Correlation between gene mutation status and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1NZ868Q
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/C1NZ868Q
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 Fisher's exact test
TP53 213 (70%) 93 1.65e-11
(5.72e-09) 		1.75e-19
(6.06e-17) 		0.0858
(1.00) 		0.0628
(1.00) 		0.00847
(1.00) 		0.000199
(0.0672) 		0.0243
(1.00) 		0.00022
(0.0736) 		0.0867
(1.00) 		0.0129
(1.00)
CASP8 27 (9%) 279 2.07e-05
(0.00704) 		7.55e-11
(2.6e-08) 		0.0168
(1.00) 		0.311
(1.00) 		1.62e-08
(5.57e-06) 		2.85e-06
(0.000974) 		0.144
(1.00) 		0.838
(1.00) 		0.493
(1.00) 		0.00182
(0.587)
CSMD3 70 (23%) 236 0.00105
(0.345) 		0.000217
(0.0728) 		0.013
(1.00) 		0.15
(1.00) 		8.26e-06
(0.00282) 		1.41e-06
(0.000483) 		0.000515
(0.17) 		0.00138
(0.449) 		0.00177
(0.57) 		0.000974
(0.321)
NSD1 33 (11%) 273 0.0327
(1.00) 		4.47e-24
(1.56e-21) 		0.0974
(1.00) 		0.459
(1.00) 		0.000292
(0.0965) 		6.04e-05
(0.0204) 		0.0144
(1.00) 		0.00477
(1.00) 		0.0387
(1.00) 		0.028
(1.00)
NOTCH1 57 (19%) 249 0.229
(1.00) 		0.00638
(1.00) 		0.0577
(1.00) 		0.0267
(1.00) 		0.00195
(0.627) 		0.000267
(0.0886) 		3.26e-05
(0.011) 		0.23
(1.00) 		0.0185
(1.00) 		0.0209
(1.00)
HRAS 10 (3%) 296 0.000211
(0.0709) 		0.0109
(1.00) 		0.389
(1.00) 		0.234
(1.00) 		0.00131
(0.427) 		0.00286
(0.914) 		0.541
(1.00) 		0.0521
(1.00) 		0.757
(1.00) 		0.414
(1.00)
NFE2L2 17 (6%) 289 0.882
(1.00) 		0.000228
(0.0761) 		0.348
(1.00) 		1
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.301
(1.00) 		0.697
(1.00)
PIK3CA 64 (21%) 242 0.0292
(1.00) 		0.0646
(1.00) 		0.702
(1.00) 		0.881
(1.00) 		0.0956
(1.00) 		0.468
(1.00) 		0.00886
(1.00) 		0.155
(1.00) 		0.0803
(1.00) 		0.265
(1.00)
CDKN2A 65 (21%) 241 0.0857
(1.00) 		0.00508
(1.00) 		0.0012
(0.393) 		0.307
(1.00) 		0.183
(1.00) 		0.213
(1.00) 		0.371
(1.00) 		0.0623
(1.00) 		0.368
(1.00) 		0.318
(1.00)
FAT1 69 (23%) 237 0.334
(1.00) 		0.0629
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.109
(1.00) 		0.219
(1.00) 		0.0969
(1.00) 		0.402
(1.00) 		0.859
(1.00) 		0.131
(1.00)
JUB 18 (6%) 288 0.424
(1.00) 		0.151
(1.00) 		0.397
(1.00) 		0.466
(1.00) 		0.127
(1.00) 		0.19
(1.00) 		0.0779
(1.00) 		1
(1.00) 		0.0411
(1.00) 		1
(1.00)
MLL2 53 (17%) 253 0.0114
(1.00) 		0.045
(1.00) 		0.5
(1.00) 		0.811
(1.00) 		0.082
(1.00) 		0.0641
(1.00) 		0.0706
(1.00) 		0.00499
(1.00) 		0.0939
(1.00) 		0.0329
(1.00)
FBXW7 15 (5%) 291 0.667
(1.00) 		0.138
(1.00) 		0.416
(1.00) 		0.134
(1.00) 		0.653
(1.00) 		0.438
(1.00) 		0.794
(1.00) 		0.602
(1.00) 		1
(1.00) 		1
(1.00)
ZNF750 13 (4%) 293 0.445
(1.00) 		0.131
(1.00) 		0.805
(1.00) 		0.526
(1.00) 		0.0793
(1.00) 		0.1
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.817
(1.00)
EPHA2 13 (4%) 293 0.554
(1.00) 		0.00158
(0.512) 		0.741
(1.00) 		0.902
(1.00) 		0.0631
(1.00) 		0.228
(1.00) 		0.323
(1.00) 		0.239
(1.00) 		0.725
(1.00) 		0.0275
(1.00)
FLG 47 (15%) 259 0.367
(1.00) 		0.15
(1.00) 		0.548
(1.00) 		0.762
(1.00) 		0.0643
(1.00) 		0.222
(1.00) 		0.0567
(1.00) 		0.108
(1.00) 		0.105
(1.00) 		0.0254
(1.00)
B2M 7 (2%) 299 0.11
(1.00) 		0.0635
(1.00) 		0.584
(1.00) 		0.383
(1.00) 		0.286
(1.00) 		0.705
(1.00) 		0.764
(1.00) 		0.847
(1.00)
EP300 24 (8%) 282 0.235
(1.00) 		0.388
(1.00) 		0.573
(1.00) 		0.278
(1.00) 		0.00482
(1.00) 		0.113
(1.00) 		0.424
(1.00) 		0.379
(1.00) 		1
(1.00) 		0.65
(1.00)
RHOA 4 (1%) 302 0.235
(1.00) 		0.122
(1.00) 		0.138
(1.00) 		0.449
(1.00) 		0.823
(1.00) 		0.156
(1.00) 		0.0769
(1.00) 		0.308
(1.00) 		0.114
(1.00) 		0.0604
(1.00)
HLA-A 9 (3%) 297 0.0759
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.189
(1.00) 		0.697
(1.00) 		0.202
(1.00) 		0.318
(1.00) 		0.541
(1.00) 		0.781
(1.00)
CTCF 11 (4%) 295 0.276
(1.00) 		0.0164
(1.00) 		0.616
(1.00) 		0.856
(1.00) 		0.426
(1.00) 		0.928
(1.00) 		0.793
(1.00) 		0.763
(1.00) 		0.47
(1.00) 		0.414
(1.00)
RB1 10 (3%) 296 0.00771
(1.00) 		0.381
(1.00) 		0.327
(1.00) 		0.123
(1.00) 		0.0558
(1.00) 		0.259
(1.00) 		0.143
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.781
(1.00)
TGFBR2 10 (3%) 296 0.163
(1.00) 		0.0148
(1.00) 		0.438
(1.00) 		1
(1.00) 		0.229
(1.00) 		0.921
(1.00) 		1
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.0275
(1.00)
NECAB1 6 (2%) 300 0.914
(1.00) 		0.176
(1.00) 		0.872
(1.00) 		0.659
(1.00) 		0.0715
(1.00) 		0.0992
(1.00) 		0.505
(1.00) 		0.407
(1.00) 		0.535
(1.00) 		0.279
(1.00)
MAPK1 4 (1%) 302 0.13
(1.00) 		0.856
(1.00) 		1
(1.00) 		0.743
(1.00) 		0.689
(1.00) 		0.69
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.499
(1.00) 		0.527
(1.00)
EPB41L3 16 (5%) 290 0.0728
(1.00) 		0.0257
(1.00) 		0.675
(1.00) 		0.128
(1.00) 		0.0717
(1.00) 		0.00889
(1.00) 		0.253
(1.00) 		0.0724
(1.00) 		0.13
(1.00) 		0.362
(1.00)
RAC1 9 (3%) 297 0.0789
(1.00) 		0.49
(1.00) 		1
(1.00) 		0.743
(1.00) 		0.189
(1.00) 		0.222
(1.00) 		0.251
(1.00) 		0.0879
(1.00) 		0.326
(1.00) 		0.333
(1.00)
CUL3 10 (3%) 296 0.304
(1.00) 		0.123
(1.00) 		0.377
(1.00) 		0.199
(1.00) 		0.469
(1.00) 		0.787
(1.00) 		0.918
(1.00) 		0.326
(1.00) 		0.185
(1.00) 		0.378
(1.00)
PRB1 7 (2%) 299 0.157
(1.00) 		0.147
(1.00) 		0.357
(1.00) 		0.659
(1.00) 		0.804
(1.00) 		0.571
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.0736
(1.00) 		0.363
(1.00)
TRPV4 7 (2%) 299 0.661
(1.00) 		0.922
(1.00) 		1
(1.00) 		1
(1.00) 		0.494
(1.00) 		0.306
(1.00) 		0.377
(1.00) 		0.247
(1.00) 		0.764
(1.00) 		0.395
(1.00)
EPDR1 6 (2%) 300 0.704
(1.00) 		0.36
(1.00) 		0.714
(1.00) 		0.773
(1.00) 		0.331
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.168
(1.00) 		1
(1.00)
SLC26A7 8 (3%) 298 0.887
(1.00) 		0.51
(1.00) 		0.394
(1.00) 		0.289
(1.00) 		0.128
(1.00) 		0.399
(1.00) 		0.809
(1.00) 		0.479
(1.00) 		0.672
(1.00) 		0.175
(1.00)
KCNA3 8 (3%) 298 0.342
(1.00) 		0.801
(1.00) 		0.0452
(1.00) 		0.592
(1.00) 		0.603
(1.00) 		0.446
(1.00) 		0.809
(1.00) 		0.479
(1.00) 		0.639
(1.00) 		0.0644
(1.00)
HIST1H1B 7 (2%) 299 0.443
(1.00) 		0.00632
(1.00) 		0.945
(1.00) 		0.648
(1.00) 		0.641
(1.00) 		0.267
(1.00) 		0.786
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.0156
(1.00)
STEAP4 10 (3%) 296 0.495
(1.00) 		0.601
(1.00) 		0.171
(1.00) 		0.12
(1.00) 		0.108
(1.00) 		0.339
(1.00) 		0.239
(1.00) 		0.745
(1.00) 		0.515
(1.00) 		0.898
(1.00)
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0292 (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 CLUS_4
ALL 114 68 103 17
PIK3CA MUTATED 14 19 26 3
PIK3CA WILD-TYPE 100 49 77 14

