Correlation between gene mutation status and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1TD9VR8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1TD9VR8
Overview
Introduction

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

Summary

Testing the association between mutation status of 35 genes and 10 molecular subtypes across 306 patients, 19 significant findings detected with P value < 0.05 and Q value < 0.25.

  • HRAS mutation correlated to 'CN_CNMF'.

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

  • NFE2L2 mutation correlated to 'METHLYATION_CNMF'.

  • NOTCH1 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • NSD1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • CASP8 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • CSMD3 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 35 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, 19 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Chi-square 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 Chi-square test
TP53 213 (70%) 93 8.22e-13
(2.84e-10) 		1.4e-19
(4.84e-17) 		0.0858
(1.00) 		0.0628
(1.00) 		0.00584
(1.00) 		0.000164
(0.0548) 		0.0511
(1.00) 		0.000232
(0.0772) 		0.0472
(1.00) 		0.00367
(1.00)
CASP8 27 (9%) 279 7.37e-07
(0.000252) 		4.67e-11
(1.61e-08) 		0.0168
(1.00) 		0.311
(1.00) 		2.22e-08
(7.65e-06) 		2.55e-08
(8.73e-06) 		0.052
(1.00) 		0.209
(1.00) 		0.192
(1.00) 		0.126
(1.00)
CSMD3 70 (23%) 236 0.00471
(1.00) 		8.17e-05
(0.0275) 		0.013
(1.00) 		0.15
(1.00) 		1.09e-05
(0.00369) 		1.04e-05
(0.00354) 		0.000372
(0.123) 		0.0133
(1.00) 		0.00438
(1.00) 		0.0045
(1.00)
NSD1 33 (11%) 273 0.0667
(1.00) 		2.78e-23
(9.69e-21) 		0.0974
(1.00) 		0.459
(1.00) 		0.000214
(0.0714) 		1.09e-05
(0.00369) 		0.0807
(1.00) 		0.0153
(1.00) 		0.0341
(1.00) 		0.0482
(1.00)
NOTCH1 57 (19%) 249 0.115
(1.00) 		0.00818
(1.00) 		0.0577
(1.00) 		0.0267
(1.00) 		0.00339
(1.00) 		0.000549
(0.181) 		0.000269
(0.0892) 		0.23
(1.00) 		0.0337
(1.00) 		0.0119
(1.00)
HRAS 10 (3%) 296 0.000127
(0.0427) 		0.00165
(0.535) 		0.389
(1.00) 		0.234
(1.00) 		0.00141
(0.462) 		0.0012
(0.396) 		0.262
(1.00) 		0.23
(1.00) 		0.626
(1.00) 		0.411
(1.00)
NFE2L2 17 (6%) 289 0.916
(1.00) 		3.02e-05
(0.0102) 		0.348
(1.00) 		1
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.724
(1.00) 		0.209
(1.00) 		0.397
(1.00) 		0.419
(1.00)
PIK3CA 64 (21%) 242 0.173
(1.00) 		0.0298
(1.00) 		0.702
(1.00) 		0.881
(1.00) 		0.08
(1.00) 		0.356
(1.00) 		0.0445
(1.00) 		0.485
(1.00) 		0.789
(1.00) 		0.49
(1.00)
CDKN2A 65 (21%) 241 0.142
(1.00) 		0.00193
(0.625) 		0.0012
(0.396) 		0.307
(1.00) 		0.214
(1.00) 		0.357
(1.00) 		0.312
(1.00) 		0.166
(1.00) 		0.639
(1.00) 		0.569
(1.00)
FAT1 69 (23%) 237 0.681
(1.00) 		0.13
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.254
(1.00) 		0.0842
(1.00) 		0.235
(1.00) 		0.93
(1.00) 		0.484
(1.00)
JUB 18 (6%) 288 0.275
(1.00) 		0.0796
(1.00) 		0.397
(1.00) 		0.466
(1.00) 		0.141
(1.00) 		0.503
(1.00) 		0.0962
(1.00) 		1
(1.00) 		0.0779
(1.00) 		0.953
(1.00)
MLL2 53 (17%) 253 0.141
(1.00) 		0.0405
(1.00) 		0.5
(1.00) 		0.811
(1.00) 		0.112
(1.00) 		0.187
(1.00) 		0.0677
(1.00) 		0.00182
(0.59) 		0.499
(1.00) 		0.195
(1.00)
FBXW7 15 (5%) 291 0.471
(1.00) 		0.125
(1.00) 		0.416
(1.00) 		0.134
(1.00) 		0.653
(1.00) 		1
(1.00) 		0.81
(1.00) 		0.766
(1.00) 		0.546
(1.00) 		0.0465
(1.00)
ZNF750 13 (4%) 293 1
(1.00) 		0.136
(1.00) 		0.805
(1.00) 		0.526
(1.00) 		0.079
(1.00) 		0.105
(1.00) 		0.708
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.764
(1.00)
EPHA2 13 (4%) 293 0.213
(1.00) 		0.00144
(0.469) 		0.741
(1.00) 		0.902
(1.00) 		0.071
(1.00) 		0.114
(1.00) 		0.101
(1.00) 		0.0059
(1.00) 		0.138
(1.00) 		0.229
(1.00)
FLG 47 (15%) 259 0.919
(1.00) 		0.0844
(1.00) 		0.548
(1.00) 		0.762
(1.00) 		0.0493
(1.00) 		0.0791
(1.00) 		0.0405
(1.00) 		0.149
(1.00) 		0.4
(1.00) 		0.26
(1.00)
B2M 7 (2%) 299 0.219
(1.00) 		0.067
(1.00) 		0.585
(1.00) 		0.45
(1.00) 		0.33
(1.00) 		0.787
(1.00) 		0.658
(1.00) 		0.856
(1.00)
EP300 24 (8%) 282 0.419
(1.00) 		0.503
(1.00) 		0.573
(1.00) 		0.278
(1.00) 		0.00561
(1.00) 		0.0174
(1.00) 		0.41
(1.00) 		0.847
(1.00) 		0.735
(1.00) 		0.267
(1.00)
RHOA 4 (1%) 302 0.0599
(1.00) 		0.0921
(1.00) 		0.138
(1.00) 		0.449
(1.00) 		0.825
(1.00) 		0.212
(1.00) 		0.0734
(1.00) 		0.431
(1.00) 		0.0375
(1.00) 		0.0398
(1.00)
HLA-A 9 (3%) 297 0.367
(1.00) 		0.186
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.19
(1.00) 		0.23
(1.00) 		0.612
(1.00) 		0.0573
(1.00) 		0.695
(1.00) 		0.381
(1.00)
CTCF 11 (4%) 295 0.182
(1.00) 		0.0296
(1.00) 		0.616
(1.00) 		0.856
(1.00) 		0.425
(1.00) 		0.445
(1.00) 		0.484
(1.00) 		0.534
(1.00) 		0.715
(1.00) 		0.972
(1.00)
RB1 10 (3%) 296 0.703
(1.00) 		0.406
(1.00) 		0.327
(1.00) 		0.123
(1.00) 		0.0459
(1.00) 		0.0314
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.532
(1.00) 		0.0629
(1.00)
TGFBR2 10 (3%) 296 0.542
(1.00) 		0.0274
(1.00) 		0.438
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.596
(1.00) 		0.918
(1.00) 		1
(1.00) 		0.897
(1.00) 		0.244
(1.00)
NECAB1 6 (2%) 300 0.362
(1.00) 		0.157
(1.00) 		0.872
(1.00) 		0.659
(1.00) 		0.0746
(1.00) 		0.018
(1.00) 		0.581
(1.00) 		0.554
(1.00) 		0.512
(1.00) 		0.167
(1.00)
MAPK1 4 (1%) 302 0.297
(1.00) 		0.885
(1.00) 		1
(1.00) 		0.743
(1.00) 		0.688
(1.00) 		0.351
(1.00) 		0.682
(1.00) 		0.197
(1.00) 		0.697
(1.00) 		0.984
(1.00)
EPB41L3 16 (5%) 290 0.203
(1.00) 		0.0296
(1.00) 		0.675
(1.00) 		0.128
(1.00) 		0.0688
(1.00) 		0.0154
(1.00) 		0.131
(1.00) 		0.117
(1.00) 		0.326
(1.00) 		0.323
(1.00)
RAC1 9 (3%) 297 0.233
(1.00) 		0.509
(1.00) 		1
(1.00) 		0.743
(1.00) 		0.19
(1.00) 		0.0372
(1.00) 		0.28
(1.00) 		0.156
(1.00) 		0.375
(1.00) 		0.137
(1.00)
CUL3 10 (3%) 296 0.277
(1.00) 		0.122
(1.00) 		0.377
(1.00) 		0.199
(1.00) 		0.47
(1.00) 		0.781
(1.00) 		0.649
(1.00) 		0.504
(1.00) 		0.375
(1.00) 		0.686
(1.00)
PRB1 7 (2%) 299 0.0588
(1.00) 		0.149
(1.00) 		0.357
(1.00) 		0.659
(1.00) 		0.889
(1.00) 		0.485
(1.00) 		0.242
(1.00) 		0.304
(1.00) 		0.00226
(0.728) 		0.987
(1.00)
TRPV4 7 (2%) 299 0.847
(1.00) 		0.91
(1.00) 		1
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.261
(1.00) 		0.113
(1.00) 		0.459
(1.00) 		0.714
(1.00) 		0.0778
(1.00)
EPDR1 6 (2%) 300 0.544
(1.00) 		0.302
(1.00) 		0.714
(1.00) 		0.773
(1.00) 		0.33
(1.00) 		0.655
(1.00) 		1
(1.00) 		0.772
(1.00) 		0.0556
(1.00) 		0.697
(1.00)
SLC26A7 8 (3%) 298 0.643
(1.00) 		0.403
(1.00) 		0.394
(1.00) 		0.289
(1.00) 		0.128
(1.00) 		0.0795
(1.00) 		0.573
(1.00) 		0.642
(1.00) 		0.297
(1.00) 		0.571
(1.00)
KCNA3 8 (3%) 298 0.869
(1.00) 		0.842
(1.00) 		0.0452
(1.00) 		0.592
(1.00) 		0.549
(1.00) 		0.215
(1.00) 		0.811
(1.00) 		0.642
(1.00) 		0.568
(1.00) 		0.21
(1.00)
HIST1H1B 7 (2%) 299 0.605
(1.00) 		0.284
(1.00) 		0.945
(1.00) 		0.648
(1.00) 		0.721
(1.00) 		0.435
(1.00) 		0.611
(1.00) 		0.0188
(1.00) 		0.714
(1.00) 		0.0789
(1.00)
STEAP4 10 (3%) 296 0.147
(1.00) 		0.595
(1.00) 		0.171
(1.00) 		0.12
(1.00) 		0.0993
(1.00) 		0.215
(1.00) 		0.285
(1.00) 		0.584
(1.00) 		0.715
(1.00) 		0.381
(1.00)
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

