Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 38 genes and 10 molecular subtypes across 194 patients, 16 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • HLA-A mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • EP300 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • PIK3CA mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • ERBB3 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 38 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, 16 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
KRAS 11 (6%) 183 0.565
(0.893) 		0.00384
(0.145) 		0.806
(1.00) 		0.219
(0.728) 		0.00448
(0.145) 		0.00165
(0.125) 		0.00322
(0.145) 		0.00074
(0.0937) 		0.0372
(0.389) 		0.00019
(0.0722)
ARID1A 14 (7%) 180 0.00691
(0.202) 		0.00423
(0.145) 		0.926
(1.00) 		0.124
(0.636) 		0.167
(0.691) 		0.00066
(0.0937) 		0.102
(0.578) 		0.00444
(0.145) 		0.701
(0.955) 		0.00457
(0.145)
HLA-A 16 (8%) 178 0.259
(0.758) 		0.0943
(0.56) 		0.223
(0.728) 		0.0176
(0.341) 		0.00101
(0.0959) 		0.067
(0.498) 		0.433
(0.85) 		0.00789
(0.214) 		0.692
(0.952) 		0.419
(0.848)
EP300 21 (11%) 173 1
(1.00) 		0.0264
(0.386) 		0.247
(0.754) 		0.0379
(0.389) 		0.135
(0.651) 		0.0722
(0.498) 		0.84
(1.00) 		0.00965
(0.24) 		1
(1.00) 		0.25
(0.754)
PIK3CA 53 (27%) 141 0.0354
(0.389) 		0.283
(0.777) 		0.432
(0.85) 		0.299
(0.777) 		0.35
(0.805) 		0.00392
(0.145) 		0.333
(0.804) 		0.347
(0.804) 		0.483
(0.855) 		0.233
(0.736)
ERBB3 11 (6%) 183 0.0726
(0.498) 		0.125
(0.636) 		0.914
(1.00) 		0.791
(1.00) 		0.0324
(0.389) 		0.0101
(0.24) 		0.0784
(0.523) 		0.029
(0.389) 		0.93
(1.00) 		0.334
(0.804)
FBXW7 19 (10%) 175 0.496
(0.857) 		0.259
(0.758) 		0.946
(1.00) 		0.971
(1.00) 		0.339
(0.804) 		0.679
(0.952) 		0.402
(0.827) 		0.457
(0.85) 		0.226
(0.728) 		0.543
(0.883)
HLA-B 11 (6%) 183 0.519
(0.866) 		0.164
(0.691) 		0.685
(0.952) 		0.327
(0.804) 		0.238
(0.738) 		0.0923
(0.557) 		0.0192
(0.347) 		0.134
(0.651) 		0.0135
(0.302) 		0.0478
(0.454)
PTEN 15 (8%) 179 0.566
(0.893) 		0.343
(0.804) 		0.905
(1.00) 		0.591
(0.908) 		0.0261
(0.386) 		0.228
(0.728) 		0.434
(0.85) 		0.194
(0.706) 		1
(1.00) 		0.418
(0.848)
MAPK1 9 (5%) 185 0.552
(0.888) 		0.227
(0.728) 		0.322
(0.804) 		0.975
(1.00) 		0.0904
(0.554) 		0.055
(0.475) 		0.182
(0.706) 		0.0826
(0.541) 		0.021
(0.363) 		0.0222
(0.366)
NFE2L2 12 (6%) 182 0.927
(1.00) 		0.0979
(0.572) 		0.299
(0.777) 		0.0501
(0.465) 		0.458
(0.85) 		0.0465
(0.453) 		0.0362
(0.389) 		0.0179
(0.341) 		0.386
(0.827) 		0.0734
(0.498)
FAT2 11 (6%) 183 0.613
(0.911) 		0.0516
(0.467) 		0.9
(1.00) 		0.623
(0.917) 		0.0646
(0.498) 		0.482
(0.855) 		0.583
(0.904) 		0.762
(1.00) 		0.0704
(0.498) 		0.0895
(0.554)
ZNF750 10 (5%) 184 0.0854
(0.55) 		0.367
(0.823) 		0.9
(1.00) 		0.154
(0.691) 		0.509
(0.866) 		0.29
(0.777) 		0.182
(0.706) 		0.19
(0.706) 		0.471
(0.854) 		0.0726
(0.498)
BAP1 4 (2%) 190 0.141
(0.662) 		0.0583
(0.48) 		0.511
(0.866) 		0.454
(0.85) 		0.69
(0.952) 		0.353
(0.806) 		0.257
(0.758) 		0.172
(0.697)
RAB35 4 (2%) 190 0.259
(0.758) 		0.454
(0.85) 		0.769
(1.00) 		0.454
(0.85) 		0.474
(0.854) 		0.107
(0.587) 		0.292
(0.777) 		0.0312
(0.389)
SMAD4 7 (4%) 187 0.488
(0.855) 		0.346
(0.804) 		0.573
(0.893) 		0.92
(1.00) 		0.515
(0.866) 		1
(1.00) 		0.723
(0.977) 		0.599
(0.908) 		1
(1.00) 		0.945
(1.00)
TCTE1 5 (3%) 189 0.182
(0.706) 		0.318
(0.804) 		0.312
(0.801) 		0.0428
(0.428) 		0.0172
(0.341) 		0.405
(0.827) 		0.0247
(0.386) 		0.101
(0.578) 		0.2
(0.706) 		0.337
(0.804)
NHS 12 (6%) 182 0.862
(1.00) 		0.978
(1.00) 		0.642
(0.939) 		0.926
(1.00) 		0.759
(1.00) 		0.276
(0.777) 		0.933
(1.00) 		0.831
(1.00) 		0.424
(0.85) 		0.434
(0.85)
LIN9 7 (4%) 187 0.157
(0.691) 		0.374
(0.825) 		0.69
(0.952) 		0.373
(0.825) 		0.534
(0.883) 		0.869
(1.00) 		0.888
(1.00) 		0.269
(0.776) 		0.297
(0.777) 		0.893
(1.00)
C12ORF43 4 (2%) 190 0.199
(0.706) 		0.145
(0.674) 		0.912
(1.00) 		0.456
(0.85) 		0.472
(0.854) 		0.204
(0.706) 		0.292
(0.777) 		0.162
(0.691)
MED1 11 (6%) 183 0.923
(1.00) 		0.133
(0.651) 		0.169
(0.692) 		0.156
(0.691) 		0.235
(0.738) 		0.103
(0.578) 		0.187
(0.706) 		0.239
(0.738) 		0.507
(0.866) 		0.122
(0.636)
USP28 4 (2%) 190 0.199
(0.706) 		0.541
(0.883) 		0.321
(0.804) 		0.91
(1.00) 		0.604
(0.908) 		1
(1.00) 		0.389
(0.827) 		0.938
(1.00) 		0.202
(0.706) 		0.822
(1.00)
IDS 7 (4%) 187 0.189
(0.706) 		0.534
(0.883) 		0.248
(0.754) 		0.537
(0.883) 		1
(1.00) 		0.87
(1.00) 		0.493
(0.856) 		0.222
(0.728) 		0.438
(0.85) 		0.714
(0.968)
TRIM9 8 (4%) 186 0.334
(0.804) 		0.786
(1.00) 		0.687
(0.952) 		0.88
(1.00) 		0.0904
(0.554) 		0.661
(0.952) 		0.544
(0.883) 		0.0378
(0.389) 		0.565
(0.893) 		0.358
(0.811)
SEMA4B 7 (4%) 187 1
(1.00) 		0.891
(1.00) 		0.368
(0.823) 		0.87
(1.00) 		0.0607
(0.48) 		0.287
(0.777) 		0.389
(0.827) 		0.129
(0.643)
ARHGAP4 6 (3%) 188 1
(1.00) 		0.686
(0.952) 		0.852
(1.00) 		0.686
(0.952) 		0.346
(0.804) 		1
(1.00) 		0.509
(0.866) 		0.228
(0.728) 		0.69
(0.952) 		1
(1.00)
POU2F1 3 (2%) 191 0.449
(0.85) 		0.266
(0.77) 		0.614
(0.911) 		0.701
(0.955) 		0.627
(0.92) 		0.488
(0.855) 		0.294
(0.777) 		0.162
(0.691)
IFNGR1 6 (3%) 188 1
(1.00) 		0.742
(0.989) 		0.603
(0.908) 		0.911
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.325
(0.804) 		0.0342
(0.389) 		0.0531
(0.469) 		0.784
(1.00)
IGFN1 11 (6%) 183 0.214
(0.728) 		0.38
(0.825) 		0.685
(0.952) 		0.7
(0.955) 		1
(1.00) 		0.593
(0.908) 		0.354
(0.806) 		0.966
(1.00) 		0.331
(0.804) 		0.849
(1.00)
RPGR 9 (5%) 185 1
(1.00) 		0.923
(1.00) 		0.688
(0.952) 		0.404
(0.827) 		0.393
(0.827) 		0.879
(1.00) 		0.916
(1.00) 		0.952
(1.00) 		0.761
(1.00) 		0.803
(1.00)
CASP8 9 (5%) 185 0.672
(0.952) 		0.477
(0.855) 		0.517
(0.866) 		0.167
(0.691) 		0.219
(0.728) 		0.463
(0.854) 		0.57
(0.893) 		0.448
(0.85) 		0.123
(0.636) 		0.435
(0.85)
GAS6 4 (2%) 190 0.816
(1.00) 		0.11
(0.598) 		0.458
(0.85) 		0.281
(0.777) 		0.767
(1.00) 		0.454
(0.85) 		1
(1.00) 		0.389
(0.827) 		0.292
(0.777) 		0.756
(1.00)
ABCD1 7 (4%) 187 0.605
(0.908) 		0.925
(1.00) 		0.573
(0.893) 		0.592
(0.908) 		0.179
(0.706) 		0.0338
(0.389) 		0.489
(0.855) 		0.52
(0.866) 		0.0573
(0.48) 		0.376
(0.825)
RPAP1 4 (2%) 190 0.683
(0.952) 		0.608
(0.909) 		0.601
(0.908) 		1
(1.00) 		1
(1.00) 		0.742
(0.989) 		1
(1.00) 		0.904
(1.00)
HIST1H4E 4 (2%) 190 0.199
(0.706) 		0.734
(0.988) 		0.397
(0.827) 		0.308
(0.797) 		0.474
(0.854) 		0.831
(1.00) 		0.401
(0.827) 		0.38
(0.825)
NLRC5 7 (4%) 187 0.681
(0.952) 		0.274
(0.777) 		0.203
(0.706) 		0.736
(0.988) 		0.68
(0.952) 		0.196
(0.706) 		0.138
(0.656) 		0.277
(0.777) 		0.566
(0.893) 		0.161
(0.691)
DDX41 5 (3%) 189 0.0291
(0.389) 		0.115
(0.616) 		0.567
(0.893) 		0.402
(0.827) 		0.331
(0.804) 		0.779
(1.00) 		1
(1.00) 		0.546
(0.883)
MCM7 3 (2%) 191 0.0711
(0.498) 		0.616
(0.911) 		0.467
(0.854) 		1
(1.00) 		0.491
(0.855) 		0.0598
(0.48) 		0.163
(0.691)
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
KRAS MUTATED 7 1 3
KRAS WILD-TYPE 83 39 58
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
KRAS MUTATED 9 0 1 0 0 1
KRAS WILD-TYPE 41 32 35 36 7 32