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

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0646 (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 42 56 64 44 38 47 15
PIK3CA MUTATED 5 8 17 16 7 9 2
PIK3CA WILD-TYPE 37 48 47 28 31 38 13
'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 = 0.0956 (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 124 95 85
PIK3CA MUTATED 31 13 20
PIK3CA WILD-TYPE 93 82 65
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.468 (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 100 92 112
PIK3CA MUTATED 17 21 26
PIK3CA WILD-TYPE 83 71 86
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00886 (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 62 132 110
PIK3CA MUTATED 16 35 13
PIK3CA WILD-TYPE 46 97 97

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 = 0.155 (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
ALL 124 180
PIK3CA MUTATED 21 43
PIK3CA WILD-TYPE 103 137
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0803 (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
ALL 41 126 101
PIK3CA MUTATED 8 34 15
PIK3CA WILD-TYPE 33 92 86
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.265 (Fisher's exact 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
ALL 101 143 24
PIK3CA MUTATED 17 36 4
PIK3CA WILD-TYPE 84 107 20
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0857 (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 CLUS_4
ALL 114 68 103 17
CDKN2A MUTATED 28 14 16 7
CDKN2A WILD-TYPE 86 54 87 10
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00508 (Chi-square test), Q value = 1

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 42 56 64 44 38 47 15
CDKN2A MUTATED 5 18 19 1 9 10 3
CDKN2A WILD-TYPE 37 38 45 43 29 37 12

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 = 0.39

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 = 0.183 (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 124 95 85
CDKN2A MUTATED 22 19 24
CDKN2A WILD-TYPE 102 76 61
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.213 (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 100 92 112
CDKN2A MUTATED 25 22 18
CDKN2A WILD-TYPE 75 70 94
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.371 (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 62 132 110
CDKN2A MUTATED 12 24 28
CDKN2A WILD-TYPE 50 108 82
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0623 (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
ALL 124 180
CDKN2A MUTATED 33 31
CDKN2A WILD-TYPE 91 149
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.368 (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
ALL 41 126 101
CDKN2A MUTATED 12 24 22
CDKN2A WILD-TYPE 29 102 79
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.318 (Fisher's exact 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
ALL 101 143 24
CDKN2A MUTATED 26 26 6
CDKN2A WILD-TYPE 75 117 18
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 68 103 17
HRAS MUTATED 0 0 10 0
HRAS WILD-TYPE 114 68 93 17

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 = 0.0109 (Chi-square test), Q value = 1

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 42 56 64 44 38 47 15
HRAS MUTATED 1 1 0 0 5 2 1
HRAS WILD-TYPE 41 55 64 44 33 45 14

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 = 0.00131 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
HRAS MUTATED 1 1 8
HRAS WILD-TYPE 123 94 77