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

Table S1.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
PIK3CA MUTATED 27 29 6
PIK3CA WILD-TYPE 135 84 21
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0298 (Chi-square test), Q value = 1

Table S2.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
PIK3CA MUTATED 5 6 17 16 9 10 1
PIK3CA WILD-TYPE 38 46 46 28 32 41 11

Figure S1.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
PIK3CA MUTATED 12 9 8 10
PIK3CA WILD-TYPE 43 43 27 56
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
PIK3CA MUTATED 2 14 23
PIK3CA WILD-TYPE 15 59 95
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.08 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
PIK3CA MUTATED 31 13 20
PIK3CA WILD-TYPE 91 83 66
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
PIK3CA MUTATED 28 16 20
PIK3CA WILD-TYPE 93 49 98
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
PIK3CA MUTATED 17 33 14
PIK3CA WILD-TYPE 46 103 91

Figure S2.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
PIK3CA MUTATED 2 22 40
PIK3CA WILD-TYPE 12 99 129
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
PIK3CA MUTATED 8 15 23 11
PIK3CA WILD-TYPE 27 47 84 53
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.49 (Chi-square test), Q value = 1

Table S10.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
PIK3CA MUTATED 2 2 7 11 19 16
PIK3CA WILD-TYPE 2 5 39 33 83 49
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S11.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
CDKN2A MUTATED 39 18 8
CDKN2A WILD-TYPE 123 95 19
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00193 (Chi-square test), Q value = 0.62

Table S12.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
CDKN2A MUTATED 5 17 19 1 11 11 1
CDKN2A WILD-TYPE 38 35 44 43 30 40 11

Figure S3.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.4

Table S13.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CDKN2A MUTATED 11 6 17 19
CDKN2A WILD-TYPE 44 46 18 47

Figure S4.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
CDKN2A MUTATED 2 22 29
CDKN2A WILD-TYPE 15 51 89
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
CDKN2A MUTATED 22 19 24
CDKN2A WILD-TYPE 100 77 62
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
CDKN2A MUTATED 21 16 28
CDKN2A WILD-TYPE 100 49 90
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S17.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
CDKN2A MUTATED 13 24 27
CDKN2A WILD-TYPE 50 112 78
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
CDKN2A MUTATED 3 32 29
CDKN2A WILD-TYPE 11 89 140
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
CDKN2A MUTATED 10 11 24 13
CDKN2A WILD-TYPE 25 51 83 51
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.569 (Chi-square test), Q value = 1

Table S20.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
CDKN2A MUTATED 2 1 7 10 25 13
CDKN2A WILD-TYPE 2 6 39 34 77 52
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
HRAS MUTATED 0 10 0
HRAS WILD-TYPE 162 103 27

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

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00165 (Chi-square test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
HRAS MUTATED 1 1 0 0 6 2 0
HRAS WILD-TYPE 42 51 63 44 35 49 12

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

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
HRAS MUTATED 1 1 3 2
HRAS WILD-TYPE 54 51 32 64
'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
HRAS MUTATED 1 4 2
HRAS WILD-TYPE 16 69 116
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
HRAS MUTATED 1 1 8
HRAS WILD-TYPE 121 95 78

Figure S7.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
HRAS MUTATED 1 7 2
HRAS WILD-TYPE 120 58 116

Figure S8.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
HRAS MUTATED 3 2 5
HRAS WILD-TYPE 60 134 100
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
HRAS MUTATED 1 2 7
HRAS WILD-TYPE 13 119 162
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
HRAS MUTATED 2 2 5 1
HRAS WILD-TYPE 33 60 102 63
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.411 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
HRAS MUTATED 0 0 2 4 3 1
HRAS WILD-TYPE 4 7 44 40 99 64
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.22e-13 (Fisher's exact test), Q value = 2.8e-10