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

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
KRAS MUTATED 3 1 4
KRAS WILD-TYPE 39 30 56
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
KRAS MUTATED 2 2 1 0 3
KRAS WILD-TYPE 25 38 31 18 13
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
KRAS MUTATED 4 0 6 1
KRAS WILD-TYPE 33 65 43 41

Figure S2.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
KRAS MUTATED 8 2 1
KRAS WILD-TYPE 41 118 23

Figure S3.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
KRAS MUTATED 7 4 0
KRAS WILD-TYPE 52 52 79

Figure S4.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.094

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
KRAS MUTATED 8 0 2 1 0
KRAS WILD-TYPE 33 50 56 14 30

Figure S5.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
KRAS MUTATED 6 5 0
KRAS WILD-TYPE 63 52 58

Figure S6.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.072

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
KRAS MUTATED 9 1 0 1
KRAS WILD-TYPE 33 31 28 81

Figure S7.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.76

Table S11.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HLA-A MUTATED 9 4 2
HLA-A WILD-TYPE 81 36 59
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0943 (Fisher's exact test), Q value = 0.56

Table S12.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
HLA-A MUTATED 1 3 5 6 0 1
HLA-A WILD-TYPE 49 29 31 30 7 32
'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.73

Table S13.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
HLA-A MUTATED 5 3 2
HLA-A WILD-TYPE 37 28 58
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.34

Table S14.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
HLA-A MUTATED 5 0 4 1 0
HLA-A WILD-TYPE 22 40 28 17 16

Figure S8.  Get High-res Image Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.096

Table S15.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
HLA-A MUTATED 1 6 0 9
HLA-A WILD-TYPE 36 59 49 33

Figure S9.  Get High-res Image Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.067 (Fisher's exact test), Q value = 0.5

Table S16.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
HLA-A MUTATED 1 11 4
HLA-A WILD-TYPE 48 109 20
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.85

Table S17.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HLA-A MUTATED 3 4 9
HLA-A WILD-TYPE 56 52 70
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00789 (Fisher's exact test), Q value = 0.21

Table S18.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HLA-A MUTATED 0 4 3 3 6
HLA-A WILD-TYPE 41 46 55 12 24

Figure S10.  Get High-res Image Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.95

Table S19.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HLA-A MUTATED 4 4 6
HLA-A WILD-TYPE 65 53 52
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.419 (Fisher's exact test), Q value = 0.85

Table S20.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HLA-A MUTATED 1 2 2 9
HLA-A WILD-TYPE 41 30 26 73
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.86

Table S21.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
FBXW7 MUTATED 11 3 4
FBXW7 WILD-TYPE 79 37 57
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.76

Table S22.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
FBXW7 MUTATED 6 4 4 5 0 0
FBXW7 WILD-TYPE 44 28 32 31 7 33
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
FBXW7 MUTATED 6 4 7
FBXW7 WILD-TYPE 36 27 53
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.971 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
FBXW7 MUTATED 3 5 4 2 3
FBXW7 WILD-TYPE 24 35 28 16 13
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.8

Table S25.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
FBXW7 MUTATED 1 9 5 4
FBXW7 WILD-TYPE 36 56 44 38
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.95

Table S26.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
FBXW7 MUTATED 6 12 1
FBXW7 WILD-TYPE 43 108 23
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 0.83

Table S27.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
FBXW7 MUTATED 6 3 10
FBXW7 WILD-TYPE 53 53 69
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 0.85

Table S28.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
FBXW7 MUTATED 4 8 3 1 3
FBXW7 WILD-TYPE 37 42 55 14 27
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.73

Table S29.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
FBXW7 MUTATED 10 3 6
FBXW7 WILD-TYPE 59 54 52
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.88

Table S30.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
FBXW7 MUTATED 5 1 3 10
FBXW7 WILD-TYPE 37 31 25 72
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 0.87

Table S31.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HLA-B MUTATED 7 2 2
HLA-B WILD-TYPE 83 38 59
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.69