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 = 0.00286 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 92 112
HRAS MUTATED 1 8 1
HRAS WILD-TYPE 99 84 111

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 = 0.541 (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 62 132 110
HRAS MUTATED 3 3 4
HRAS WILD-TYPE 59 129 106
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0521 (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
ALL 124 180
HRAS MUTATED 1 9
HRAS WILD-TYPE 123 171
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.757 (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
ALL 41 126 101
HRAS MUTATED 2 5 3
HRAS WILD-TYPE 39 121 98
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.414 (Fisher's exact 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
ALL 101 143 24
HRAS MUTATED 3 5 2
HRAS WILD-TYPE 98 138 22
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.65e-11 (Fisher's exact test), Q value = 5.7e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 68 103 17
TP53 MUTATED 102 52 48 9
TP53 WILD-TYPE 12 16 55 8

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 = 1.75e-19 (Chi-square test), Q value = 6.1e-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 42 56 64 44 38 47 15
TP53 MUTATED 34 50 55 4 23 34 13
TP53 WILD-TYPE 8 6 9 40 15 13 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 = 0.00847 (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 124 95 85
TP53 MUTATED 77 77 58
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 = 0.000199 (Fisher's exact test), Q value = 0.067

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 92 112
TP53 MUTATED 83 65 64
TP53 WILD-TYPE 17 27 48

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 = 0.0243 (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 62 132 110
TP53 MUTATED 41 84 87
TP53 WILD-TYPE 21 48 23

Figure S13.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.074

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

nPatients CLUS_1 CLUS_2
ALL 124 180
TP53 MUTATED 101 111
TP53 WILD-TYPE 23 69

Figure S14.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0867 (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
ALL 41 126 101
TP53 MUTATED 25 84 78
TP53 WILD-TYPE 16 42 23
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact 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
ALL 101 143 24
TP53 MUTATED 81 91 15
TP53 WILD-TYPE 20 52 9

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 = 0.882 (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 CLUS_4
ALL 114 68 103 17
NFE2L2 MUTATED 6 3 7 1
NFE2L2 WILD-TYPE 108 65 96 16
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000228 (Chi-square test), Q value = 0.076

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 42 56 64 44 38 47 15
NFE2L2 MUTATED 0 0 10 0 5 2 0
NFE2L2 WILD-TYPE 42 56 54 44 33 45 15

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 124 95 85
NFE2L2 MUTATED 7 5 5
NFE2L2 WILD-TYPE 117 90 80
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.755 (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 100 92 112
NFE2L2 MUTATED 6 6 5
NFE2L2 WILD-TYPE 94 86 107
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.287 (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 62 132 110
NFE2L2 MUTATED 1 8 8
NFE2L2 WILD-TYPE 61 124 102
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (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
ALL 124 180
NFE2L2 MUTATED 7 10
NFE2L2 WILD-TYPE 117 170
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.301 (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
ALL 41 126 101
NFE2L2 MUTATED 1 6 9
NFE2L2 WILD-TYPE 40 120 92
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.697 (Fisher's exact 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
ALL 101 143 24
NFE2L2 MUTATED 5 9 2
NFE2L2 WILD-TYPE 96 134 22
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.229 (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 CLUS_4
ALL 114 68 103 17
NOTCH1 MUTATED 24 7 22 3
NOTCH1 WILD-TYPE 90 61 81 14
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00638 (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 42 56 64 44 38 47 15
NOTCH1 MUTATED 3 13 10 2 12 13 4
NOTCH1 WILD-TYPE 39 43 54 42 26 34 11

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 = 0.00195 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
NOTCH1 MUTATED 12 22 23
NOTCH1 WILD-TYPE 112 73 62

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 = 0.000267 (Fisher's exact test), Q value = 0.089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 92 112
NOTCH1 MUTATED 21 27 9
NOTCH1 WILD-TYPE 79 65 103

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 = 3.26e-05 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 132 110
NOTCH1 MUTATED 19 10 27
NOTCH1 WILD-TYPE 43 122 83

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
ALL 124 180
NOTCH1 MUTATED 27 29
NOTCH1 WILD-TYPE 97 151
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (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
ALL 41 126 101
NOTCH1 MUTATED 9 14 25
NOTCH1 WILD-TYPE 32 112 76

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 = 0.0209 (Fisher's exact 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
ALL 101 143 24
NOTCH1 MUTATED 22 18 8
NOTCH1 WILD-TYPE 79 125 16

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 = 0.0327 (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 CLUS_4
ALL 114 68 103 17
NSD1 MUTATED 11 14 8 0
NSD1 WILD-TYPE 103 54 95 17

Figure S24.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NSD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.47e-24 (Chi-square test), Q value = 1.6e-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 42 56 64 44 38 47 15
NSD1 MUTATED 25 1 0 3 3 1 0
NSD1 WILD-TYPE 17 55 64 41 35 46 15

Figure S25.  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 = 0.000292 (Fisher's exact test), Q value = 0.097

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
NSD1 MUTATED 24 3 6
NSD1 WILD-TYPE 100 92 79

Figure S26.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.04e-05 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 92 112
NSD1 MUTATED 4 5 24
NSD1 WILD-TYPE 96 87 88

Figure S27.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0144 (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 62 132 110
NSD1 MUTATED 7 21 5
NSD1 WILD-TYPE 55 111 105

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

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00477 (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
ALL 124 180
NSD1 MUTATED 6 27
NSD1 WILD-TYPE 118 153

Figure S29.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0387 (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
ALL 41 126 101
NSD1 MUTATED 5 19 5
NSD1 WILD-TYPE 36 107 96

Figure S30.  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 = 0.028 (Fisher's exact 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
ALL 101 143 24
NSD1 MUTATED 5 22 2
NSD1 WILD-TYPE 96 121 22

Figure S31.  Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.334 (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 CLUS_4
ALL 114 68 103 17
FAT1 MUTATED 20 19 26 3
FAT1 WILD-TYPE 94 49 77 14
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0629 (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 42 56 64 44 38 47 15
FAT1 MUTATED 11 11 17 3 14 10 3
FAT1 WILD-TYPE 31 45 47 41 24 37 12
'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 = 0.109 (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 124 95 85
FAT1 MUTATED 21 27 21
FAT1 WILD-TYPE 103 68 64
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.219 (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 100 92 112
FAT1 MUTATED 28 21 20
FAT1 WILD-TYPE 72 71 92
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0969 (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 62 132 110
FAT1 MUTATED 10 26 32
FAT1 WILD-TYPE 52 106 78
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.402 (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
ALL 124 180
FAT1 MUTATED 31 37
FAT1 WILD-TYPE 93 143
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.859 (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
ALL 41 126 101
FAT1 MUTATED 9 29 26
FAT1 WILD-TYPE 32 97 75
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.131 (Fisher's exact 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
ALL 101 143 24
FAT1 MUTATED 31 28 5
FAT1 WILD-TYPE 70 115 19
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.007

