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 44 genes and 10 molecular subtypes across 498 patients, 44 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • PTEN mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • MLL2 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • CTNNB1 mutation correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • KDM6A mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • FOXA1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • MLL3 mutation correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • IDH1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • SMG7 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • CDKN1B mutation correlated to 'RPPA_CHIERARCHICAL'.

  • ERN1 mutation correlated to 'METHLYATION_CNMF'.

  • ZFHX3 mutation correlated to 'MIRSEQ_CNMF'.

  • ZMYM3 mutation correlated to 'METHLYATION_CNMF'.

  • EMG1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • KRT25 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 44 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, 44 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
TP53 57 (11%) 441 1e-05
(0.00055) 		0.00436
(0.103) 		0.00174
(0.0547) 		0.0563
(0.435) 		0.00234
(0.0606) 		5e-05
(0.00244) 		0.0711
(0.447) 		0.00731
(0.128) 		0.0193
(0.208) 		0.0611
(0.447)
FOXA1 28 (6%) 470 0.001
(0.041) 		1e-05
(0.00055) 		0.0062
(0.128) 		0.0785
(0.466) 		1e-05
(0.00055) 		1e-05
(0.00055) 		0.0977
(0.489) 		0.00663
(0.128) 		0.191
(0.631) 		0.239
(0.666)
SPOP 57 (11%) 441 1e-05
(0.00055) 		1e-05
(0.00055) 		0.0906
(0.48) 		0.886
(1.00) 		1e-05
(0.00055) 		1e-05
(0.00055) 		0.163
(0.582) 		0.161
(0.58) 		0.122
(0.51) 		0.336
(0.728)
CTNNB1 13 (3%) 485 0.185
(0.62) 		0.0102
(0.142) 		0.101
(0.493) 		0.0121
(0.156) 		0.0655
(0.447) 		0.207
(0.658) 		0.0651
(0.447) 		0.00757
(0.128) 		0.0209
(0.209) 		0.112
(0.51)
PIK3CA 14 (3%) 484 0.0811
(0.466) 		0.0129
(0.156) 		0.0637
(0.447) 		0.586
(0.892) 		0.00466
(0.103) 		0.00704
(0.128) 		0.0416
(0.352) 		0.0103
(0.142) 		0.548
(0.88) 		0.157
(0.57)
KDM6A 13 (3%) 485 0.5
(0.863) 		0.0201
(0.209) 		0.494
(0.86) 		0.705
(0.937) 		0.00998
(0.142) 		0.00876
(0.138) 		0.0804
(0.466) 		0.264
(0.682) 		0.303
(0.712) 		0.436
(0.813)
PTEN 17 (3%) 481 0.536
(0.88) 		0.523
(0.879) 		0.351
(0.75) 		0.495
(0.86) 		0.0121
(0.156) 		0.00113
(0.041) 		0.541
(0.88) 		0.13
(0.523) 		0.675
(0.916) 		0.882
(1.00)
MLL2 29 (6%) 469 0.0701
(0.447) 		0.0962
(0.489) 		0.297
(0.712) 		0.488
(0.86) 		0.0263
(0.257) 		0.00848
(0.138) 		0.302
(0.712) 		0.419