Table S32.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
HLA-B MUTATED 0 4 3 2 0 2
HLA-B WILD-TYPE 50 28 33 34 7 31
'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.95

Table S33.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
HLA-B MUTATED 4 2 3
HLA-B WILD-TYPE 38 29 57
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.327 (Fisher's exact test), Q value = 0.8

Table S34.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
HLA-B MUTATED 3 1 4 1 0
HLA-B WILD-TYPE 24 39 28 17 16
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.74

Table S35.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
HLA-B MUTATED 1 4 1 5
HLA-B WILD-TYPE 36 61 48 37
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0923 (Fisher's exact test), Q value = 0.56

Table S36.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
HLA-B MUTATED 0 10 1
HLA-B WILD-TYPE 49 110 23
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.35

Table S37.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HLA-B MUTATED 1 1 9
HLA-B WILD-TYPE 58 55 70

Figure S11.  Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.65

Table S38.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HLA-B MUTATED 0 5 2 1 3
HLA-B WILD-TYPE 41 45 56 14 27
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.3

Table S39.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HLA-B MUTATED 3 0 7
HLA-B WILD-TYPE 66 57 51

Figure S12.  Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.45

Table S40.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HLA-B MUTATED 0 0 2 8
HLA-B WILD-TYPE 42 32 26 74

Figure S13.  Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
PTEN MUTATED 9 3 3
PTEN WILD-TYPE 81 37 58
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
PTEN MUTATED 5 2 3 1 2 2
PTEN WILD-TYPE 45 30 33 35 5 31
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
PTEN MUTATED 2 2 5
PTEN WILD-TYPE 40 29 55
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
PTEN MUTATED 2 2 4 0 1
PTEN WILD-TYPE 25 38 28 18 15
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
PTEN MUTATED 5 8 2 0
PTEN WILD-TYPE 32 57 47 42

Figure S14.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
PTEN MUTATED 6 9 0
PTEN WILD-TYPE 43 111 24
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
PTEN MUTATED 7 3 5
PTEN WILD-TYPE 52 53 74
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
PTEN MUTATED 4 6 3 2 0
PTEN WILD-TYPE 37 44 55 13 30
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
PTEN MUTATED 6 4 5
PTEN WILD-TYPE 63 53 53
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
PTEN MUTATED 4 4 3 4
PTEN WILD-TYPE 38 28 25 78
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00691 (Fisher's exact test), Q value = 0.2

Table S51.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ARID1A MUTATED 11 3 0
ARID1A WILD-TYPE 79 37 61

Figure S15.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.14

Table S52.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
ARID1A MUTATED 10 2 2 0 0 0
ARID1A WILD-TYPE 40 30 34 36 7 33

Figure S16.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
ARID1A MUTATED 3 3 5
ARID1A WILD-TYPE 39 28 55
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.64

Table S54.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
ARID1A MUTATED 2 2 3 0 4
ARID1A WILD-TYPE 25 38 29 18 12
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.69

Table S55.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
ARID1A MUTATED 5 2 5 2
ARID1A WILD-TYPE 32 63 44 40
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.094

Table S56.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
ARID1A MUTATED 10 4 0
ARID1A WILD-TYPE 39 116 24

Figure S17.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.58

Table S57.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ARID1A MUTATED 8 2 4
ARID1A WILD-TYPE 51 54 75
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.14

Table S58.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ARID1A MUTATED 7 1 1 3 2
ARID1A WILD-TYPE 34 49 57 12 28

Figure S18.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 0.96

Table S59.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ARID1A MUTATED 6 3 3
ARID1A WILD-TYPE 63 54 55
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00457 (Fisher's exact test), Q value = 0.14

Table S60.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ARID1A MUTATED 7 0 3 2
ARID1A WILD-TYPE 35 32 25 80

Figure S19.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 0.89

Table S61.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
MAPK1 MUTATED 6 1 2
MAPK1 WILD-TYPE 84 39 59
'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.73

Table S62.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
MAPK1 MUTATED 0 2 3 1 0 3
MAPK1 WILD-TYPE 50 30 33 35 7 30
'MAPK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.8

Table S63.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
MAPK1 MUTATED 3 0 4
MAPK1 WILD-TYPE 39 31 56
'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.975 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
MAPK1 MUTATED 2 2 1 1 1
MAPK1 WILD-TYPE 25 38 31 17 15
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0904 (Fisher's exact test), Q value = 0.55

Table S65.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
MAPK1 MUTATED 2 6 0 1
MAPK1 WILD-TYPE 35 59 49 41
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.055 (Fisher's exact test), Q value = 0.47

Table S66.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
MAPK1 MUTATED 0 9 0
MAPK1 WILD-TYPE 49 111 24
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.71

Table S67.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MAPK1 MUTATED 1 5 3
MAPK1 WILD-TYPE 58 51 76
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0826 (Fisher's exact test), Q value = 0.54

Table S68.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MAPK1 MUTATED 0 2 6 1 0
MAPK1 WILD-TYPE 41 48 52 14 30
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.36

Table S69.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MAPK1 MUTATED 0 5 4
MAPK1 WILD-TYPE 69 52 54

Figure S20.  Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.37

Table S70.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MAPK1 MUTATED 0 5 1 3
MAPK1 WILD-TYPE 42 27 27 79

Figure S21.  Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'CN_CNMF'

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

Table S71.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
EP300 MUTATED 10 4 6
EP300 WILD-TYPE 80 36 55
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.39

Table S72.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
EP300 MUTATED 2 7 5 1 2 4
EP300 WILD-TYPE 48 25 31 35 5 29

Figure S22.  Get High-res Image Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.75

Table S73.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
EP300 MUTATED 2 4 9
EP300 WILD-TYPE 40 27 51
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.39

Table S74.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
EP300 MUTATED 2 5 8 0 0
EP300 WILD-TYPE 25 35 24 18 16

Figure S23.  Get High-res Image Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.65

Table S75.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
EP300 MUTATED 6 10 2 3
EP300 WILD-TYPE 31 55 47 39
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0722 (Fisher's exact test), Q value = 0.5

Table S76.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
EP300 MUTATED 2 18 1
EP300 WILD-TYPE 47 102 23
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
EP300 MUTATED 6 5 10
EP300 WILD-TYPE 53 51 69
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00965 (Fisher's exact test), Q value = 0.24

Table S78.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
EP300 MUTATED 1 9 10 1 0
EP300 WILD-TYPE 40 41 48 14 30

Figure S24.  Get High-res Image Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S79.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
EP300 MUTATED 7 5 6
EP300 WILD-TYPE 62 52 52
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 0.75

Table S80.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
EP300 MUTATED 2 3 1 12
EP300 WILD-TYPE 40 29 27 70
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.39

Table S81.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
PIK3CA MUTATED 33 7 13
PIK3CA WILD-TYPE 57 33 48

Figure S25.  Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.78

Table S82.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
PIK3CA MUTATED 18 8 11 5 1 10
PIK3CA WILD-TYPE 32 24 25 31 6 23
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 0.85

Table S83.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
PIK3CA MUTATED 12 5 12
PIK3CA WILD-TYPE 30 26 48
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.78

Table S84.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
PIK3CA MUTATED 9 8 4 3 5
PIK3CA WILD-TYPE 18 32 28 15 11
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.81

Table S85.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
PIK3CA MUTATED 10 19 16 7
PIK3CA WILD-TYPE 27 46 33 35
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00392 (Fisher's exact test), Q value = 0.14

Table S86.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
PIK3CA MUTATED 19 32 1
PIK3CA WILD-TYPE 30 88 23

Figure S26.  Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.8

Table S87.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
PIK3CA MUTATED 20 12 21
PIK3CA WILD-TYPE 39 44 58
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 0.8

Table S88.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
PIK3CA MUTATED 14 17 13 4 5
PIK3CA WILD-TYPE 27 33 45 11 25
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.86