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 68 103 17
CASP8 MUTATED 3 1 20 2
CASP8 WILD-TYPE 111 67 83 15

Figure S32.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.55e-11 (Chi-square test), Q value = 2.6e-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 42 56 64 44 38 47 15
CASP8 MUTATED 2 2 0 0 15 6 2
CASP8 WILD-TYPE 40 54 64 44 23 41 13

Figure S33.  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 S34.  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 = 1.62e-08 (Fisher's exact test), Q value = 5.6e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
CASP8 MUTATED 1 5 21
CASP8 WILD-TYPE 123 90 64

Figure S35.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.85e-06 (Fisher's exact test), Q value = 0.00097

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 92 112
CASP8 MUTATED 7 19 1
CASP8 WILD-TYPE 93 73 111

Figure S36.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.144 (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 62 132 110
CASP8 MUTATED 8 7 11
CASP8 WILD-TYPE 54 125 99
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.838 (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
ALL 124 180
CASP8 MUTATED 10 16
CASP8 WILD-TYPE 114 164
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.493 (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
ALL 41 126 101
CASP8 MUTATED 5 9 10
CASP8 WILD-TYPE 36 117 91
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 143 24
CASP8 MUTATED 10 7 7
CASP8 WILD-TYPE 91 136 17

Figure S37.  Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'JUB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.424 (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 CLUS_4
ALL 114 68 103 17
JUB MUTATED 10 3 4 1
JUB WILD-TYPE 104 65 99 16
'JUB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.151 (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 42 56 64 44 38 47 15
JUB MUTATED 0 6 5 1 3 1 2
JUB WILD-TYPE 42 50 59 43 35 46 13
'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 = 0.127 (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 124 95 85
JUB MUTATED 5 4 9
JUB WILD-TYPE 119 91 76
'JUB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.19 (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 100 92 112
JUB MUTATED 5 9 4
JUB WILD-TYPE 95 83 108
'JUB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0779 (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 62 132 110
JUB MUTATED 7 8 3
JUB WILD-TYPE 55 124 107
'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
ALL 124 180
JUB MUTATED 7 11
JUB WILD-TYPE 117 169
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0411 (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
ALL 41 126 101
JUB MUTATED 6 9 3
JUB WILD-TYPE 35 117 98

Figure S38.  Get High-res Image Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact 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
ALL 101 143 24
JUB MUTATED 7 10 1
JUB WILD-TYPE 94 133 23
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0114 (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 CLUS_4
ALL 114 68 103 17
MLL2 MUTATED 20 20 10 3
MLL2 WILD-TYPE 94 48 93 14

Figure S39.  Get High-res Image Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.045 (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 42 56 64 44 38 47 15
MLL2 MUTATED 11 8 17 9 3 4 1
MLL2 WILD-TYPE 31 48 47 35 35 43 14

Figure S40.  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 = 0.082 (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 124 95 85
MLL2 MUTATED 29 12 12
MLL2 WILD-TYPE 95 83 73
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0641 (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 100 92 112
MLL2 MUTATED 11 16 26
MLL2 WILD-TYPE 89 76 86
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0706 (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 62 132 110
MLL2 MUTATED 11 29 12
MLL2 WILD-TYPE 51 103 98
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00499 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2
ALL 124 180
MLL2 MUTATED 12 40
MLL2 WILD-TYPE 112 140

Figure S41.  Get High-res Image Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0939 (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
ALL 41 126 101
MLL2 MUTATED 5 28 12
MLL2 WILD-TYPE 36 98 89
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact 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
ALL 101 143 24
MLL2 MUTATED 10 32 3
MLL2 WILD-TYPE 91 111 21

Figure S42.  Get High-res Image Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.667 (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 CLUS_4
ALL 114 68 103 17
FBXW7 MUTATED 6 5 4 0
FBXW7 WILD-TYPE 108 63 99 17
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.138 (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 42 56 64 44 38 47 15
FBXW7 MUTATED 4 0 5 1 2 1 2
FBXW7 WILD-TYPE 38 56 59 43 36 46 13
'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 124 95 85
FBXW7 MUTATED 7 3 5
FBXW7 WILD-TYPE 117 92 80
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.438 (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 100 92 112
FBXW7 MUTATED 4 3 8
FBXW7 WILD-TYPE 96 89 104
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.794 (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 62 132 110
FBXW7 MUTATED 4 6 5
FBXW7 WILD-TYPE 58 126 105
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.602 (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
ALL 124 180
FBXW7 MUTATED 5 10
FBXW7 WILD-TYPE 119 170
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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
ALL 41 126 101
FBXW7 MUTATED 2 6 4
FBXW7 WILD-TYPE 39 120 97
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact 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
ALL 101 143 24
FBXW7 MUTATED 4 7 1
FBXW7 WILD-TYPE 97 136 23
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.445 (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 CLUS_4
ALL 114 68 103 17
ZNF750 MUTATED 3 5 5 0
ZNF750 WILD-TYPE 111 63 98 17
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (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 42 56 64 44 38 47 15
ZNF750 MUTATED 1 0 4 5 1 2 0
ZNF750 WILD-TYPE 41 56 60 39 37 45 15
'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 = 0.0793 (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 124 95 85
ZNF750 MUTATED 9 3 1
ZNF750 WILD-TYPE 115 92 84
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.1 (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 100 92 112
ZNF750 MUTATED 4 1 8
ZNF750 WILD-TYPE 96 91 104
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.755 (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 62 132 110
ZNF750 MUTATED 2 7 4
ZNF750 WILD-TYPE 60 125 106
'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
ALL 124 180
ZNF750 MUTATED 5 8
ZNF750 WILD-TYPE 119 172
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.37 (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
ALL 41 126 101
ZNF750 MUTATED 0 7 5
ZNF750 WILD-TYPE 41 119 96
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.817 (Fisher's exact 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
ALL 101 143 24
ZNF750 MUTATED 5 7 0
ZNF750 WILD-TYPE 96 136 24
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.554 (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 CLUS_4
ALL 114 68 103 17
EPHA2 MUTATED 5 1 5 1
EPHA2 WILD-TYPE 109 67 98 16
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00158 (Chi-square test), Q value = 0.51

