYPE 43 36 71 47
'ZFP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.36

Table S304.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ZFP3 MUTATED 8 0 0
ZFP3 WILD-TYPE 79 79 54

Figure S71.  Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S305.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ZFP3 MUTATED 0 3 1 2
ZFP3 WILD-TYPE 40 64 23 24
'ZFP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S306.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ZFP3 MUTATED 0 5 1
ZFP3 WILD-TYPE 11 121 19
'ZFP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S307.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ZFP3 MUTATED 0 0 3 5
ZFP3 WILD-TYPE 14 6 26 166
'ZFP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.16

Table S308.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
ZFP3 MUTATED 1 0 0 0 0 4 3
ZFP3 WILD-TYPE 0 5 1 1 130 31 44

Figure S72.  Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ZFP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S309.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ZFP3 MUTATED 0 0 8
ZFP3 WILD-TYPE 3 9 186
'ZFP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00718 (Fisher's exact test), Q value = 1

Table S310.  Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ZFP3 MUTATED 2 0 6
ZFP3 WILD-TYPE 5 62 131

Figure S73.  Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RWDD2B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 1

Table S311.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
RWDD2B MUTATED 4 1 0 2
RWDD2B WILD-TYPE 38 56 67 37

Figure S74.  Get High-res Image Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RWDD2B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S312.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
RWDD2B MUTATED 3 1 2 1
RWDD2B WILD-TYPE 45 36 71 46
'RWDD2B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 1

Table S313.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
RWDD2B MUTATED 6 0 1
RWDD2B WILD-TYPE 81 79 53

Figure S75.  Get High-res Image Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RWDD2B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S314.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
RWDD2B MUTATED 1 1 0 1
RWDD2B WILD-TYPE 39 66 24 25
'RWDD2B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S315.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
RWDD2B MUTATED 0 2 1
RWDD2B WILD-TYPE 11 124 19
'RWDD2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S316.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
RWDD2B MUTATED 0 0 1 6
RWDD2B WILD-TYPE 14 6 28 165
'RWDD2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S317.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
RWDD2B MUTATED 0 0 0 0 2 1 4
RWDD2B WILD-TYPE 1 5 1 1 128 34 43
'RWDD2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S318.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
RWDD2B MUTATED 0 0 6
RWDD2B WILD-TYPE 3 9 188
'RWDD2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.23

Table S319.  Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
RWDD2B MUTATED 3 1 2
RWDD2B WILD-TYPE 4 61 135

Figure S76.  Get High-res Image Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TBC1D10C MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S320.  Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
TBC1D10C MUTATED 1 0 1 1
TBC1D10C WILD-TYPE 41 57 66 38
'TBC1D10C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S321.  Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
TBC1D10C MUTATED 2 0 0 1
TBC1D10C WILD-TYPE 46 37 73 46
'TBC1D10C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S322.  Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
TBC1D10C MUTATED 2 1 0
TBC1D10C WILD-TYPE 85 78 54
'TBC1D10C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S323.  Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
TBC1D10C MUTATED 0 0 0 3
TBC1D10C WILD-TYPE 14 6 29 168
'TBC1D10C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S324.  Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
TBC1D10C MUTATED 0 0 0 0 1 2 0
TBC1D10C WILD-TYPE 1 5 1 1 129 33 47
'TBC1D10C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S325.  Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
TBC1D10C MUTATED 0 0 3
TBC1D10C WILD-TYPE 3 9 191
'TBC1D10C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S326.  Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
TBC1D10C MUTATED 0 0 3
TBC1D10C WILD-TYPE 7 62 134
'ERCC6L MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 1

Table S327.  Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ERCC6L MUTATED 4 0 0 1
ERCC6L WILD-TYPE 38 57 67 38

Figure S77.  Get High-res Image Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ERCC6L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S328.  Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ERCC6L MUTATED 2 0 1 2
ERCC6L WILD-TYPE 46 37 72 45
'ERCC6L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 1

Table S329.  Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ERCC6L MUTATED 4 1 0
ERCC6L WILD-TYPE 83 78 54
'ERCC6L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S330.  Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ERCC6L MUTATED 0 0 1 4
ERCC6L WILD-TYPE 14 6 28 167
'ERCC6L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S331.  Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
ERCC6L MUTATED 0 0 0 0 3 1 1
ERCC6L WILD-TYPE 1 5 1 1 127 34 46
'ERCC6L MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S332.  Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ERCC6L MUTATED 0 0 5
ERCC6L WILD-TYPE 3 9 189
'ERCC6L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S333.  Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ERCC6L MUTATED 1 1 3
ERCC6L WILD-TYPE 6 61 134
'ERBB3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S334.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ERBB3 MUTATED 5 3 1 2
ERBB3 WILD-TYPE 37 54 66 37
'ERBB3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 1