Table S89.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
PIK3CA MUTATED 22 13 14
PIK3CA WILD-TYPE 47 44 44
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.74

Table S90.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
PIK3CA MUTATED 16 9 7 17
PIK3CA WILD-TYPE 26 23 21 65
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
NFE2L2 MUTATED 5 3 4
NFE2L2 WILD-TYPE 85 37 57
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0979 (Fisher's exact test), Q value = 0.57

Table S92.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
NFE2L2 MUTATED 0 4 2 2 0 4
NFE2L2 WILD-TYPE 50 28 34 34 7 29
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.78

Table S93.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
NFE2L2 MUTATED 4 3 2
NFE2L2 WILD-TYPE 38 28 58
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0501 (Fisher's exact test), Q value = 0.46

Table S94.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
NFE2L2 MUTATED 1 0 4 3 1
NFE2L2 WILD-TYPE 26 40 28 15 15
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.85

Table S95.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
NFE2L2 MUTATED 2 5 1 4
NFE2L2 WILD-TYPE 35 60 48 38
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.45

Table S96.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
NFE2L2 MUTATED 0 11 1
NFE2L2 WILD-TYPE 49 109 23

Figure S27.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.39

Table S97.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
NFE2L2 MUTATED 0 5 7
NFE2L2 WILD-TYPE 59 51 72

Figure S28.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.34

Table S98.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
NFE2L2 MUTATED 0 1 6 3 2
NFE2L2 WILD-TYPE 41 49 52 12 28

Figure S29.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.83

Table S99.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
NFE2L2 MUTATED 2 4 5
NFE2L2 WILD-TYPE 67 53 53
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0734 (Fisher's exact test), Q value = 0.5

Table S100.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
NFE2L2 MUTATED 0 2 4 5
NFE2L2 WILD-TYPE 42 30 24 77
'FAT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.613 (Fisher's exact test), Q value = 0.91

Table S101.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
FAT2 MUTATED 6 3 2
FAT2 WILD-TYPE 84 37 59
'FAT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0516 (Fisher's exact test), Q value = 0.47

Table S102.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
FAT2 MUTATED 1 5 2 2 1 0
FAT2 WILD-TYPE 49 27 34 34 6 33
'FAT2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S103.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
FAT2 MUTATED 3 2 3
FAT2 WILD-TYPE 39 29 57
'FAT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 0.92

Table S104.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
FAT2 MUTATED 1 2 3 2 0
FAT2 WILD-TYPE 26 38 29 16 16
'FAT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0646 (Fisher's exact test), Q value = 0.5

Table S105.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
FAT2 MUTATED 0 5 1 5
FAT2 WILD-TYPE 37 60 48 37
'FAT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.86

Table S106.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
FAT2 MUTATED 1 9 1
FAT2 WILD-TYPE 48 111 23
'FAT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 0.9

Table S107.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
FAT2 MUTATED 2 3 6
FAT2 WILD-TYPE 57 53 73
'FAT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S108.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
FAT2 MUTATED 1 4 4 0 2
FAT2 WILD-TYPE 40 46 54 15 28
'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0704 (Fisher's exact test), Q value = 0.5

Table S109.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
FAT2 MUTATED 3 1 7
FAT2 WILD-TYPE 66 56 51
'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0895 (Fisher's exact test), Q value = 0.55

Table S110.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
FAT2 MUTATED 1 0 1 9
FAT2 WILD-TYPE 41 32 27 73
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0854 (Fisher's exact test), Q value = 0.55

Table S111.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ZNF750 MUTATED 8 0 2
ZNF750 WILD-TYPE 82 40 59
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.82

Table S112.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
ZNF750 MUTATED 1 3 4 1 0 1
ZNF750 WILD-TYPE 49 29 32 35 7 32
'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S113.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
ZNF750 MUTATED 3 2 3
ZNF750 WILD-TYPE 39 29 57
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.69

Table S114.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
ZNF750 MUTATED 4 1 3 0 0
ZNF750 WILD-TYPE 23 39 29 18 16
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.87

Table S115.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
ZNF750 MUTATED 1 5 1 3
ZNF750 WILD-TYPE 36 60 48 39
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.78

Table S116.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
ZNF750 MUTATED 1 9 0
ZNF750 WILD-TYPE 48 111 24
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.71

Table S117.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ZNF750 MUTATED 2 1 7
ZNF750 WILD-TYPE 57 55 72
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.71

Table S118.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ZNF750 MUTATED 0 5 2 1 2
ZNF750 WILD-TYPE 41 45 56 14 28
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.85

Table S119.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ZNF750 MUTATED 4 1 4
ZNF750 WILD-TYPE 65 56 54
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0726 (Fisher's exact test), Q value = 0.5

Table S120.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ZNF750 MUTATED 0 0 2 7
ZNF750 WILD-TYPE 42 32 26 75
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.66

Table S121.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
BAP1 MUTATED 4 0 0
BAP1 WILD-TYPE 86 40 61
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0583 (Fisher's exact test), Q value = 0.48

Table S122.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
BAP1 MUTATED 0 3 1 0 0 0
BAP1 WILD-TYPE 50 29 35 36 7 33
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.87

Table S123.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
BAP1 MUTATED 0 3 1 0
BAP1 WILD-TYPE 37 62 48 42
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.85

Table S124.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
BAP1 MUTATED 0 4 0
BAP1 WILD-TYPE 49 116 24
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 0.95

Table S125.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
BAP1 MUTATED 1 2 1
BAP1 WILD-TYPE 58 54 78
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.353 (Fisher's exact test), Q value = 0.81

Table S126.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
BAP1 MUTATED 0 2 1 1 0
BAP1 WILD-TYPE 41 48 57 14 30
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.76

Table S127.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
BAP1 MUTATED 0 2 2
BAP1 WILD-TYPE 69 55 56
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.7

Table S128.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
BAP1 MUTATED 0 2 1 1
BAP1 WILD-TYPE 42 30 27 81
'RAB35 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.76

Table S129.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
RAB35 MUTATED 1 0 3
RAB35 WILD-TYPE 89 40 58
'RAB35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.85

Table S130.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
RAB35 MUTATED 0 0 2 1 0 1
RAB35 WILD-TYPE 50 32 34 35 7 32
'RAB35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
RAB35 MUTATED 1 2 0 1
RAB35 WILD-TYPE 36 63 49 41
'RAB35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.85

Table S132.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
RAB35 MUTATED 0 4 0
RAB35 WILD-TYPE 49 116 24
'RAB35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.85

Table S133.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
RAB35 MUTATED 0 2 2
RAB35 WILD-TYPE 59 54 77
'RAB35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.59

Table S134.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
RAB35 MUTATED 0 0 3 1 0
RAB35 WILD-TYPE 41 50 55 14 30
'RAB35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.78

Table S135.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
RAB35 MUTATED 0 1 2
RAB35 WILD-TYPE 69 56 56
'RAB35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.39

Table S136.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
RAB35 MUTATED 0 1 2 0
RAB35 WILD-TYPE 42 31 26 82

Figure S30.  Get High-res Image Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0726 (Fisher's exact test), Q value = 0.5

Table S137.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ERBB3 MUTATED 5 5 1
ERBB3 WILD-TYPE 85 35 60
'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.64

Table S138.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
ERBB3 MUTATED 7 2 1 1 0 0
ERBB3 WILD-TYPE 43 30 35 35 7 33
'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S139.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
ERBB3 MUTATED 4 2 4
ERBB3 WILD-TYPE 38 29 56
'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
ERBB3 MUTATED 2 2 2 2 2
ERBB3 WILD-TYPE 25 38 30 16 14
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.39

Table S141.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
ERBB3 MUTATED 1 1 7 2
ERBB3 WILD-TYPE 36 64 42 40