Table S31.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
TP53 MUTATED 142 54 15
TP53 WILD-TYPE 20 59 12

Figure S9.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.4e-19 (Chi-square test), Q value = 4.8e-17

Table S32.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
TP53 MUTATED 35 48 54 4 26 36 10
TP53 WILD-TYPE 8 4 9 40 15 15 2

Figure S10.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0858 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
TP53 MUTATED 45 33 28 54
TP53 WILD-TYPE 10 19 7 12
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S34.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
TP53 MUTATED 9 57 94
TP53 WILD-TYPE 8 16 24
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
TP53 MUTATED 75 78 59
TP53 WILD-TYPE 47 18 27

Figure S11.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.055

Table S36.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
TP53 MUTATED 72 42 98
TP53 WILD-TYPE 49 23 20

Figure S12.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0511 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
TP53 MUTATED 39 91 82
TP53 WILD-TYPE 24 45 23
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000232 (Fisher's exact test), Q value = 0.077

Table S38.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
TP53 MUTATED 11 99 102
TP53 WILD-TYPE 3 22 67

Figure S13.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
TP53 MUTATED 21 38 76 52
TP53 WILD-TYPE 14 24 31 12

Figure S14.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00367 (Chi-square test), Q value = 1

Table S40.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
TP53 MUTATED 2 4 22 30 82 47
TP53 WILD-TYPE 2 3 24 14 20 18

Figure S15.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S41.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
NFE2L2 MUTATED 9 7 1
NFE2L2 WILD-TYPE 153 106 26
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.02e-05 (Chi-square test), Q value = 0.01

Table S42.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
NFE2L2 MUTATED 0 0 11 0 5 1 0
NFE2L2 WILD-TYPE 43 52 52 44 36 50 12

Figure S16.  Get High-res Image Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S43.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
NFE2L2 MUTATED 4 6 2 2
NFE2L2 WILD-TYPE 51 46 33 64
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S44.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
NFE2L2 MUTATED 1 5 8
NFE2L2 WILD-TYPE 16 68 110
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S45.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
NFE2L2 MUTATED 7 5 5
NFE2L2 WILD-TYPE 115 91 81
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S46.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
NFE2L2 MUTATED 6 4 7
NFE2L2 WILD-TYPE 115 61 111
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S47.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
NFE2L2 MUTATED 2 9 6
NFE2L2 WILD-TYPE 61 127 99
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
NFE2L2 MUTATED 2 5 10
NFE2L2 WILD-TYPE 12 116 159
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
NFE2L2 MUTATED 0 3 8 5
NFE2L2 WILD-TYPE 35 59 99 59
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.419 (Chi-square test), Q value = 1

Table S50.  Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
NFE2L2 MUTATED 1 0 1 4 6 4
NFE2L2 WILD-TYPE 3 7 45 40 96 61
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
NOTCH1 MUTATED 24 24 8
NOTCH1 WILD-TYPE 138 89 19
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00818 (Chi-square test), Q value = 1

Table S52.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
NOTCH1 MUTATED 3 13 10 2 12 14 3
NOTCH1 WILD-TYPE 40 39 53 42 29 37 9

Figure S17.  Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0577 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
NOTCH1 MUTATED 15 4 6 14
NOTCH1 WILD-TYPE 40 48 29 52
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S54.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
NOTCH1 MUTATED 2 21 16
NOTCH1 WILD-TYPE 15 52 102

Figure S18.  Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
NOTCH1 MUTATED 12 23 22
NOTCH1 WILD-TYPE 110 73 64

Figure S19.  Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000549 (Fisher's exact test), Q value = 0.18

Table S56.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
NOTCH1 MUTATED 11 20 26
NOTCH1 WILD-TYPE 110 45 92

Figure S20.  Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.089

Table S57.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
NOTCH1 MUTATED 15 12 29
NOTCH1 WILD-TYPE 48 124 76

Figure S21.  Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
NOTCH1 MUTATED 4 26 26
NOTCH1 WILD-TYPE 10 95 143
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
NOTCH1 MUTATED 8 4 21 15
NOTCH1 WILD-TYPE 27 58 86 49

Figure S22.  Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Chi-square test), Q value = 1

Table S60.  Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
NOTCH1 MUTATED 1 2 4 14 22 5
NOTCH1 WILD-TYPE 3 5 42 30 80 60

Figure S23.  Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0667 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
NSD1 MUTATED 24 7 2
NSD1 WILD-TYPE 138 106 25
'NSD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.78e-23 (Chi-square test), Q value = 9.7e-21

Table S62.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
NSD1 MUTATED 25 1 0 3 3 1 0
NSD1 WILD-TYPE 18 51 63 41 38 50 12

Figure S24.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0974 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
NSD1 MUTATED 7 7 5 2
NSD1 WILD-TYPE 48 45 30 64
'NSD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
NSD1 MUTATED 0 8 13
NSD1 WILD-TYPE 17 65 105
'NSD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.071

Table S65.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
NSD1 MUTATED 24 3 6
NSD1 WILD-TYPE 98 93 80

Figure S25.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0037

Table S66.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
NSD1 MUTATED 26 2 5
NSD1 WILD-TYPE 95 63 113

Figure S26.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0807 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
NSD1 MUTATED 7 20 6
NSD1 WILD-TYPE 56 116 99
'NSD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S68.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
NSD1 MUTATED 2 6 25
NSD1 WILD-TYPE 12 115 144

Figure S27.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
NSD1 MUTATED 3 13 10 3
NSD1 WILD-TYPE 32 49 97 61

Figure S28.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0482 (Chi-square test), Q value = 1

Table S70.  Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
NSD1 MUTATED 0 0 8 4 5 12
NSD1 WILD-TYPE 4 7 38 40 97 53

Figure S29.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
FAT1 MUTATED 38 26 4
FAT1 WILD-TYPE 124 87 23
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Chi-square test), Q value = 1

Table S72.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
FAT1 MUTATED 11 10 16 3 13 12 4
FAT1 WILD-TYPE 32 42 47 41 28 39 8
'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
FAT1 MUTATED 12 11 7 17
FAT1 WILD-TYPE 43 41 28 49
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S74.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
FAT1 MUTATED 4 16 27
FAT1 WILD-TYPE 13 57 91
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S75.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
FAT1 MUTATED 21 27 21
FAT1 WILD-TYPE 101 69 65
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 1

Table S76.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
FAT1 MUTATED 22 15 32
FAT1 WILD-TYPE 99 50 86
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0842 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
FAT1 MUTATED 10 27 31
FAT1 WILD-TYPE 53 109 74
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
FAT1 MUTATED 4 32 32
FAT1 WILD-TYPE 10 89 137
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
FAT1 MUTATED 8 13 27 16
FAT1 WILD-TYPE 27 49 80 48
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.484 (Chi-square test), Q value = 1

Table S80.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
FAT1 MUTATED 1 1 8 12 30 12
FAT1 WILD-TYPE 3 6 38 32 72 53
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.37e-07 (Fisher's exact test), Q value = 0.00025

Table S81.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
CASP8 MUTATED 2 21 3
CASP8 WILD-TYPE 160 92 24

Figure S30.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.67e-11 (Chi-square test), Q value = 1.6e-08

Table S82.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
CASP8 MUTATED 2 2 0 0 16 6 1
CASP8 WILD-TYPE 41 50 63 44 25 45 11