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 42 56 64 44 38 47 15
EPHA2 MUTATED 1 3 0 1 6 0 2
EPHA2 WILD-TYPE 41 53 64 43 32 47 13

Figure S43.  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 = 0.0631 (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 124 95 85
EPHA2 MUTATED 2 4 7
EPHA2 WILD-TYPE 122 91 78
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (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 100 92 112
EPHA2 MUTATED 5 6 2
EPHA2 WILD-TYPE 95 86 110
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.323 (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 62 132 110
EPHA2 MUTATED 4 3 5
EPHA2 WILD-TYPE 58 129 105
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.239 (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
ALL 124 180
EPHA2 MUTATED 7 5
EPHA2 WILD-TYPE 117 175
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.725 (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
ALL 41 126 101
EPHA2 MUTATED 2 3 4
EPHA2 WILD-TYPE 39 123 97
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact 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
ALL 101 143 24
EPHA2 MUTATED 4 2 3
EPHA2 WILD-TYPE 97 141 21

Figure S44.  Get High-res Image Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.367 (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 CLUS_4
ALL 114 68 103 17
FLG MUTATED 13 14 17 3
FLG WILD-TYPE 101 54 86 14
'FLG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.15 (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 42 56 64 44 38 47 15
FLG MUTATED 5 5 16 7 8 4 2
FLG WILD-TYPE 37 51 48 37 30 43 13
'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 = 0.0643 (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 124 95 85
FLG MUTATED 26 9 12
FLG WILD-TYPE 98 86 73
'FLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (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 100 92 112
FLG MUTATED 11 14 22
FLG WILD-TYPE 89 78 90
'FLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0567 (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 62 132 110
FLG MUTATED 11 26 10
FLG WILD-TYPE 51 106 100
'FLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.108 (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
ALL 124 180
FLG MUTATED 14 33
FLG WILD-TYPE 110 147
'FLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.105 (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
ALL 41 126 101
FLG MUTATED 5 25 10
FLG WILD-TYPE 36 101 91
'FLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact 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
ALL 101 143 24
FLG MUTATED 10 29 1
FLG WILD-TYPE 91 114 23

Figure S45.  Get High-res Image Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'B2M MUTATION STATUS' versus 'CN_CNMF'

P value = 0.11 (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 CLUS_4
ALL 114 68 103 17
B2M MUTATED 0 3 4 0
B2M WILD-TYPE 114 65 99 17
'B2M MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0635 (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 42 56 64 44 38 47 15
B2M MUTATED 0 0 1 4 1 1 0
B2M WILD-TYPE 42 56 63 40 37 46 15
'B2M MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.584 (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 124 95 85
B2M MUTATED 4 1 1
B2M WILD-TYPE 120 94 84
'B2M MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.383 (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 100 92 112
B2M MUTATED 1 1 4
B2M WILD-TYPE 99 91 108
'B2M MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.286 (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 62 132 110
B2M MUTATED 0 5 2
B2M WILD-TYPE 62 127 108
'B2M MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.705 (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
ALL 124 180
B2M MUTATED 2 5
B2M WILD-TYPE 122 175
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.764 (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
ALL 41 126 101
B2M MUTATED 0 4 3
B2M WILD-TYPE 41 122 98
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.847 (Fisher's exact 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
ALL 101 143 24
B2M MUTATED 2 5 0
B2M WILD-TYPE 99 138 24
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.235 (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 CLUS_4
ALL 114 68 103 17
EP300 MUTATED 7 3 12 2
EP300 WILD-TYPE 107 65 91 15
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.388 (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 42 56 64 44 38 47 15
EP300 MUTATED 2 2 4 5 6 4 1
EP300 WILD-TYPE 40 54 60 39 32 43 14
'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 = 0.00482 (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 124 95 85
EP300 MUTATED 5 5 14
EP300 WILD-TYPE 119 90 71

Figure S46.  Get High-res Image Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.113 (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 100 92 112
EP300 MUTATED 6 12 6
EP300 WILD-TYPE 94 80 106
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.424 (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 62 132 110
EP300 MUTATED 7 8 8
EP300 WILD-TYPE 55 124 102
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.379 (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
ALL 124 180
EP300 MUTATED 7 16
EP300 WILD-TYPE 117 164
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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
ALL 41 126 101
EP300 MUTATED 3 11 8
EP300 WILD-TYPE 38 115 93
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.65 (Fisher's exact 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
ALL 101 143 24
EP300 MUTATED 8 11 3
EP300 WILD-TYPE 93 132 21
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.235 (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 CLUS_4
ALL 114 68 103 17
RHOA MUTATED 2 0 1 1
RHOA WILD-TYPE 112 68 102 16
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.122 (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 42 56 64 44 38 47 15
RHOA MUTATED 0 3 0 0 0 1 0
RHOA WILD-TYPE 42 53 64 44 38 46 15
'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 = 0.823 (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 124 95 85
RHOA MUTATED 1 2 1
RHOA WILD-TYPE 123 93 84
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.156 (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 100 92 112
RHOA MUTATED 3 1 0
RHOA WILD-TYPE 97 91 112
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0769 (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 62 132 110
RHOA MUTATED 2 0 2
RHOA WILD-TYPE 60 132 108
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.308 (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
ALL 124 180
RHOA MUTATED 3 1
RHOA WILD-TYPE 121 179
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.114 (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
ALL 41 126 101
RHOA MUTATED 1 0 3
RHOA WILD-TYPE 40 126 98
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0604 (Fisher's exact 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
ALL 101 143 24
RHOA MUTATED 3 0 1
RHOA WILD-TYPE 98 143 23
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0759 (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 CLUS_4
ALL 114 68 103 17
HLA-A MUTATED 3 0 4 2
HLA-A WILD-TYPE 111 68 99 15
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.132 (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 42 56 64 44 38 47 15
HLA-A MUTATED 0 1 2 1 4 1 0
HLA-A WILD-TYPE 42 55 62 43 34 46 15
'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 = 0.189 (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 124 95 85
HLA-A MUTATED 3 1 5
HLA-A WILD-TYPE 121 94 80
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.697 (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 100 92 112
HLA-A MUTATED 2 4 3
HLA-A WILD-TYPE 98 88 109
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.202 (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 62 132 110
HLA-A MUTATED 4 3 2
HLA-A WILD-TYPE 58 129 108
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.318 (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
ALL 124 180
HLA-A MUTATED 2 7
HLA-A WILD-TYPE 122 173
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.541 (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
ALL 41 126 101
HLA-A MUTATED 2 5 2
HLA-A WILD-TYPE 39 121 99
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.781 (Fisher's exact 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
ALL 101 143 24
HLA-A MUTATED 3 6 0
HLA-A WILD-TYPE 98 137 24
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.276 (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 CLUS_4
ALL 114 68 103 17
CTCF MUTATED 2 2 7 0
CTCF WILD-TYPE 112 66 96 17
'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0164 (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 42 56 64 44 38 47 15
CTCF MUTATED 3 1 0 1 5 1 0
CTCF WILD-TYPE 39 55 64 43 33 46 15