Figure S31.  Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.24

Table S142.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
ERBB3 MUTATED 7 3 1
ERBB3 WILD-TYPE 42 117 23

Figure S32.  Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0784 (Fisher's exact test), Q value = 0.52

Table S143.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ERBB3 MUTATED 5 5 1
ERBB3 WILD-TYPE 54 51 78
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.39

Table S144.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ERBB3 MUTATED 7 2 1 0 1
ERBB3 WILD-TYPE 34 48 57 15 29

Figure S33.  Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S145.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ERBB3 MUTATED 4 4 3
ERBB3 WILD-TYPE 65 53 55
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.8

Table S146.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ERBB3 MUTATED 5 2 1 3
ERBB3 WILD-TYPE 37 30 27 79
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 0.86

Table S147.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
SMAD4 MUTATED 4 0 2
SMAD4 WILD-TYPE 86 40 59
'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.8

Table S148.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
SMAD4 MUTATED 2 0 3 0 0 2
SMAD4 WILD-TYPE 48 32 33 36 7 31
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.89

Table S149.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
SMAD4 MUTATED 3 1 2
SMAD4 WILD-TYPE 39 30 58
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S150.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
SMAD4 MUTATED 2 2 1 1 0
SMAD4 WILD-TYPE 25 38 31 17 16
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.87

Table S151.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
SMAD4 MUTATED 0 2 3 2
SMAD4 WILD-TYPE 37 63 46 40
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
SMAD4 MUTATED 2 4 1
SMAD4 WILD-TYPE 47 116 23
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 0.98

Table S153.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
SMAD4 MUTATED 2 1 4
SMAD4 WILD-TYPE 57 55 75
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 0.91

Table S154.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
SMAD4 MUTATED 1 3 1 0 2
SMAD4 WILD-TYPE 40 47 57 15 28
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S155.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
SMAD4 MUTATED 3 2 2
SMAD4 WILD-TYPE 66 55 56
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S156.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
SMAD4 MUTATED 1 1 1 4
SMAD4 WILD-TYPE 41 31 27 78
'TCTE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.71

Table S157.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
TCTE1 MUTATED 3 2 0
TCTE1 WILD-TYPE 87 38 61
'TCTE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.8

Table S158.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
TCTE1 MUTATED 0 2 1 2 0 0
TCTE1 WILD-TYPE 50 30 35 34 7 33
'TCTE1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.8

Table S159.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
TCTE1 MUTATED 3 0 2
TCTE1 WILD-TYPE 39 31 58
'TCTE1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.43

Table S160.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
TCTE1 MUTATED 1 0 1 3 0
TCTE1 WILD-TYPE 26 40 31 15 16

Figure S34.  Get High-res Image Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TCTE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.34

Table S161.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
TCTE1 MUTATED 0 1 0 4
TCTE1 WILD-TYPE 37 64 49 38

Figure S35.  Get High-res Image Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TCTE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.83

Table S162.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
TCTE1 MUTATED 0 4 1
TCTE1 WILD-TYPE 49 116 23
'TCTE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.39

Table S163.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
TCTE1 MUTATED 0 0 5
TCTE1 WILD-TYPE 59 56 74

Figure S36.  Get High-res Image Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TCTE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.58

Table S164.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
TCTE1 MUTATED 0 1 1 2 1
TCTE1 WILD-TYPE 41 49 57 13 29
'TCTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.71

Table S165.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
TCTE1 MUTATED 1 0 3
TCTE1 WILD-TYPE 68 57 55
'TCTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 0.8

Table S166.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
TCTE1 MUTATED 0 0 0 4
TCTE1 WILD-TYPE 42 32 28 78
'NHS MUTATION STATUS' versus 'CN_CNMF'

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

Table S167.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
NHS MUTATED 6 3 3
NHS WILD-TYPE 84 37 58
'NHS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S168.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
NHS MUTATED 3 3 2 2 0 2
NHS WILD-TYPE 47 29 34 34 7 31
'NHS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.94

Table S169.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
NHS MUTATED 4 1 5
NHS WILD-TYPE 38 30 55
'NHS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S170.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
NHS MUTATED 2 2 3 2 1
NHS WILD-TYPE 25 38 29 16 15
'NHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
NHS MUTATED 2 4 2 4
NHS WILD-TYPE 35 61 47 38
'NHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.78

Table S172.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
NHS MUTATED 3 6 3
NHS WILD-TYPE 46 114 21
'NHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S173.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
NHS MUTATED 3 4 5
NHS WILD-TYPE 56 52 74
'NHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
NHS MUTATED 3 3 3 0 3
NHS WILD-TYPE 38 47 55 15 27
'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.85

Table S175.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
NHS MUTATED 6 3 2
NHS WILD-TYPE 63 54 56
'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 0.85

Table S176.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
NHS MUTATED 3 1 0 7
NHS WILD-TYPE 39 31 28 75
'LIN9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.69

Table S177.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
LIN9 MUTATED 1 1 4
LIN9 WILD-TYPE 89 39 57
'LIN9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.82

Table S178.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
LIN9 MUTATED 1 2 1 0 0 3
LIN9 WILD-TYPE 49 30 35 36 7 30
'LIN9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 0.95

Table S179.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
LIN9 MUTATED 1 2 4
LIN9 WILD-TYPE 41 29 56
'LIN9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.82

Table S180.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
LIN9 MUTATED 0 3 1 1 2
LIN9 WILD-TYPE 27 37 31 17 14
'LIN9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 0.88

Table S181.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
LIN9 MUTATED 3 2 1 1
LIN9 WILD-TYPE 34 63 48 41
'LIN9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S182.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
LIN9 MUTATED 1 5 1
LIN9 WILD-TYPE 48 115 23
'LIN9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S183.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
LIN9 MUTATED 3 2 2
LIN9 WILD-TYPE 56 54 77
'LIN9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 0.78

Table S184.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
LIN9 MUTATED 0 2 4 1 0
LIN9 WILD-TYPE 41 48 54 14 30
'LIN9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.78

Table S185.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
LIN9 MUTATED 1 2 4
LIN9 WILD-TYPE 68 55 54
'LIN9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S186.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
LIN9 MUTATED 1 2 1 3
LIN9 WILD-TYPE 41 30 27 79
'C12ORF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.71

Table S187.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
C12ORF43 MUTATED 2 2 0
C12ORF43 WILD-TYPE 88 38 61
'C12ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.67

Table S188.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
C12ORF43 MUTATED 0 1 1 1 1 0
C12ORF43 WILD-TYPE 50 31 35 35 6 33
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S189.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
C12ORF43 MUTATED 0 2 1 1
C12ORF43 WILD-TYPE 37 63 48 41
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.85

Table S190.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
C12ORF43 MUTATED 0 4 0
C12ORF43 WILD-TYPE 49 116 24
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.85

Table S191.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
C12ORF43 MUTATED 0 2 2
C12ORF43 WILD-TYPE 59 54 77
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.71

Table S192.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
C12ORF43 MUTATED 0 0 2 1 1
C12ORF43 WILD-TYPE 41 50 56 14 29
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.78

Table S193.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
C12ORF43 MUTATED 0 1 2
C12ORF43 WILD-TYPE 69 56 56
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.69

Table S194.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
C12ORF43 MUTATED 0 0 2 1
C12ORF43 WILD-TYPE 42 32 26 81
'MED1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S195.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
MED1 MUTATED 6 2 3
MED1 WILD-TYPE 84 38 58
'MED1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.65

Table S196.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
MED1 MUTATED 0 1 3 3 0 4
MED1 WILD-TYPE 50 31 33 33 7 29
'MED1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.69

Table S197.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
MED1 MUTATED 6 1 3
MED1 WILD-TYPE 36 30 57
'MED1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 0.69