Figure S31.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CASP8 MUTATED 5 1 8 8
CASP8 WILD-TYPE 50 51 27 58

Figure S32.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
CASP8 MUTATED 1 11 10
CASP8 WILD-TYPE 16 62 108
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.22e-08 (Fisher's exact test), Q value = 7.6e-06

Table S85.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
CASP8 MUTATED 1 5 21
CASP8 WILD-TYPE 121 91 65

Figure S33.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.55e-08 (Fisher's exact test), Q value = 8.7e-06

Table S86.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
CASP8 MUTATED 1 18 8
CASP8 WILD-TYPE 120 47 110

Figure S34.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.052 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
CASP8 MUTATED 7 6 13
CASP8 WILD-TYPE 56 130 92
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
CASP8 MUTATED 3 10 13
CASP8 WILD-TYPE 11 111 156
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S89.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
CASP8 MUTATED 5 2 12 5
CASP8 WILD-TYPE 30 60 95 59
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.126 (Chi-square test), Q value = 1

Table S90.  Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
CASP8 MUTATED 1 1 4 7 10 1
CASP8 WILD-TYPE 3 6 42 37 92 64
'JUB MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
JUB MUTATED 13 4 1
JUB WILD-TYPE 149 109 26
'JUB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0796 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
JUB MUTATED 0 6 5 1 3 1 2
JUB WILD-TYPE 43 46 58 43 38 50 10
'JUB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
JUB MUTATED 5 2 3 2
JUB WILD-TYPE 50 50 32 64
'JUB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
JUB MUTATED 1 6 5
JUB WILD-TYPE 16 67 113
'JUB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
JUB MUTATED 5 4 9
JUB WILD-TYPE 117 92 77
'JUB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
JUB MUTATED 5 5 8
JUB WILD-TYPE 116 60 110
'JUB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0962 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
JUB MUTATED 7 8 3
JUB WILD-TYPE 56 128 102
'JUB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
JUB MUTATED 0 7 11
JUB WILD-TYPE 14 114 158
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0779 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
JUB MUTATED 6 3 7 2
JUB WILD-TYPE 29 59 100 62
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.953 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
JUB MUTATED 0 0 4 3 7 4
JUB WILD-TYPE 4 7 42 41 95 61
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S101.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
MLL2 MUTATED 35 14 4
MLL2 WILD-TYPE 127 99 23
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0405 (Chi-square test), Q value = 1

Table S102.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
MLL2 MUTATED 11 7 17 9 4 5 0
MLL2 WILD-TYPE 32 45 46 35 37 46 12

Figure S35.  Get High-res Image Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S103.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
MLL2 MUTATED 7 11 8 10
MLL2 WILD-TYPE 48 41 27 56
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S104.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
MLL2 MUTATED 3 14 19
MLL2 WILD-TYPE 14 59 99
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S105.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
MLL2 MUTATED 28 12 13
MLL2 WILD-TYPE 94 84 73
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S106.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
MLL2 MUTATED 26 12 15
MLL2 WILD-TYPE 95 53 103
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0677 (Fisher's exact test), Q value = 1

Table S107.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
MLL2 MUTATED 12 29 11
MLL2 WILD-TYPE 51 107 94
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.59

Table S108.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
MLL2 MUTATED 0 12 40
MLL2 WILD-TYPE 14 109 129

Figure S36.  Get High-res Image Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S109.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
MLL2 MUTATED 5 14 18 8
MLL2 WILD-TYPE 30 48 89 56
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.195 (Chi-square test), Q value = 1

Table S110.  Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
MLL2 MUTATED 0 1 10 10 10 14
MLL2 WILD-TYPE 4 6 36 34 92 51
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
FBXW7 MUTATED 10 5 0
FBXW7 WILD-TYPE 152 108 27
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.125 (Chi-square test), Q value = 1

Table S112.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
FBXW7 MUTATED 3 0 5 1 3 1 2
FBXW7 WILD-TYPE 40 52 58 43 38 50 10
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
FBXW7 MUTATED 1 4 1 5
FBXW7 WILD-TYPE 54 48 34 61
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
FBXW7 MUTATED 1 1 9
FBXW7 WILD-TYPE 16 72 109
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
FBXW7 MUTATED 7 3 5
FBXW7 WILD-TYPE 115 93 81
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
FBXW7 MUTATED 6 3 6
FBXW7 WILD-TYPE 115 62 112
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
FBXW7 MUTATED 4 6 5
FBXW7 WILD-TYPE 59 130 100
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
FBXW7 MUTATED 0 5 10
FBXW7 WILD-TYPE 14 116 159
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
FBXW7 MUTATED 1 5 4 2
FBXW7 WILD-TYPE 34 57 103 62
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0465 (Chi-square test), Q value = 1

Table S120.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
FBXW7 MUTATED 0 2 1 1 4 4
FBXW7 WILD-TYPE 4 5 45 43 98 61

Figure S37.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

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

Table S121.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
ZNF750 MUTATED 7 5 1
ZNF750 WILD-TYPE 155 108 26
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.136 (Chi-square test), Q value = 1

Table S122.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
ZNF750 MUTATED 1 0 4 5 1 2 0
ZNF750 WILD-TYPE 42 52 59 39 40 49 12
'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S123.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
ZNF750 MUTATED 2 2 0 2
ZNF750 WILD-TYPE 53 50 35 64
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
ZNF750 MUTATED 1 2 3
ZNF750 WILD-TYPE 16 71 115
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.079 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
ZNF750 MUTATED 9 3 1
ZNF750 WILD-TYPE 113 93 85
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S126.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
ZNF750 MUTATED 9 1 3
ZNF750 WILD-TYPE 112 64 115
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S127.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
ZNF750 MUTATED 3 7 3
ZNF750 WILD-TYPE 60 129 102
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S128.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
ZNF750 MUTATED 0 5 8
ZNF750 WILD-TYPE 14 116 161
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S129.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
ZNF750 MUTATED 0 4 4 4
ZNF750 WILD-TYPE 35 58 103 60
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.764 (Chi-square test), Q value = 1

Table S130.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
ZNF750 MUTATED 0 1 3 2 4 2
ZNF750 WILD-TYPE 4 6 43 42 98 63
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
EPHA2 MUTATED 4 6 2
EPHA2 WILD-TYPE 158 107 25
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00144 (Chi-square test), Q value = 0.47

Table S132.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
EPHA2 MUTATED 1 3 0 1 6 0 2
EPHA2 WILD-TYPE 42 49 63 43 35 51 10

Figure S38.  Get High-res Image Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
EPHA2 MUTATED 4 2 1 5
EPHA2 WILD-TYPE 51 50 34 61
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S134.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
EPHA2 MUTATED 1 5 6
EPHA2 WILD-TYPE 16 68 112
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.071 (Fisher's exact test), Q value = 1

Table S135.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
EPHA2 MUTATED 2 4 7
EPHA2 WILD-TYPE 120 92 79
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S136.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
EPHA2 MUTATED 2 5 6
EPHA2 WILD-TYPE 119 60 112
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S137.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
EPHA2 MUTATED 4 2 6
EPHA2 WILD-TYPE 59 134 99
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0059 (Fisher's exact test), Q value = 1

Table S138.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
EPHA2 MUTATED 3 6 3
EPHA2 WILD-TYPE 11 115 166