Table S335.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ERBB3 MUTATED 6 1 4 0
ERBB3 WILD-TYPE 42 36 69 47

Figure S78.  Get High-res Image Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 1

Table S336.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ERBB3 MUTATED 9 2 3
ERBB3 WILD-TYPE 78 77 51
'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S337.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ERBB3 MUTATED 2 6 1 3
ERBB3 WILD-TYPE 38 61 23 23
'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S338.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ERBB3 MUTATED 0 10 2
ERBB3 WILD-TYPE 11 116 18
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S339.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ERBB3 MUTATED 0 0 2 11
ERBB3 WILD-TYPE 14 6 27 160
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 1

Table S340.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
ERBB3 MUTATED 0 0 0 0 4 5 4
ERBB3 WILD-TYPE 1 5 1 1 126 30 43
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S341.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ERBB3 MUTATED 0 0 12
ERBB3 WILD-TYPE 3 9 182
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0542 (Fisher's exact test), Q value = 1

Table S342.  Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ERBB3 MUTATED 2 4 6
ERBB3 WILD-TYPE 5 58 131
'KLK2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S343.  Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
KLK2 MUTATED 1 1 0 1
KLK2 WILD-TYPE 41 56 67 38
'KLK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S344.  Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
KLK2 MUTATED 2 1 0 0
KLK2 WILD-TYPE 46 36 73 47
'KLK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S345.  Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
KLK2 MUTATED 2 0 1
KLK2 WILD-TYPE 85 79 53
'KLK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S346.  Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
KLK2 MUTATED 0 0 0 3
KLK2 WILD-TYPE 14 6 29 168
'KLK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S347.  Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
KLK2 MUTATED 0 0 0 0 1 1 1
KLK2 WILD-TYPE 1 5 1 1 129 34 46
'TAPBP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 1

Table S348.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
TAPBP MUTATED 1 0 1 3
TAPBP WILD-TYPE 41 57 66 36
'TAPBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S349.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
TAPBP MUTATED 2 1 2 0
TAPBP WILD-TYPE 46 36 71 47
'TAPBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 1

Table S350.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
TAPBP MUTATED 4 1 0
TAPBP WILD-TYPE 83 78 54
'TAPBP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S351.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
TAPBP MUTATED 1 2 0 1
TAPBP WILD-TYPE 39 65 24 25
'TAPBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S352.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
TAPBP MUTATED 1 2 1
TAPBP WILD-TYPE 10 124 19
'TAPBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 1

Table S353.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
TAPBP MUTATED 0 0 2 3
TAPBP WILD-TYPE 14 6 27 168
'TAPBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S354.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
TAPBP MUTATED 0 0 0 0 1 2 2
TAPBP WILD-TYPE 1 5 1 1 129 33 45
'TAPBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S355.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
TAPBP MUTATED 0 0 5
TAPBP WILD-TYPE 3 9 189
'TAPBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 1

Table S356.  Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
TAPBP MUTATED 2 1 2
TAPBP WILD-TYPE 5 61 135

Figure S79.  Get High-res Image Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S357.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ERBB2 MUTATED 3 1 2 3
ERBB2 WILD-TYPE 39 56 65 36
'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S358.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ERBB2 MUTATED 4 1 4 0
ERBB2 WILD-TYPE 44 36 69 47
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S359.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ERBB2 MUTATED 5 3 1
ERBB2 WILD-TYPE 82 76 53
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0767 (Fisher's exact test), Q value = 1

Table S360.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ERBB2 MUTATED 3 1 0 3
ERBB2 WILD-TYPE 37 66 24 23
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S361.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ERBB2 MUTATED 0 5 2
ERBB2 WILD-TYPE 11 121 18
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S362.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ERBB2 MUTATED 0 0 3 6
ERBB2 WILD-TYPE 14 6 26 165
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 1

Table S363.  Gene #42: '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 1 5 1 1 130 35 47
ERBB2 MUTATED 0 1 0 0 3 1 4
ERBB2 WILD-TYPE 1 4 1 1 127 34 43
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S364.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ERBB2 MUTATED 0 1 7
ERBB2 WILD-TYPE 3 8 187
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S365.  Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ERBB2 MUTATED 0 0 8
ERBB2 WILD-TYPE 7 62 129
'MORC2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S366.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
MORC2 MUTATED 2 1 0 2
MORC2 WILD-TYPE 40 56 67 37
'MORC2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S367.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
MORC2 MUTATED 2 1 2 0
MORC2 WILD-TYPE 46 36 71 47
'MORC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S368.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
MORC2 MUTATED 4 0 1
MORC2 WILD-TYPE 83 79 53
'MORC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S369.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
MORC2 MUTATED 0 1 0 2
MORC2 WILD-TYPE 40 66 24 24
'MORC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S370.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
MORC2 MUTATED 0 2 1
MORC2 WILD-TYPE 11 124 19
'MORC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S371.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
MORC2 MUTATED 0 0 1 4
MORC2 WILD-TYPE 14 6 28 167
'MORC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 1