Table S198.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
MED1 MUTATED 4 2 1 3 0
MED1 WILD-TYPE 23 38 31 15 16
'MED1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.74

Table S199.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
MED1 MUTATED 1 4 1 5
MED1 WILD-TYPE 36 61 48 37
'MED1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.58

Table S200.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
MED1 MUTATED 0 9 2
MED1 WILD-TYPE 49 111 22
'MED1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.71

Table S201.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MED1 MUTATED 1 3 7
MED1 WILD-TYPE 58 53 72
'MED1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.74

Table S202.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MED1 MUTATED 0 4 4 0 3
MED1 WILD-TYPE 41 46 54 15 27
'MED1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.87

Table S203.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MED1 MUTATED 3 2 5
MED1 WILD-TYPE 66 55 53
'MED1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.64

Table S204.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MED1 MUTATED 0 1 3 6
MED1 WILD-TYPE 42 31 25 76
'USP28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.71

Table S205.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
USP28 MUTATED 2 2 0
USP28 WILD-TYPE 88 38 61
'USP28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.88

Table S206.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
USP28 MUTATED 1 2 1 0 0 0
USP28 WILD-TYPE 49 30 35 36 7 33
'USP28 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.8

Table S207.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
USP28 MUTATED 0 0 3
USP28 WILD-TYPE 42 31 57
'USP28 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S208.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
USP28 MUTATED 0 2 1 0 0
USP28 WILD-TYPE 27 38 31 18 16
'USP28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 0.91

Table S209.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
USP28 MUTATED 0 1 1 2
USP28 WILD-TYPE 37 64 48 40
'USP28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S210.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
USP28 MUTATED 1 3 0
USP28 WILD-TYPE 48 117 24
'USP28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.83

Table S211.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 58 56 76
'USP28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S212.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
USP28 MUTATED 1 1 2 0 0
USP28 WILD-TYPE 40 49 56 15 30
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.71

Table S213.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 68 57 55
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S214.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
USP28 MUTATED 1 0 0 3
USP28 WILD-TYPE 41 32 28 79
'IDS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.71

Table S215.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
IDS MUTATED 4 2 0
IDS WILD-TYPE 86 38 61
'IDS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 0.88

Table S216.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
IDS MUTATED 2 3 1 0 0 1
IDS WILD-TYPE 48 29 35 36 7 32
'IDS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.75

Table S217.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
IDS MUTATED 0 2 3
IDS WILD-TYPE 42 29 57
'IDS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 0.88

Table S218.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
IDS MUTATED 0 3 1 0 1
IDS WILD-TYPE 27 37 31 18 15
'IDS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S219.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
IDS MUTATED 1 3 2 1
IDS WILD-TYPE 36 62 47 41
'IDS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S220.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
IDS MUTATED 2 5 0
IDS WILD-TYPE 47 115 24
'IDS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 0.86

Table S221.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
IDS MUTATED 1 3 3
IDS WILD-TYPE 58 53 76
'IDS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.73

Table S222.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
IDS MUTATED 1 1 3 2 0
IDS WILD-TYPE 40 49 55 13 30
'IDS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.85

Table S223.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
IDS MUTATED 1 3 3
IDS WILD-TYPE 68 54 55
'IDS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 0.97

Table S224.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
IDS MUTATED 2 2 0 3
IDS WILD-TYPE 40 30 28 79
'TRIM9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.8

Table S225.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
TRIM9 MUTATED 6 1 1
TRIM9 WILD-TYPE 84 39 60
'TRIM9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S226.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
TRIM9 MUTATED 3 2 1 2 0 0
TRIM9 WILD-TYPE 47 30 35 34 7 33
'TRIM9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 0.95

Table S227.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
TRIM9 MUTATED 1 2 4
TRIM9 WILD-TYPE 41 29 56
'TRIM9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S228.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
TRIM9 MUTATED 1 3 2 0 1
TRIM9 WILD-TYPE 26 37 30 18 15
'TRIM9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0904 (Fisher's exact test), Q value = 0.55

Table S229.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
TRIM9 MUTATED 0 1 3 4
TRIM9 WILD-TYPE 37 64 46 38
'TRIM9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 0.95

Table S230.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
TRIM9 MUTATED 3 4 1
TRIM9 WILD-TYPE 46 116 23
'TRIM9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 0.88

Table S231.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
TRIM9 MUTATED 2 1 5
TRIM9 WILD-TYPE 57 55 74
'TRIM9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.39

Table S232.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
TRIM9 MUTATED 3 1 0 2 2
TRIM9 WILD-TYPE 38 49 58 13 28

Figure S37.  Get High-res Image Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TRIM9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.89

Table S233.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
TRIM9 MUTATED 4 1 2
TRIM9 WILD-TYPE 65 56 56
'TRIM9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 0.81

Table S234.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
TRIM9 MUTATED 3 0 0 4
TRIM9 WILD-TYPE 39 32 28 78
'SEMA4B MUTATION STATUS' versus 'CN_CNMF'

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

Table S235.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
SEMA4B MUTATED 4 1 2
SEMA4B WILD-TYPE 86 39 59
'SEMA4B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S236.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
SEMA4B MUTATED 1 2 1 2 0 1
SEMA4B WILD-TYPE 49 30 35 34 7 32
'SEMA4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.82

Table S237.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
SEMA4B MUTATED 0 3 1 3
SEMA4B WILD-TYPE 37 62 48 39
'SEMA4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S238.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
SEMA4B MUTATED 1 5 1
SEMA4B WILD-TYPE 48 115 23
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0607 (Fisher's exact test), Q value = 0.48

Table S239.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
SEMA4B MUTATED 1 0 6
SEMA4B WILD-TYPE 58 56 73
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.78

Table S240.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
SEMA4B MUTATED 0 2 2 0 3
SEMA4B WILD-TYPE 41 48 56 15 27
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.83

Table S241.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
SEMA4B MUTATED 2 1 4
SEMA4B WILD-TYPE 67 56 54
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 0.64

Table S242.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
SEMA4B MUTATED 0 0 1 6
SEMA4B WILD-TYPE 42 32 27 76
'ARHGAP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S243.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ARHGAP4 MUTATED 3 1 2
ARHGAP4 WILD-TYPE 87 39 59
'ARHGAP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.95

Table S244.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
ARHGAP4 MUTATED 1 2 1 2 0 0
ARHGAP4 WILD-TYPE 49 30 35 34 7 33
'ARHGAP4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S245.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
ARHGAP4 MUTATED 1 1 3
ARHGAP4 WILD-TYPE 41 30 57
'ARHGAP4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 0.95

Table S246.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
ARHGAP4 MUTATED 2 1 2 0 0
ARHGAP4 WILD-TYPE 25 39 30 18 16
'ARHGAP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.8

Table S247.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
ARHGAP4 MUTATED 0 2 1 3
ARHGAP4 WILD-TYPE 37 63 48 39
'ARHGAP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S248.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
ARHGAP4 MUTATED 1 4 1
ARHGAP4 WILD-TYPE 48 116 23
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.87

Table S249.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ARHGAP4 MUTATED 1 1 4
ARHGAP4 WILD-TYPE 58 55 75
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.73

Table S250.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ARHGAP4 MUTATED 1 1 2 2 0
ARHGAP4 WILD-TYPE 40 49 56 13 30
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 0.95

Table S251.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ARHGAP4 MUTATED 1 2 1
ARHGAP4 WILD-TYPE 68 55 57
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S252.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ARHGAP4 MUTATED 1 1 0 2
ARHGAP4 WILD-TYPE 41 31 28 80
'POU2F1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.85

Table S253.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
POU2F1 MUTATED 2 1 0
POU2F1 WILD-TYPE 88 39 61
'POU2F1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.77