Figure S39.  Get High-res Image Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S139.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
EPHA2 MUTATED 2 0 6 1
EPHA2 WILD-TYPE 33 62 101 63
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.229 (Chi-square test), Q value = 1

Table S140.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
EPHA2 MUTATED 0 1 1 3 4 0
EPHA2 WILD-TYPE 4 6 45 41 98 65
'FLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
FLG MUTATED 24 19 4
FLG WILD-TYPE 138 94 23
'FLG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0844 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
FLG MUTATED 6 4 15 7 10 4 1
FLG WILD-TYPE 37 48 48 37 31 47 11
'FLG MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
FLG MUTATED 9 9 7 7
FLG WILD-TYPE 46 43 28 59
'FLG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
FLG MUTATED 2 13 17
FLG WILD-TYPE 15 60 101
'FLG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
FLG MUTATED 26 9 12
FLG WILD-TYPE 96 87 74

Figure S40.  Get High-res Image Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0791 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
FLG MUTATED 25 10 12
FLG WILD-TYPE 96 55 106
'FLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
FLG MUTATED 11 27 9
FLG WILD-TYPE 52 109 96

Figure S41.  Get High-res Image Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S148.  Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
FLG MUTATED 2 13 32
FLG WILD-TYPE 12 108 137
'FLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S149.  Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
FLG MUTATED 3 13 16 8
FLG WILD-TYPE 32 49 91 56
'FLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.26 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
FLG MUTATED 0 0 9 8 10 13
FLG WILD-TYPE 4 7 37 36 92 52
'B2M MUTATION STATUS' versus 'CN_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
B2M MUTATED 2 5 0
B2M WILD-TYPE 160 108 27
'B2M MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.067 (Chi-square test), Q value = 1

Table S152.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
B2M MUTATED 0 0 1 4 1 1 0
B2M WILD-TYPE 43 52 62 40 40 50 12
'B2M MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S153.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
B2M MUTATED 4 1 1
B2M WILD-TYPE 118 95 85
'B2M MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S154.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
B2M MUTATED 4 1 1
B2M WILD-TYPE 117 64 117
'B2M MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S155.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
B2M MUTATED 0 5 2
B2M WILD-TYPE 63 131 103
'B2M MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S156.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
B2M MUTATED 0 2 5
B2M WILD-TYPE 14 119 164
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S157.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
B2M MUTATED 0 3 3 1
B2M WILD-TYPE 35 59 104 63
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.856 (Chi-square test), Q value = 1

Table S158.  Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
B2M MUTATED 0 0 2 2 2 1
B2M WILD-TYPE 4 7 44 42 100 64
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S159.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
EP300 MUTATED 10 12 2
EP300 WILD-TYPE 152 101 25
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.503 (Chi-square test), Q value = 1

Table S160.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
EP300 MUTATED 2 2 4 5 6 4 1
EP300 WILD-TYPE 41 50 59 39 35 47 11
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S161.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
EP300 MUTATED 3 2 4 4
EP300 WILD-TYPE 52 50 31 62
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S162.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
EP300 MUTATED 1 7 5
EP300 WILD-TYPE 16 66 113
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00561 (Fisher's exact test), Q value = 1

Table S163.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
EP300 MUTATED 5 5 14
EP300 WILD-TYPE 117 91 72

Figure S42.  Get High-res Image Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S164.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
EP300 MUTATED 6 11 7
EP300 WILD-TYPE 115 54 111

Figure S43.  Get High-res Image Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
EP300 MUTATED 7 8 8
EP300 WILD-TYPE 56 128 97
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S166.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
EP300 MUTATED 1 8 14
EP300 WILD-TYPE 13 113 155
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S167.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
EP300 MUTATED 3 3 10 6
EP300 WILD-TYPE 32 59 97 58
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.267 (Chi-square test), Q value = 1

Table S168.  Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
EP300 MUTATED 1 0 6 5 8 2
EP300 WILD-TYPE 3 7 40 39 94 63
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0599 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
RHOA MUTATED 1 1 2
RHOA WILD-TYPE 161 112 25
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0921 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
RHOA MUTATED 0 3 0 0 0 1 0
RHOA WILD-TYPE 43 49 63 44 41 50 12
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
RHOA MUTATED 0 0 0 3
RHOA WILD-TYPE 55 52 35 63
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
RHOA MUTATED 0 0 3
RHOA WILD-TYPE 17 73 115
'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
RHOA MUTATED 1 2 1
RHOA WILD-TYPE 121 94 85
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S174.  Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
RHOA MUTATED 0 1 3
RHOA WILD-TYPE 121 64 115
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0734 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
RHOA MUTATED 2 0 2
RHOA WILD-TYPE 61 136 103
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
RHOA MUTATED 0 3 1
RHOA WILD-TYPE 14 118 168
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 1

Table S177.  Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
RHOA MUTATED 1 0 0 3
RHOA WILD-TYPE 34 62 107 61

Figure S44.  Get High-res Image Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0398 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
RHOA MUTATED 0 1 0 0 3 0
RHOA WILD-TYPE 4 6 46 44 99 65

Figure S45.  Get High-res Image Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
HLA-A MUTATED 3 5 1
HLA-A WILD-TYPE 159 108 26
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.186 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
HLA-A MUTATED 0 1 2 1 4 1 0
HLA-A WILD-TYPE 43 51 61 43 37 50 12
'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S181.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
HLA-A MUTATED 1 1 1 2
HLA-A WILD-TYPE 54 51 34 64
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S182.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
HLA-A MUTATED 1 1 3
HLA-A WILD-TYPE 16 72 115
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S183.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
HLA-A MUTATED 3 1 5
HLA-A WILD-TYPE 119 95 81
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
HLA-A MUTATED 2 4 3
HLA-A WILD-TYPE 119 61 115
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S185.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
HLA-A MUTATED 3 3 3
HLA-A WILD-TYPE 60 133 102
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0573 (Fisher's exact test), Q value = 1

Table S186.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
HLA-A MUTATED 2 2 5
HLA-A WILD-TYPE 12 119 164
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S187.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
HLA-A MUTATED 2 1 4 2
HLA-A WILD-TYPE 33 61 103 62
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.381 (Chi-square test), Q value = 1

Table S188.  Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
HLA-A MUTATED 0 0 4 1 3 1
HLA-A WILD-TYPE 4 7 42 43 99 64
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S189.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
CTCF MUTATED 4 7 0
CTCF WILD-TYPE 158 106 27
'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0296 (Chi-square test), Q value = 1

Table S190.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
CTCF MUTATED 3 1 0 1 5 1 0
CTCF WILD-TYPE 40 51 63 43 36 50 12

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

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S191.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CTCF MUTATED 2 2 0 4
CTCF WILD-TYPE 53 50 35 62
'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S192.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
CTCF MUTATED 0 2 6
CTCF WILD-TYPE 17 71 112
'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S193.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
CTCF MUTATED 4 2 5
CTCF WILD-TYPE 118 94 81
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 1

Table S194.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
CTCF MUTATED 4 4 3
CTCF WILD-TYPE 117 61 115
'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S195.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
CTCF MUTATED 3 3 5
CTCF WILD-TYPE 60 133 100
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S196.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
CTCF MUTATED 1 4 6
CTCF WILD-TYPE 13 117 163
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S197.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
CTCF MUTATED 0 3 5 2
CTCF WILD-TYPE 35 59 102 62
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.972 (Chi-square test), Q value = 1