Figure S47.  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 = 0.426 (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 124 95 85
CTCF MUTATED 4 2 5
CTCF WILD-TYPE 120 93 80
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.928 (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 100 92 112
CTCF MUTATED 3 4 4
CTCF WILD-TYPE 97 88 108
'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.793 (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 62 132 110
CTCF MUTATED 3 4 4
CTCF WILD-TYPE 59 128 106
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.763 (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
ALL 124 180
CTCF MUTATED 5 6
CTCF WILD-TYPE 119 174
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.47 (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
ALL 41 126 101
CTCF MUTATED 0 5 5
CTCF WILD-TYPE 41 121 96
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.414 (Fisher's exact 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
ALL 101 143 24
CTCF MUTATED 3 5 2
CTCF WILD-TYPE 98 138 22
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00771 (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 CLUS_4
ALL 114 68 103 17
RB1 MUTATED 0 6 4 0
RB1 WILD-TYPE 114 62 99 17

Figure S48.  Get High-res Image Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.381 (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 42 56 64 44 38 47 15
RB1 MUTATED 3 0 2 3 1 1 0
RB1 WILD-TYPE 39 56 62 41 37 46 15
'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 = 0.0558 (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 124 95 85
RB1 MUTATED 8 1 1
RB1 WILD-TYPE 116 94 84
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.259 (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 100 92 112
RB1 MUTATED 3 1 6
RB1 WILD-TYPE 97 91 106
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.143 (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 62 132 110
RB1 MUTATED 0 7 3
RB1 WILD-TYPE 62 125 107
'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
ALL 124 180
RB1 MUTATED 4 6
RB1 WILD-TYPE 120 174
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.424 (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
ALL 41 126 101
RB1 MUTATED 0 6 3
RB1 WILD-TYPE 41 120 98
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.781 (Fisher's exact 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
ALL 101 143 24
RB1 MUTATED 3 6 0
RB1 WILD-TYPE 98 137 24
'CSMD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 68 103 17
CSMD3 MUTATED 28 23 12 7
CSMD3 WILD-TYPE 86 45 91 10

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 = 0.000217 (Chi-square test), Q value = 0.073

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 42 56 64 44 38 47 15
CSMD3 MUTATED 20 8 19 11 4 5 3
CSMD3 WILD-TYPE 22 48 45 33 34 42 12

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 = 8.26e-06 (Fisher's exact test), Q value = 0.0028

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
CSMD3 MUTATED 45 9 16
CSMD3 WILD-TYPE 79 86 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 = 1.41e-06 (Fisher's exact test), Q value = 0.00048

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 92 112
CSMD3 MUTATED 9 18 43
CSMD3 WILD-TYPE 91 74 69

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 = 0.000515 (Fisher's exact test), Q value = 0.17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 132 110
CSMD3 MUTATED 14 43 13
CSMD3 WILD-TYPE 48 89 97

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 = 0.00138 (Fisher's exact test), Q value = 0.45

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

nPatients CLUS_1 CLUS_2
ALL 124 180
CSMD3 MUTATED 17 53
CSMD3 WILD-TYPE 107 127

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 = 0.00177 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 126 101
CSMD3 MUTATED 8 38 11
CSMD3 WILD-TYPE 33 88 90

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 = 0.000974 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 143 24
CSMD3 MUTATED 10 41 6
CSMD3 WILD-TYPE 91 102 18

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 = 0.163 (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 CLUS_4
ALL 114 68 103 17
TGFBR2 MUTATED 1 3 6 0
TGFBR2 WILD-TYPE 113 65 97 17
'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0148 (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 42 56 64 44 38 47 15
TGFBR2 MUTATED 3 0 0 0 4 3 0
TGFBR2 WILD-TYPE 39 56 64 44 34 44 15

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 = 0.229 (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 124 95 85
TGFBR2 MUTATED 2 3 5
TGFBR2 WILD-TYPE 122 92 80
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.921 (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 100 92 112
TGFBR2 MUTATED 4 3 3
TGFBR2 WILD-TYPE 96 89 109
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (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 62 132 110
TGFBR2 MUTATED 2 4 4
TGFBR2 WILD-TYPE 60 128 106
'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
ALL 124 180
TGFBR2 MUTATED 4 6
TGFBR2 WILD-TYPE 120 174
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.662 (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
ALL 41 126 101
TGFBR2 MUTATED 1 3 5
TGFBR2 WILD-TYPE 40 123 96
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact 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
ALL 101 143 24
TGFBR2 MUTATED 4 2 3
TGFBR2 WILD-TYPE 97 141 21

Figure S59.  Get High-res Image Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NECAB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.914 (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 CLUS_4
ALL 114 68 103 17
NECAB1 MUTATED 2 1 3 0
NECAB1 WILD-TYPE 112 67 100 17
'NECAB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.176 (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 42 56 64 44 38 47 15
NECAB1 MUTATED 2 0 0 1 2 0 1
NECAB1 WILD-TYPE 40 56 64 43 36 47 14
'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 = 0.0715 (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 124 95 85
NECAB1 MUTATED 2 0 4
NECAB1 WILD-TYPE 122 95 81
'NECAB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0992 (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 100 92 112
NECAB1 MUTATED 0 4 2
NECAB1 WILD-TYPE 100 88 110
'NECAB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.505 (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 62 132 110
NECAB1 MUTATED 2 3 1
NECAB1 WILD-TYPE 60 129 109
'NECAB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.407 (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
ALL 124 180
NECAB1 MUTATED 1 5
NECAB1 WILD-TYPE 123 175
'NECAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.535 (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
ALL 41 126 101
NECAB1 MUTATED 1 4 1
NECAB1 WILD-TYPE 40 122 100
'NECAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.279 (Fisher's exact 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
ALL 101 143 24
NECAB1 MUTATED 1 4 1
NECAB1 WILD-TYPE 100 139 23
'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.13 (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 CLUS_4
ALL 114 68 103 17
MAPK1 MUTATED 0 1 2 1
MAPK1 WILD-TYPE 114 67 101 16
'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.856 (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 42 56 64 44 38 47 15
MAPK1 MUTATED 0 0 1 1 1 1 0
MAPK1 WILD-TYPE 42 56 63 43 37 46 15
'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 = 0.689 (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 124 95 85
MAPK1 MUTATED 1 1 2
MAPK1 WILD-TYPE 123 94 83
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.69 (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 100 92 112
MAPK1 MUTATED 1 2 1
MAPK1 WILD-TYPE 99 90 111
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.342 (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 62 132 110
MAPK1 MUTATED 2 1 1
MAPK1 WILD-TYPE 60 131 109
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (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
ALL 124 180
MAPK1 MUTATED 2 2
MAPK1 WILD-TYPE 122 178
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.499 (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
ALL 41 126 101
MAPK1 MUTATED 1 1 2
MAPK1 WILD-TYPE 40 125 99
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.527 (Fisher's exact 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
ALL 101 143 24
MAPK1 MUTATED 1 2 1
MAPK1 WILD-TYPE 100 141 23
'EPB41L3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0728 (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 CLUS_4
ALL 114 68 103 17
EPB41L3 MUTATED 4 7 3 2
EPB41L3 WILD-TYPE 110 61 100 15
'EPB41L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0257 (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 42 56 64 44 38 47 15
EPB41L3 MUTATED 6 1 6 0 1 2 0
EPB41L3 WILD-TYPE 36 55 58 44 37 45 15