Table S372.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
MORC2 MUTATED 1 0 0 0 1 2 1
MORC2 WILD-TYPE 0 5 1 1 129 33 46

Figure S80.  Get High-res Image Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MORC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S373.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
MORC2 MUTATED 0 0 4
MORC2 WILD-TYPE 3 9 190
'MORC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S374.  Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
MORC2 MUTATED 1 1 2
MORC2 WILD-TYPE 6 61 135
'ABCA8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.53

Table S375.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ABCA8 MUTATED 7 2 0 3
ABCA8 WILD-TYPE 35 55 67 36

Figure S81.  Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ABCA8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 1

Table S376.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ABCA8 MUTATED 7 2 1 2
ABCA8 WILD-TYPE 41 35 72 45

Figure S82.  Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ABCA8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0057 (Fisher's exact test), Q value = 1

Table S377.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ABCA8 MUTATED 10 2 0
ABCA8 WILD-TYPE 77 77 54

Figure S83.  Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ABCA8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 1

Table S378.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ABCA8 MUTATED 2 1 0 4
ABCA8 WILD-TYPE 38 66 24 22

Figure S84.  Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ABCA8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S379.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ABCA8 MUTATED 0 5 2
ABCA8 WILD-TYPE 11 121 18
'ABCA8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S380.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ABCA8 MUTATED 0 1 1 10
ABCA8 WILD-TYPE 14 5 28 161
'ABCA8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S381.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
ABCA8 MUTATED 1 0 0 0 3 5 3
ABCA8 WILD-TYPE 0 5 1 1 127 30 44

Figure S85.  Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ABCA8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S382.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ABCA8 MUTATED 0 1 10
ABCA8 WILD-TYPE 3 8 184
'ABCA8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S383.  Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ABCA8 MUTATED 1 2 8
ABCA8 WILD-TYPE 6 60 129
'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 1

Table S384.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
SETD2 MUTATED 5 1 2 5
SETD2 WILD-TYPE 37 56 65 34

Figure S86.  Get High-res Image Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S385.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
SETD2 MUTATED 6 1 5 1
SETD2 WILD-TYPE 42 36 68 46
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.36

Table S386.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
SETD2 MUTATED 11 0 2
SETD2 WILD-TYPE 76 79 52

Figure S87.  Get High-res Image Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0929 (Fisher's exact test), Q value = 1

Table S387.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
SETD2 MUTATED 0 2 1 3
SETD2 WILD-TYPE 40 65 23 23
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S388.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
SETD2 MUTATED 0 5 1
SETD2 WILD-TYPE 11 121 19
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0929 (Fisher's exact test), Q value = 1

Table S389.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
SETD2 MUTATED 0 0 5 8
SETD2 WILD-TYPE 14 6 24 163
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.81

Table S390.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
SETD2 MUTATED 1 0 0 0 2 5 5
SETD2 WILD-TYPE 0 5 1 1 128 30 42

Figure S88.  Get High-res Image Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S391.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
SETD2 MUTATED 0 0 11
SETD2 WILD-TYPE 3 9 183
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S392.  Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
SETD2 MUTATED 1 3 7
SETD2 WILD-TYPE 6 59 130
'ESR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S393.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ESR1 MUTATED 3 1 2 4
ESR1 WILD-TYPE 39 56 65 35
'ESR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0093 (Fisher's exact test), Q value = 1

Table S394.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 37 73 47
ESR1 MUTATED 6 2 0 2
ESR1 WILD-TYPE 42 35 73 45

Figure S89.  Get High-res Image Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ESR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S395.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 79 54
ESR1 MUTATED 8 0 3
ESR1 WILD-TYPE 79 79 51

Figure S90.  Get High-res Image Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ESR1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S396.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ESR1 MUTATED 2 2 1 2
ESR1 WILD-TYPE 38 65 23 24
'ESR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S397.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 11 126 20
ESR1 MUTATED 0 5 2
ESR1 WILD-TYPE 11 121 18
'ESR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S398.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 6 29 171
ESR1 MUTATED 0 0 2 9
ESR1 WILD-TYPE 14 6 27 162
'ESR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S399.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 1 5 1 1 130 35 47
ESR1 MUTATED 0 0 0 0 3 4 4
ESR1 WILD-TYPE 1 5 1 1 127 31 43
'ESR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S400.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ESR1 MUTATED 0 0 9
ESR1 WILD-TYPE 3 9 185
'ESR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S401.  Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 62 137
ESR1 MUTATED 1 1 7
ESR1 WILD-TYPE 6 61 130
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 223

  • Number of significantly mutated genes = 46

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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