Table S198.  Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
CTCF MUTATED 0 0 2 2 3 3
CTCF WILD-TYPE 4 7 44 42 99 62
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S199.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
RB1 MUTATED 5 5 0
RB1 WILD-TYPE 157 108 27
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.406 (Chi-square test), Q value = 1

Table S200.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
RB1 MUTATED 3 0 2 3 1 1 0
RB1 WILD-TYPE 40 52 61 41 40 50 12
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 1

Table S201.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
RB1 MUTATED 0 1 0 3
RB1 WILD-TYPE 55 51 35 63
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
RB1 MUTATED 1 0 3
RB1 WILD-TYPE 16 73 115
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 1

Table S203.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
RB1 MUTATED 8 1 1
RB1 WILD-TYPE 114 95 85

Figure S47.  Get High-res Image Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 1

Table S204.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
RB1 MUTATED 8 0 2
RB1 WILD-TYPE 113 65 116

Figure S48.  Get High-res Image Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S205.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
RB1 MUTATED 0 7 3
RB1 WILD-TYPE 63 129 102
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S206.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
RB1 MUTATED 0 4 6
RB1 WILD-TYPE 14 117 163
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S207.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
RB1 MUTATED 0 3 5 1
RB1 WILD-TYPE 35 59 102 63
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0629 (Chi-square test), Q value = 1

Table S208.  Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
RB1 MUTATED 0 0 0 0 3 6
RB1 WILD-TYPE 4 7 46 44 99 59
'CSMD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 1

Table S209.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
CSMD3 MUTATED 48 15 7
CSMD3 WILD-TYPE 114 98 20

Figure S49.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CSMD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8.17e-05 (Chi-square test), Q value = 0.028

Table S210.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
CSMD3 MUTATED 21 8 18 11 4 5 3
CSMD3 WILD-TYPE 22 44 45 33 37 46 9

Figure S50.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CSMD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 1

Table S211.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CSMD3 MUTATED 15 18 8 7
CSMD3 WILD-TYPE 40 34 27 59

Figure S51.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CSMD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S212.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
CSMD3 MUTATED 6 20 22
CSMD3 WILD-TYPE 11 53 96
'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0037

Table S213.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
CSMD3 MUTATED 44 9 17
CSMD3 WILD-TYPE 78 87 69

Figure S52.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0035

Table S214.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
CSMD3 MUTATED 45 11 14
CSMD3 WILD-TYPE 76 54 104

Figure S53.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000372 (Fisher's exact test), Q value = 0.12

Table S215.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
CSMD3 MUTATED 17 42 11
CSMD3 WILD-TYPE 46 94 94

Figure S54.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 1

Table S216.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
CSMD3 MUTATED 5 18 47
CSMD3 WILD-TYPE 9 103 122

Figure S55.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00438 (Fisher's exact test), Q value = 1

Table S217.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
CSMD3 MUTATED 6 20 26 5
CSMD3 WILD-TYPE 29 42 81 59

Figure S56.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0045 (Chi-square test), Q value = 1

Table S218.  Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
CSMD3 MUTATED 1 0 10 10 12 24
CSMD3 WILD-TYPE 3 7 36 34 90 41

Figure S57.  Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TGFBR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S219.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
TGFBR2 MUTATED 4 5 1
TGFBR2 WILD-TYPE 158 108 26
'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0274 (Chi-square test), Q value = 1

Table S220.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
TGFBR2 MUTATED 3 0 0 0 4 3 0
TGFBR2 WILD-TYPE 40 52 63 44 37 48 12

Figure S58.  Get High-res Image Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TGFBR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

Table S221.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
TGFBR2 MUTATED 3 1 0 4
TGFBR2 WILD-TYPE 52 51 35 62
'TGFBR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S222.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
TGFBR2 MUTATED 0 3 5
TGFBR2 WILD-TYPE 17 70 113
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S223.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
TGFBR2 MUTATED 2 3 5
TGFBR2 WILD-TYPE 120 93 81
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
TGFBR2 MUTATED 3 3 4
TGFBR2 WILD-TYPE 118 62 114
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S225.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
TGFBR2 MUTATED 2 4 4
TGFBR2 WILD-TYPE 61 132 101
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S226.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
TGFBR2 MUTATED 0 4 6
TGFBR2 WILD-TYPE 14 117 163
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S227.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
TGFBR2 MUTATED 1 1 4 3
TGFBR2 WILD-TYPE 34 61 103 61
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.244 (Chi-square test), Q value = 1

Table S228.  Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
TGFBR2 MUTATED 0 1 0 3 4 1
TGFBR2 WILD-TYPE 4 6 46 41 98 64
'NECAB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S229.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
NECAB1 MUTATED 2 4 0
NECAB1 WILD-TYPE 160 109 27
'NECAB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.157 (Chi-square test), Q value = 1

Table S230.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
NECAB1 MUTATED 2 0 0 1 2 0 1
NECAB1 WILD-TYPE 41 52 63 43 39 51 11
'NECAB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S231.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
NECAB1 MUTATED 1 0 1 1
NECAB1 WILD-TYPE 54 52 34 65
'NECAB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S232.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
NECAB1 MUTATED 0 2 1
NECAB1 WILD-TYPE 17 71 117
'NECAB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0746 (Fisher's exact test), Q value = 1

Table S233.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
NECAB1 MUTATED 2 0 4
NECAB1 WILD-TYPE 120 96 82
'NECAB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 1

Table S234.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
NECAB1 MUTATED 2 4 0
NECAB1 WILD-TYPE 119 61 118

Figure S59.  Get High-res Image Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NECAB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S235.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
NECAB1 MUTATED 2 3 1
NECAB1 WILD-TYPE 61 133 104
'NECAB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S236.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
NECAB1 MUTATED 0 1 5
NECAB1 WILD-TYPE 14 120 164
'NECAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 1

Table S237.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
NECAB1 MUTATED 1 2 3 0
NECAB1 WILD-TYPE 34 60 104 64
'NECAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.167 (Chi-square test), Q value = 1

Table S238.  Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
NECAB1 MUTATED 0 1 0 2 1 2
NECAB1 WILD-TYPE 4 6 46 42 101 63
'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S239.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
MAPK1 MUTATED 1 2 1
MAPK1 WILD-TYPE 161 111 26
'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.885 (Chi-square test), Q value = 1

Table S240.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
MAPK1 MUTATED 0 0 1 1 1 1 0
MAPK1 WILD-TYPE 43 52 62 43 40 50 12
'MAPK1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S241.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
MAPK1 MUTATED 1 1 1 1
MAPK1 WILD-TYPE 54 51 34 65
'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S242.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
MAPK1 MUTATED 0 2 2
MAPK1 WILD-TYPE 17 71 116
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 1

Table S243.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
MAPK1 MUTATED 1 1 2
MAPK1 WILD-TYPE 121 95 84
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S244.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
MAPK1 MUTATED 1 2 1
MAPK1 WILD-TYPE 120 63 117
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S245.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
MAPK1 MUTATED 1 1 2
MAPK1 WILD-TYPE 62 135 103
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S246.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
MAPK1 MUTATED 1 1 2
MAPK1 WILD-TYPE 13 120 167
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S247.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
MAPK1 MUTATED 1 0 2 1
MAPK1 WILD-TYPE 34 62 105 63
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.984 (Chi-square test), Q value = 1