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 = 0.0717 (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 124 95 85
EPB41L3 MUTATED 11 2 3
EPB41L3 WILD-TYPE 113 93 82
'EPB41L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00889 (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 100 92 112
EPB41L3 MUTATED 2 2 12
EPB41L3 WILD-TYPE 98 90 100

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 = 0.253 (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 62 132 110
EPB41L3 MUTATED 3 10 3
EPB41L3 WILD-TYPE 59 122 107
'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0724 (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
ALL 124 180
EPB41L3 MUTATED 3 13
EPB41L3 WILD-TYPE 121 167
'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.13 (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
ALL 41 126 101
EPB41L3 MUTATED 2 10 2
EPB41L3 WILD-TYPE 39 116 99
'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.362 (Fisher's exact 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
ALL 101 143 24
EPB41L3 MUTATED 3 10 1
EPB41L3 WILD-TYPE 98 133 23
'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0789 (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 CLUS_4
ALL 114 68 103 17
RAC1 MUTATED 1 1 7 0
RAC1 WILD-TYPE 113 67 96 17
'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.49 (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 42 56 64 44 38 47 15
RAC1 MUTATED 0 1 1 1 2 3 1
RAC1 WILD-TYPE 42 55 63 43 36 44 14
'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 = 0.189 (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 124 95 85
RAC1 MUTATED 3 1 5
RAC1 WILD-TYPE 121 94 80
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (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 100 92 112
RAC1 MUTATED 1 5 3
RAC1 WILD-TYPE 99 87 109
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.251 (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 62 132 110
RAC1 MUTATED 2 6 1
RAC1 WILD-TYPE 60 126 109
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0879 (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
ALL 124 180
RAC1 MUTATED 1 8
RAC1 WILD-TYPE 123 172
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.326 (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
ALL 41 126 101
RAC1 MUTATED 1 5 1
RAC1 WILD-TYPE 40 121 100
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.333 (Fisher's exact 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
ALL 101 143 24
RAC1 MUTATED 1 6 0
RAC1 WILD-TYPE 100 137 24
'CUL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.304 (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 CLUS_4
ALL 114 68 103 17
CUL3 MUTATED 3 5 2 0
CUL3 WILD-TYPE 111 63 101 17
'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.123 (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 42 56 64 44 38 47 15
CUL3 MUTATED 3 1 5 0 0 1 0
CUL3 WILD-TYPE 39 55 59 44 38 46 15
'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 = 0.469 (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 124 95 85
CUL3 MUTATED 5 4 1
CUL3 WILD-TYPE 119 91 84
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.787 (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 100 92 112
CUL3 MUTATED 4 2 4
CUL3 WILD-TYPE 96 90 108
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.918 (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 62 132 110
CUL3 MUTATED 2 5 3
CUL3 WILD-TYPE 60 127 107
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.326 (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
ALL 124 180
CUL3 MUTATED 6 4
CUL3 WILD-TYPE 118 176
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.185 (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
ALL 41 126 101
CUL3 MUTATED 3 3 2
CUL3 WILD-TYPE 38 123 99
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.378 (Fisher's exact 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
ALL 101 143 24
CUL3 MUTATED 5 3 0
CUL3 WILD-TYPE 96 140 24
'PRB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.157 (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 CLUS_4
ALL 114 68 103 17
PRB1 MUTATED 5 2 0 0
PRB1 WILD-TYPE 109 66 103 17
'PRB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.147 (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 42 56 64 44 38 47 15
PRB1 MUTATED 3 1 3 0 0 0 0
PRB1 WILD-TYPE 39 55 61 44 38 47 15
'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 = 0.804 (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 124 95 85
PRB1 MUTATED 3 3 1
PRB1 WILD-TYPE 121 92 84
'PRB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.571 (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 100 92 112
PRB1 MUTATED 2 1 4
PRB1 WILD-TYPE 98 91 108
'PRB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.244 (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 62 132 110
PRB1 MUTATED 3 3 1
PRB1 WILD-TYPE 59 129 109
'PRB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (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
ALL 124 180
PRB1 MUTATED 3 4
PRB1 WILD-TYPE 121 176
'PRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0736 (Fisher's exact test), Q value = 1