Table S254.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
POU2F1 MUTATED 0 1 2 0 0 0
POU2F1 WILD-TYPE 50 31 34 36 7 33
'POU2F1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 0.91

Table S255.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
POU2F1 MUTATED 0 2 0 1
POU2F1 WILD-TYPE 37 63 49 41
'POU2F1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.701 (Fisher's exact test), Q value = 0.96

Table S256.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
POU2F1 MUTATED 0 3 0
POU2F1 WILD-TYPE 49 117 24
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 0.92

Table S257.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
POU2F1 MUTATED 0 1 2
POU2F1 WILD-TYPE 59 55 77
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 0.86

Table S258.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
POU2F1 MUTATED 0 0 2 0 1
POU2F1 WILD-TYPE 41 50 56 15 29
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 0.78

Table S259.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
POU2F1 MUTATED 0 1 2
POU2F1 WILD-TYPE 69 56 56
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.69

Table S260.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
POU2F1 MUTATED 0 0 2 1
POU2F1 WILD-TYPE 42 32 26 81
'IFNGR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S261.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
IFNGR1 MUTATED 3 1 2
IFNGR1 WILD-TYPE 87 39 59
'IFNGR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 0.99

Table S262.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
IFNGR1 MUTATED 2 2 0 1 0 1
IFNGR1 WILD-TYPE 48 30 36 35 7 32
'IFNGR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.91

Table S263.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
IFNGR1 MUTATED 0 1 2
IFNGR1 WILD-TYPE 42 30 58
'IFNGR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S264.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
IFNGR1 MUTATED 0 2 1 0 0
IFNGR1 WILD-TYPE 27 38 31 18 16
'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S265.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
IFNGR1 MUTATED 2 2 1 1
IFNGR1 WILD-TYPE 35 63 48 41
'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S266.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
IFNGR1 MUTATED 2 4 0
IFNGR1 WILD-TYPE 47 116 24
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.8

Table S267.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
IFNGR1 MUTATED 3 0 3
IFNGR1 WILD-TYPE 56 56 76
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.39

Table S268.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
IFNGR1 MUTATED 1 3 0 2 0
IFNGR1 WILD-TYPE 40 47 58 13 30

Figure S38.  Get High-res Image Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0531 (Fisher's exact test), Q value = 0.47

Table S269.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
IFNGR1 MUTATED 5 0 1
IFNGR1 WILD-TYPE 64 57 57
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S270.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
IFNGR1 MUTATED 2 0 1 3
IFNGR1 WILD-TYPE 40 32 27 79
'IGFN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.73

Table S271.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
IGFN1 MUTATED 7 0 4
IGFN1 WILD-TYPE 83 40 57
'IGFN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.82

Table S272.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
IGFN1 MUTATED 2 4 2 1 1 1
IGFN1 WILD-TYPE 48 28 34 35 6 32
'IGFN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.95

Table S273.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
IGFN1 MUTATED 1 2 4
IGFN1 WILD-TYPE 41 29 56
'IGFN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.7 (Fisher's exact test), Q value = 0.96

Table S274.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
IGFN1 MUTATED 2 2 3 0 0
IGFN1 WILD-TYPE 25 38 29 18 16
'IGFN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S275.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
IGFN1 MUTATED 2 4 3 2
IGFN1 WILD-TYPE 35 61 46 40
'IGFN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.91

Table S276.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
IGFN1 MUTATED 3 8 0
IGFN1 WILD-TYPE 46 112 24
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.81

Table S277.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
IGFN1 MUTATED 4 1 6
IGFN1 WILD-TYPE 55 55 73
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S278.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
IGFN1 MUTATED 3 3 3 1 1
IGFN1 WILD-TYPE 38 47 55 14 29
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.8

Table S279.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
IGFN1 MUTATED 5 1 4
IGFN1 WILD-TYPE 64 56 54
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S280.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
IGFN1 MUTATED 2 1 1 6
IGFN1 WILD-TYPE 40 31 27 76
'RPGR MUTATION STATUS' versus 'CN_CNMF'

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

Table S281.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
RPGR MUTATED 4 2 3
RPGR WILD-TYPE 86 38 58
'RPGR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S282.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
RPGR MUTATED 3 2 1 1 0 2
RPGR WILD-TYPE 47 30 35 35 7 31
'RPGR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.95

Table S283.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
RPGR MUTATED 1 2 4
RPGR WILD-TYPE 41 29 56
'RPGR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.83

Table S284.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
RPGR MUTATED 0 3 1 2 1
RPGR WILD-TYPE 27 37 31 16 15
'RPGR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.83

Table S285.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
RPGR MUTATED 0 3 4 2
RPGR WILD-TYPE 37 62 45 40
'RPGR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S286.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
RPGR MUTATED 3 5 1
RPGR WILD-TYPE 46 115 23
'RPGR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S287.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
RPGR MUTATED 3 3 3
RPGR WILD-TYPE 56 53 76
'RPGR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.952 (Fisher's exact test), Q value = 1

Table S288.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
RPGR MUTATED 2 2 4 0 1
RPGR WILD-TYPE 39 48 54 15 29
'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S289.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
RPGR MUTATED 3 2 4
RPGR WILD-TYPE 66 55 54
'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S290.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
RPGR MUTATED 3 2 1 3
RPGR WILD-TYPE 39 30 27 79
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 0.95

Table S291.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
CASP8 MUTATED 3 2 4
CASP8 WILD-TYPE 87 38 57
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 0.85

Table S292.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
CASP8 MUTATED 1 1 3 2 1 1
CASP8 WILD-TYPE 49 31 33 34 6 32
'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.87

Table S293.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
CASP8 MUTATED 2 2 1
CASP8 WILD-TYPE 40 29 59
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.69

Table S294.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
CASP8 MUTATED 1 0 2 2 0
CASP8 WILD-TYPE 26 40 30 16 16
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.73

Table S295.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
CASP8 MUTATED 0 5 1 3
CASP8 WILD-TYPE 37 60 48 39
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 0.85

Table S296.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
CASP8 MUTATED 1 6 2
CASP8 WILD-TYPE 48 114 22
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.89

Table S297.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
CASP8 MUTATED 3 1 5
CASP8 WILD-TYPE 56 55 74
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 0.85

Table S298.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
CASP8 MUTATED 0 3 3 1 2
CASP8 WILD-TYPE 41 47 55 14 28
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.64

Table S299.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
CASP8 MUTATED 4 0 4
CASP8 WILD-TYPE 65 57 54
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 0.85

Table S300.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
CASP8 MUTATED 1 0 1 6
CASP8 WILD-TYPE 41 32 27 76
'GAS6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 1

Table S301.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
GAS6 MUTATED 2 0 2
GAS6 WILD-TYPE 88 40 59
'GAS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.6

Table S302.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
GAS6 MUTATED 0 0 3 1 0 0
GAS6 WILD-TYPE 50 32 33 35 7 33
'GAS6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.85

Table S303.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
GAS6 MUTATED 2 0 1
GAS6 WILD-TYPE 40 31 59
'GAS6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.78

Table S304.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
GAS6 MUTATED 2 0 1 0 0
GAS6 WILD-TYPE 25 40 31 18 16
'GAS6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S305.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
GAS6 MUTATED 1 2 0 1
GAS6 WILD-TYPE 36 63 49 41
'GAS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.85

Table S306.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
GAS6 MUTATED 0 4 0
GAS6 WILD-TYPE 49 116 24
'GAS6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S307.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
GAS6 MUTATED 1 1 2
GAS6 WILD-TYPE 58 55 77
'GAS6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.83

Table S308.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
GAS6 MUTATED 0 3 1 0 0
GAS6 WILD-TYPE 41 47 57 15 30
'GAS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.78