Table S248.  Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
MAPK1 MUTATED 0 0 1 1 1 1
MAPK1 WILD-TYPE 4 7 45 43 101 64
'EPB41L3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S249.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
EPB41L3 MUTATED 11 3 2
EPB41L3 WILD-TYPE 151 110 25
'EPB41L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0296 (Chi-square test), Q value = 1

Table S250.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
EPB41L3 MUTATED 6 1 6 0 1 2 0
EPB41L3 WILD-TYPE 37 51 57 44 40 49 12

Figure S60.  Get High-res Image Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPB41L3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S251.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
EPB41L3 MUTATED 1 3 2 4
EPB41L3 WILD-TYPE 54 49 33 62
'EPB41L3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S252.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
EPB41L3 MUTATED 0 1 9
EPB41L3 WILD-TYPE 17 72 109
'EPB41L3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0688 (Fisher's exact test), Q value = 1

Table S253.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
EPB41L3 MUTATED 11 2 3
EPB41L3 WILD-TYPE 111 94 83
'EPB41L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 1

Table S254.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
EPB41L3 MUTATED 12 1 3
EPB41L3 WILD-TYPE 109 64 115

Figure S61.  Get High-res Image Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S255.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
EPB41L3 MUTATED 4 10 2
EPB41L3 WILD-TYPE 59 126 103
'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S256.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
EPB41L3 MUTATED 0 3 13
EPB41L3 WILD-TYPE 14 118 156
'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S257.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
EPB41L3 MUTATED 2 6 4 2
EPB41L3 WILD-TYPE 33 56 103 62
'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Chi-square test), Q value = 1

Table S258.  Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
EPB41L3 MUTATED 0 0 2 2 3 7
EPB41L3 WILD-TYPE 4 7 44 42 99 58
'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S259.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
RAC1 MUTATED 3 6 0
RAC1 WILD-TYPE 159 107 27
'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.509 (Chi-square test), Q value = 1

Table S260.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
RAC1 MUTATED 0 1 1 1 2 3 1
RAC1 WILD-TYPE 43 51 62 43 39 48 11
'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S261.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
RAC1 MUTATED 1 1 1 1
RAC1 WILD-TYPE 54 51 34 65
'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S262.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
RAC1 MUTATED 0 2 2
RAC1 WILD-TYPE 17 71 116
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S263.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
RAC1 MUTATED 3 1 5
RAC1 WILD-TYPE 119 95 81
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 1

Table S264.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
RAC1 MUTATED 3 5 1
RAC1 WILD-TYPE 118 60 117

Figure S62.  Get High-res Image Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S265.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
RAC1 MUTATED 3 5 1
RAC1 WILD-TYPE 60 131 104
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S266.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
RAC1 MUTATED 0 1 8
RAC1 WILD-TYPE 14 120 161
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S267.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
RAC1 MUTATED 1 3 3 0
RAC1 WILD-TYPE 34 59 104 64
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Chi-square test), Q value = 1

Table S268.  Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
RAC1 MUTATED 0 0 4 1 1 1
RAC1 WILD-TYPE 4 7 42 43 101 64
'CUL3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S269.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
CUL3 MUTATED 8 2 0
CUL3 WILD-TYPE 154 111 27
'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.122 (Chi-square test), Q value = 1

Table S270.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
CUL3 MUTATED 3 1 5 0 0 1 0
CUL3 WILD-TYPE 40 51 58 44 41 50 12
'CUL3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S271.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CUL3 MUTATED 2 4 0 2
CUL3 WILD-TYPE 53 48 35 64
'CUL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S272.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
CUL3 MUTATED 2 2 4
CUL3 WILD-TYPE 15 71 114
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S273.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
CUL3 MUTATED 5 4 1
CUL3 WILD-TYPE 117 92 85
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S274.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
CUL3 MUTATED 5 1 4
CUL3 WILD-TYPE 116 64 114
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 1

Table S275.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
CUL3 MUTATED 2 6 2
CUL3 WILD-TYPE 61 130 103
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S276.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
CUL3 MUTATED 0 6 4
CUL3 WILD-TYPE 14 115 165
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S277.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
CUL3 MUTATED 1 4 2 1
CUL3 WILD-TYPE 34 58 105 63
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.686 (Chi-square test), Q value = 1

Table S278.  Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
CUL3 MUTATED 0 0 1 0 5 2
CUL3 WILD-TYPE 4 7 45 44 97 63
'PRB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S279.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
PRB1 MUTATED 7 0 0
PRB1 WILD-TYPE 155 113 27
'PRB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.149 (Chi-square test), Q value = 1

Table S280.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
PRB1 MUTATED 3 0 3 0 0 1 0
PRB1 WILD-TYPE 40 52 60 44 41 50 12
'PRB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S281.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
PRB1 MUTATED 2 1 0 0
PRB1 WILD-TYPE 53 51 35 66
'PRB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S282.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
PRB1 MUTATED 0 2 1
PRB1 WILD-TYPE 17 71 117
'PRB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S283.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
PRB1 MUTATED 2 3 2
PRB1 WILD-TYPE 120 93 84
'PRB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S284.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
PRB1 MUTATED 3 0 4
PRB1 WILD-TYPE 118 65 114
'PRB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S285.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
PRB1 MUTATED 3 3 1
PRB1 WILD-TYPE 60 133 104
'PRB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 1

Table S286.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
PRB1 MUTATED 1 3 3
PRB1 WILD-TYPE 13 118 166
'PRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.73

Table S287.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
PRB1 MUTATED 3 3 0 0
PRB1 WILD-TYPE 32 59 107 64

Figure S63.  Get High-res Image Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.987 (Chi-square test), Q value = 1

Table S288.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
PRB1 MUTATED 0 0 1 1 3 1
PRB1 WILD-TYPE 4 7 45 43 99 64
'TRPV4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S289.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
TRPV4 MUTATED 5 2 0
TRPV4 WILD-TYPE 157 111 27
'TRPV4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.91 (Chi-square test), Q value = 1

Table S290.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
TRPV4 MUTATED 0 2 2 1 1 1 0
TRPV4 WILD-TYPE 43 50 61 43 40 50 12
'TRPV4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S291.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
TRPV4 MUTATED 2 1 1 2
TRPV4 WILD-TYPE 53 51 34 64
'TRPV4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S292.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
TRPV4 MUTATED 0 2 4
TRPV4 WILD-TYPE 17 71 114
'TRPV4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S293.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
TRPV4 MUTATED 3 1 3
TRPV4 WILD-TYPE 119 95 83
'TRPV4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S294.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
TRPV4 MUTATED 3 3 1
TRPV4 WILD-TYPE 118 62 117
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S295.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
TRPV4 MUTATED 0 6 1
TRPV4 WILD-TYPE 63 130 104
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S296.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
TRPV4 MUTATED 0 1 6
TRPV4 WILD-TYPE 14 120 163
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S297.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
TRPV4 MUTATED 0 1 3 3
TRPV4 WILD-TYPE 35 61 104 61
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0778 (Chi-square test), Q value = 1

Table S298.  Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
TRPV4 MUTATED 0 0 0 4 1 2
TRPV4 WILD-TYPE 4 7 46 40 101 63
'EPDR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S299.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
EPDR1 MUTATED 5 1 0
EPDR1 WILD-TYPE 157 112 27
'EPDR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.302 (Chi-square test), Q value = 1