Table S287.  Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 126 101
PRB1 MUTATED 2 4 0
PRB1 WILD-TYPE 39 122 101
'PRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.363 (Fisher's exact 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
ALL 101 143 24
PRB1 MUTATED 3 2 1
PRB1 WILD-TYPE 98 141 23
'TRPV4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.661 (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 CLUS_4
ALL 114 68 103 17
TRPV4 MUTATED 4 2 1 0
TRPV4 WILD-TYPE 110 66 102 17
'TRPV4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.922 (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 42 56 64 44 38 47 15
TRPV4 MUTATED 0 2 2 1 1 1 0
TRPV4 WILD-TYPE 42 54 62 43 37 46 15
'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 = 0.494 (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 124 95 85
TRPV4 MUTATED 3 1 3
TRPV4 WILD-TYPE 121 94 82
'TRPV4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.306 (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 100 92 112
TRPV4 MUTATED 1 4 2
TRPV4 WILD-TYPE 99 88 110
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.377 (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 62 132 110
TRPV4 MUTATED 1 5 1
TRPV4 WILD-TYPE 61 127 109
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.247 (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
ALL 124 180
TRPV4 MUTATED 1 6
TRPV4 WILD-TYPE 123 174
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.764 (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
ALL 41 126 101
TRPV4 MUTATED 0 4 3
TRPV4 WILD-TYPE 41 122 98
'TRPV4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.395 (Fisher's exact 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
ALL 101 143 24
TRPV4 MUTATED 1 5 1
TRPV4 WILD-TYPE 100 138 23
'EPDR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.704 (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 CLUS_4
ALL 114 68 103 17
EPDR1 MUTATED 4 1 1 0
EPDR1 WILD-TYPE 110 67 102 17
'EPDR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.36 (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 42 56 64 44 38 47 15
EPDR1 MUTATED 0 3 2 0 0 1 0
EPDR1 WILD-TYPE 42 53 62 44 38 46 15
'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 = 0.331 (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 124 95 85
EPDR1 MUTATED 3 3 0
EPDR1 WILD-TYPE 121 92 85
'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.686 (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 100 92 112
EPDR1 MUTATED 3 1 2
EPDR1 WILD-TYPE 97 91 110
'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 62 132 110
EPDR1 MUTATED 1 3 2
EPDR1 WILD-TYPE 61 129 108
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.691 (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
ALL 124 180
EPDR1 MUTATED 3 3
EPDR1 WILD-TYPE 121 177
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.168 (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
ALL 41 126 101
EPDR1 MUTATED 2 1 3
EPDR1 WILD-TYPE 39 125 98
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact 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
ALL 101 143 24
EPDR1 MUTATED 2 4 0
EPDR1 WILD-TYPE 99 139 24
'SLC26A7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.887 (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 CLUS_4
ALL 114 68 103 17
SLC26A7 MUTATED 4 2 2 0
SLC26A7 WILD-TYPE 110 66 101 17
'SLC26A7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.51 (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 42 56 64 44 38 47 15
SLC26A7 MUTATED 1 0 2 0 2 2 1
SLC26A7 WILD-TYPE 41 56 62 44 36 45 14
'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 124 95 85
SLC26A7 MUTATED 2 1 5
SLC26A7 WILD-TYPE 122 94 80
'SLC26A7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.399 (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 100 92 112
SLC26A7 MUTATED 1 4 3
SLC26A7 WILD-TYPE 99 88 109
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.809 (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 62 132 110
SLC26A7 MUTATED 2 4 2
SLC26A7 WILD-TYPE 60 128 108
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.479 (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
ALL 124 180
SLC26A7 MUTATED 2 6
SLC26A7 WILD-TYPE 122 174
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.672 (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
ALL 41 126 101
SLC26A7 MUTATED 2 3 2
SLC26A7 WILD-TYPE 39 123 99
'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.175 (Fisher's exact 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
ALL 101 143 24
SLC26A7 MUTATED 2 3 2
SLC26A7 WILD-TYPE 99 140 22
'KCNA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.342 (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 CLUS_4
ALL 114 68 103 17
KCNA3 MUTATED 1 3 4 0
KCNA3 WILD-TYPE 113 65 99 17
'KCNA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.801 (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 42 56 64 44 38 47 15
KCNA3 MUTATED 2 1 2 0 1 2 0
KCNA3 WILD-TYPE 40 55 62 44 37 45 15
'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 S62.  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 = 0.603 (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 124 95 85
KCNA3 MUTATED 4 1 3
KCNA3 WILD-TYPE 120 94 82
'KCNA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.446 (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 100 92 112
KCNA3 MUTATED 1 3 4
KCNA3 WILD-TYPE 99 89 108
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.809 (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 62 132 110
KCNA3 MUTATED 2 4 2
KCNA3 WILD-TYPE 60 128 108
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.479 (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
ALL 124 180
KCNA3 MUTATED 2 6
KCNA3 WILD-TYPE 122 174
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.639 (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
ALL 41 126 101
KCNA3 MUTATED 0 4 2
KCNA3 WILD-TYPE 41 122 99
'KCNA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0644 (Fisher's exact 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
ALL 101 143 24
KCNA3 MUTATED 0 6 0
KCNA3 WILD-TYPE 101 137 24
'HIST1H1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.443 (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 CLUS_4
ALL 114 68 103 17
HIST1H1B MUTATED 3 0 4 0
HIST1H1B WILD-TYPE 111 68 99 17
'HIST1H1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00632 (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 42 56 64 44 38 47 15
HIST1H1B MUTATED 0 0 3 0 4 0 0
HIST1H1B WILD-TYPE 42 56 61 44 34 47 15

Figure S63.  Get High-res Image Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'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 = 0.641 (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 124 95 85
HIST1H1B MUTATED 2 2 3
HIST1H1B WILD-TYPE 122 93 82
'HIST1H1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.267 (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 100 92 112
HIST1H1B MUTATED 2 4 1
HIST1H1B WILD-TYPE 98 88 111
'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.786 (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 62 132 110
HIST1H1B MUTATED 2 3 2
HIST1H1B WILD-TYPE 60 129 108
'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.705 (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
ALL 124 180
HIST1H1B MUTATED 2 5
HIST1H1B WILD-TYPE 122 175
'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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
ALL 41 126 101
HIST1H1B MUTATED 1 3 3
HIST1H1B WILD-TYPE 40 123 98
'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact 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
ALL 101 143 24
HIST1H1B MUTATED 1 3 3
HIST1H1B WILD-TYPE 100 140 21

Figure S64.  Get High-res Image Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'STEAP4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.495 (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 CLUS_4
ALL 114 68 103 17
STEAP4 MUTATED 4 4 2 0
STEAP4 WILD-TYPE 110 64 101 17
'STEAP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.601 (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 42 56 64 44 38 47 15
STEAP4 MUTATED 2 1 4 1 0 2 0
STEAP4 WILD-TYPE 40 55 60 43 38 45 15
'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 = 0.108 (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 124 95 85
STEAP4 MUTATED 6 4 0
STEAP4 WILD-TYPE 118 91 85
'STEAP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.339 (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 100 92 112
STEAP4 MUTATED 4 1 5
STEAP4 WILD-TYPE 96 91 107
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.239 (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 62 132 110
STEAP4 MUTATED 0 6 4
STEAP4 WILD-TYPE 62 126 106
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.745 (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
ALL 124 180
STEAP4 MUTATED 5 5
STEAP4 WILD-TYPE 119 175
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.515 (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
ALL 41 126 101
STEAP4 MUTATED 0 6 4
STEAP4 WILD-TYPE 41 120 97
'STEAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.898 (Fisher's exact 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
ALL 101 143 24
STEAP4 MUTATED 4 6 0
STEAP4 WILD-TYPE 97 137 24
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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