Table S309.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
GAS6 MUTATED 0 1 2
GAS6 WILD-TYPE 69 56 56
'GAS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S310.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
GAS6 MUTATED 0 1 0 2
GAS6 WILD-TYPE 42 31 28 80
'ABCD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 0.91

Table S311.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ABCD1 MUTATED 2 2 1
ABCD1 WILD-TYPE 88 38 60
'ABCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S312.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
ABCD1 MUTATED 1 1 2 2 0 1
ABCD1 WILD-TYPE 49 31 34 34 7 32
'ABCD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.89

Table S313.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
ABCD1 MUTATED 3 1 2
ABCD1 WILD-TYPE 39 30 58
'ABCD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.91

Table S314.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
ABCD1 MUTATED 1 1 2 2 0
ABCD1 WILD-TYPE 26 39 30 16 16
'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.71

Table S315.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
ABCD1 MUTATED 1 1 1 4
ABCD1 WILD-TYPE 36 64 48 38
'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.39

Table S316.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
ABCD1 MUTATED 0 4 3
ABCD1 WILD-TYPE 49 116 21

Figure S39.  Get High-res Image Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 0.86

Table S317.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ABCD1 MUTATED 1 3 3
ABCD1 WILD-TYPE 58 53 76
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 0.87

Table S318.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ABCD1 MUTATED 0 2 3 0 2
ABCD1 WILD-TYPE 41 48 55 15 28
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.48

Table S319.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ABCD1 MUTATED 0 4 3
ABCD1 WILD-TYPE 69 53 55
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 0.82

Table S320.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ABCD1 MUTATED 0 1 2 4
ABCD1 WILD-TYPE 42 31 26 78
'RPAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.95

Table S321.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
RPAP1 MUTATED 3 0 1
RPAP1 WILD-TYPE 87 40 60
'RPAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 0.91

Table S322.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
RPAP1 MUTATED 1 1 2 0 0 0
RPAP1 WILD-TYPE 49 31 34 36 7 33
'RPAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 0.91

Table S323.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
RPAP1 MUTATED 0 1 1 2
RPAP1 WILD-TYPE 37 64 48 40
'RPAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S324.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
RPAP1 MUTATED 1 3 0
RPAP1 WILD-TYPE 48 117 24
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S325.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
RPAP1 MUTATED 1 1 2
RPAP1 WILD-TYPE 58 55 77
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.742 (Fisher's exact test), Q value = 0.99

Table S326.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
RPAP1 MUTATED 0 2 1 0 1
RPAP1 WILD-TYPE 41 48 57 15 29
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S327.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
RPAP1 MUTATED 2 1 1
RPAP1 WILD-TYPE 67 56 57
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S328.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
RPAP1 MUTATED 1 0 1 2
RPAP1 WILD-TYPE 41 32 27 80
'HIST1H4E MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.71

Table S329.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HIST1H4E MUTATED 2 2 0
HIST1H4E WILD-TYPE 88 38 61
'HIST1H4E MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 0.99

Table S330.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
HIST1H4E MUTATED 0 1 1 1 0 1
HIST1H4E WILD-TYPE 50 31 35 35 7 32
'HIST1H4E MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.83

Table S331.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
HIST1H4E MUTATED 0 3 0 1
HIST1H4E WILD-TYPE 37 62 49 41
'HIST1H4E MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.8

Table S332.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
HIST1H4E MUTATED 0 3 1
HIST1H4E WILD-TYPE 49 117 23
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.85

Table S333.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HIST1H4E MUTATED 0 2 2
HIST1H4E WILD-TYPE 59 54 77
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S334.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HIST1H4E MUTATED 0 1 2 0 1
HIST1H4E WILD-TYPE 41 49 56 15 29
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 0.83

Table S335.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HIST1H4E MUTATED 1 2 0
HIST1H4E WILD-TYPE 68 55 58
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 0.82

Table S336.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HIST1H4E MUTATED 0 1 1 1
HIST1H4E WILD-TYPE 42 31 27 81
'NLRC5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.95

Table S337.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
NLRC5 MUTATED 4 2 1
NLRC5 WILD-TYPE 86 38 60
'NLRC5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.78

Table S338.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
NLRC5 MUTATED 4 2 0 0 0 1
NLRC5 WILD-TYPE 46 30 36 36 7 32
'NLRC5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 0.71

Table S339.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 31 60
NLRC5 MUTATED 0 2 4
NLRC5 WILD-TYPE 42 29 56
'NLRC5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 0.99

Table S340.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
NLRC5 MUTATED 0 2 2 1 1
NLRC5 WILD-TYPE 27 38 30 17 15
'NLRC5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 0.95

Table S341.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
NLRC5 MUTATED 2 1 2 2
NLRC5 WILD-TYPE 35 64 47 40
'NLRC5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.71

Table S342.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
NLRC5 MUTATED 4 3 0
NLRC5 WILD-TYPE 45 117 24
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.66

Table S343.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
NLRC5 MUTATED 4 0 3
NLRC5 WILD-TYPE 55 56 76
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.78

Table S344.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
NLRC5 MUTATED 3 0 2 1 1
NLRC5 WILD-TYPE 38 50 56 14 29
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.89

Table S345.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
NLRC5 MUTATED 4 1 2
NLRC5 WILD-TYPE 65 56 56
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.69

Table S346.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
NLRC5 MUTATED 4 0 1 2
NLRC5 WILD-TYPE 38 32 27 80
'DDX41 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.39

Table S347.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
DDX41 MUTATED 0 1 4
DDX41 WILD-TYPE 90 39 57

Figure S40.  Get High-res Image Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DDX41 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.62

Table S348.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
DDX41 MUTATED 0 3 0 1 0 1
DDX41 WILD-TYPE 50 29 36 35 7 32
'DDX41 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 0.89

Table S349.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
DDX41 MUTATED 1 3 0 1
DDX41 WILD-TYPE 36 62 49 41
'DDX41 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.83

Table S350.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
DDX41 MUTATED 0 4 1
DDX41 WILD-TYPE 49 116 23
'DDX41 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.8

Table S351.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
DDX41 MUTATED 0 2 3
DDX41 WILD-TYPE 59 54 76
'DDX41 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S352.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
DDX41 MUTATED 0 2 2 0 1
DDX41 WILD-TYPE 41 48 56 15 29
'DDX41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S353.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
DDX41 MUTATED 2 1 1
DDX41 WILD-TYPE 67 56 57
'DDX41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 0.88

Table S354.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
DDX41 MUTATED 0 1 0 3
DDX41 WILD-TYPE 42 31 28 79
'MCM7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0711 (Fisher's exact test), Q value = 0.5

Table S355.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
MCM7 MUTATED 0 0 0 1 1 1
MCM7 WILD-TYPE 50 32 36 35 6 32
'MCM7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.91

Table S356.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
MCM7 MUTATED 0 2 0 1
MCM7 WILD-TYPE 37 63 49 41
'MCM7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.85

Table S357.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
MCM7 MUTATED 0 2 1
MCM7 WILD-TYPE 49 118 23
'MCM7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S358.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MCM7 MUTATED 1 1 1
MCM7 WILD-TYPE 58 55 78
'MCM7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 0.86

Table S359.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MCM7 MUTATED 0 0 2 0 1
MCM7 WILD-TYPE 41 50 56 15 29
'MCM7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0598 (Fisher's exact test), Q value = 0.48

Table S360.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MCM7 MUTATED 0 0 3
MCM7 WILD-TYPE 69 57 55
'MCM7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.69

Table S361.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MCM7 MUTATED 0 0 2 1
MCM7 WILD-TYPE 42 32 26 81
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/15165547/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/15095897/CESC-TP.transferedmergedcluster.txt

  • Number of patients = 194

  • Number of significantly mutated genes = 38

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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