Table S300.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
EPDR1 MUTATED 0 3 2 0 0 1 0
EPDR1 WILD-TYPE 43 49 61 44 41 50 12
'EPDR1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S301.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
EPDR1 MUTATED 1 1 0 3
EPDR1 WILD-TYPE 54 51 35 63
'EPDR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S302.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
EPDR1 MUTATED 0 1 4
EPDR1 WILD-TYPE 17 72 114
'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S303.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
EPDR1 MUTATED 3 3 0
EPDR1 WILD-TYPE 119 93 86
'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S304.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
EPDR1 MUTATED 3 0 3
EPDR1 WILD-TYPE 118 65 115
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S305.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
EPDR1 MUTATED 1 3 2
EPDR1 WILD-TYPE 62 133 103
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S306.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
EPDR1 MUTATED 0 3 3
EPDR1 WILD-TYPE 14 118 166
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0556 (Fisher's exact test), Q value = 1

Table S307.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
EPDR1 MUTATED 2 2 0 2
EPDR1 WILD-TYPE 33 60 107 62
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.697 (Chi-square test), Q value = 1

Table S308.  Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
EPDR1 MUTATED 0 0 0 1 2 3
EPDR1 WILD-TYPE 4 7 46 43 100 62
'SLC26A7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S309.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
SLC26A7 MUTATED 5 2 1
SLC26A7 WILD-TYPE 157 111 26
'SLC26A7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.403 (Chi-square test), Q value = 1

Table S310.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
SLC26A7 MUTATED 1 0 3 0 2 1 1
SLC26A7 WILD-TYPE 42 52 60 44 39 50 11
'SLC26A7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S311.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
SLC26A7 MUTATED 1 2 1 0
SLC26A7 WILD-TYPE 54 50 34 66
'SLC26A7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S312.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
SLC26A7 MUTATED 0 3 1
SLC26A7 WILD-TYPE 17 70 117
'SLC26A7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S313.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
SLC26A7 MUTATED 2 1 5
SLC26A7 WILD-TYPE 120 95 81
'SLC26A7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0795 (Fisher's exact test), Q value = 1

Table S314.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
SLC26A7 MUTATED 3 4 1
SLC26A7 WILD-TYPE 118 61 117
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S315.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
SLC26A7 MUTATED 3 3 2
SLC26A7 WILD-TYPE 60 133 103
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S316.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
SLC26A7 MUTATED 0 2 6
SLC26A7 WILD-TYPE 14 119 163
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S317.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
SLC26A7 MUTATED 2 2 3 0
SLC26A7 WILD-TYPE 33 60 104 64
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.571 (Chi-square test), Q value = 1

Table S318.  Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
SLC26A7 MUTATED 0 0 1 3 2 1
SLC26A7 WILD-TYPE 4 7 45 41 100 64
'KCNA3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S319.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
KCNA3 MUTATED 4 4 0
KCNA3 WILD-TYPE 158 109 27
'KCNA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.842 (Chi-square test), Q value = 1

Table S320.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
KCNA3 MUTATED 2 1 2 0 1 2 0
KCNA3 WILD-TYPE 41 51 61 44 40 49 12
'KCNA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 1

Table S321.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
KCNA3 MUTATED 4 1 0 0
KCNA3 WILD-TYPE 51 51 35 66

Figure S64.  Get High-res Image Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KCNA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S322.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
KCNA3 MUTATED 0 3 2
KCNA3 WILD-TYPE 17 70 116
'KCNA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S323.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
KCNA3 MUTATED 4 1 3
KCNA3 WILD-TYPE 118 95 83
'KCNA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S324.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
KCNA3 MUTATED 4 3 1
KCNA3 WILD-TYPE 117 62 117
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S325.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
KCNA3 MUTATED 2 4 2
KCNA3 WILD-TYPE 61 132 103
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S326.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
KCNA3 MUTATED 0 2 6
KCNA3 WILD-TYPE 14 119 163
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S327.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
KCNA3 MUTATED 0 3 2 1
KCNA3 WILD-TYPE 35 59 105 63
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.21 (Chi-square test), Q value = 1

Table S328.  Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
KCNA3 MUTATED 0 0 1 1 0 4
KCNA3 WILD-TYPE 4 7 45 43 102 61
'HIST1H1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S329.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
HIST1H1B MUTATED 3 4 0
HIST1H1B WILD-TYPE 159 109 27
'HIST1H1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.284 (Chi-square test), Q value = 1

Table S330.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
HIST1H1B MUTATED 1 0 2 0 3 1 0
HIST1H1B WILD-TYPE 42 52 61 44 38 50 12
'HIST1H1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S331.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
HIST1H1B MUTATED 1 2 1 2
HIST1H1B WILD-TYPE 54 50 34 64
'HIST1H1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S332.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
HIST1H1B MUTATED 0 1 5
HIST1H1B WILD-TYPE 17 72 113
'HIST1H1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S333.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
HIST1H1B MUTATED 2 2 3
HIST1H1B WILD-TYPE 120 94 83
'HIST1H1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S334.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
HIST1H1B MUTATED 2 3 2
HIST1H1B WILD-TYPE 119 62 116
'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S335.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
HIST1H1B MUTATED 2 4 1
HIST1H1B WILD-TYPE 61 132 104
'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 1

Table S336.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
HIST1H1B MUTATED 2 1 4
HIST1H1B WILD-TYPE 12 120 165

Figure S65.  Get High-res Image Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S337.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
HIST1H1B MUTATED 1 1 2 3
HIST1H1B WILD-TYPE 34 61 105 61
'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0789 (Chi-square test), Q value = 1

Table S338.  Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
HIST1H1B MUTATED 1 0 1 2 1 2
HIST1H1B WILD-TYPE 3 7 45 42 101 63
'STEAP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S339.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 113 27
STEAP4 MUTATED 8 1 1
STEAP4 WILD-TYPE 154 112 26
'STEAP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.595 (Chi-square test), Q value = 1

Table S340.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 52 63 44 41 51 12
STEAP4 MUTATED 3 1 3 1 0 2 0
STEAP4 WILD-TYPE 40 51 60 43 41 49 12
'STEAP4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S341.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
STEAP4 MUTATED 1 4 0 1
STEAP4 WILD-TYPE 54 48 35 65
'STEAP4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S342.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 73 118
STEAP4 MUTATED 2 1 3
STEAP4 WILD-TYPE 15 72 115
'STEAP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0993 (Fisher's exact test), Q value = 1

Table S343.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 96 86
STEAP4 MUTATED 6 4 0
STEAP4 WILD-TYPE 116 92 86
'STEAP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S344.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 65 118
STEAP4 MUTATED 6 0 4
STEAP4 WILD-TYPE 115 65 114
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S345.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 136 105
STEAP4 MUTATED 0 6 4
STEAP4 WILD-TYPE 63 130 101
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S346.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 121 169
STEAP4 MUTATED 1 4 5
STEAP4 WILD-TYPE 13 117 164
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S347.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 62 107 64
STEAP4 MUTATED 0 3 5 2
STEAP4 WILD-TYPE 35 59 102 62
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.381 (Chi-square test), Q value = 1

Table S348.  Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 7 46 44 102 65
STEAP4 MUTATED 0 0 1 0 4 5
STEAP4 WILD-TYPE 4 7 45 44 98 60
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 306

  • Number of significantly mutated genes = 35

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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