(0.805) 		0.0047
(0.103) 		0.335
(0.728)
MLL3 29 (6%) 469 0.0394
(0.34) 		0.302
(0.712) 		0.796
(1.00) 		0.00732
(0.128) 		0.754
(0.981) 		0.71
(0.941) 		0.239
(0.666) 		0.383
(0.787) 		0.312
(0.712) 		0.0181
(0.204)
IDH1 6 (1%) 492 0.887
(1.00) 		0.0126
(0.156) 		0.418
(0.805) 		0.338
(0.729) 		0.0721
(0.447) 		0.01
(0.142) 		0.279
(0.705) 		0.111
(0.51) 		0.729
(0.961) 		0.206
(0.658)
SMG7 8 (2%) 490 0.0322
(0.295) 		0.0741
(0.453) 		0.549
(0.88) 		0.733
(0.963) 		0.0131
(0.156) 		0.00218
(0.0599) 		0.297
(0.712) 		0.0871
(0.473) 		1
(1.00) 		0.228
(0.658)
CDKN1B 6 (1%) 492 0.31
(0.712) 		0.117
(0.51) 		0.103
(0.499) 		0.0173
(0.2) 		0.562
(0.88) 		0.0958
(0.489) 		0.281
(0.705) 		0.112
(0.51) 		0.284
(0.711) 		0.84
(1.00)
ERN1 4 (1%) 494 0.367
(0.77) 		0.0194
(0.208) 		0.23
(0.658) 		0.559
(0.88) 		0.302
(0.712) 		0.799
(1.00) 		0.0642
(0.447) 		0.132
(0.523)
ZFHX3 16 (3%) 482 0.397
(0.794) 		0.17
(0.59) 		0.0815
(0.466) 		0.772
(0.995) 		0.195
(0.64) 		0.106
(0.509) 		0.0205
(0.209) 		0.316
(0.713) 		0.381
(0.787) 		0.961
(1.00)
ZMYM3 12 (2%) 486 0.335
(0.728) 		0.00121
(0.041) 		0.452
(0.833) 		0.0513
(0.403) 		0.0843
(0.468) 		0.146
(0.548) 		0.0455
(0.371) 		0.633
(0.91) 		0.246
(0.673) 		0.254
(0.673)
EMG1 4 (1%) 494 0.495
(0.86) 		0.115
(0.51) 		0.405
(0.803) 		0.222
(0.658) 		0.0443
(0.368) 		0.0011
(0.041)
KRT25 6 (1%) 492 0.604
(0.897) 		0.0803
(0.466) 		0.841
(1.00) 		0.574
(0.881) 		0.152
(0.563) 		0.875
(1.00) 		0.262
(0.681) 		0.00194
(0.0569) 		0.649
(0.914) 		0.167
(0.588)
NUDT11 11 (2%) 487 0.534
(0.88) 		0.904
(1.00) 		0.119
(0.51) 		0.0884
(0.475) 		0.851
(1.00) 		0.928
(1.00) 		0.436
(0.813) 		0.514
(0.874) 		0.685
(0.924) 		0.512
(0.873)
GAGE2A 5 (1%) 493 0.523
(0.879) 		0.663
(0.915) 		0.683
(0.924) 		0.458
(0.833) 		0.859
(1.00) 		0.589
(0.893) 		0.125
(0.519) 		0.28
(0.705)
TNRC18 9 (2%) 489 0.327
(0.726) 		0.265
(0.682) 		0.569
(0.881) 		0.307
(0.712) 		0.665
(0.915) 		0.572
(0.881) 		0.417
(0.805) 		0.21
(0.658) 		0.509
(0.872) 		0.944
(1.00)
AGAP6 5 (1%) 493 1
(1.00) 		0.659
(0.915) 		0.481
(0.86) 		0.249
(0.673) 		0.221
(0.658) 		0.458
(0.833) 		0.74
(0.969) 		0.307
(0.712) 		0.414
(0.805) 		1
(1.00)
GATA6 4 (1%) 494 0.917
(1.00) 		0.537
(0.88) 		0.657
(0.915) 		0.827
(1.00) 		1
(1.00) 		0.689
(0.924) 		0.623
(0.909) 		0.884
(1.00)
CNTNAP1 9 (2%) 489 0.222
(0.658) 		0.17
(0.59) 		0.826
(1.00) 		1
(1.00) 		0.518
(0.876) 		0.701
(0.935) 		0.926
(1.00) 		0.0687
(0.447) 		0.841
(1.00) 		0.626
(0.909)
EOMES 5 (1%) 493 0.251
(0.673) 		0.429
(0.813) 		0.67
(0.916) 		0.115
(0.51) 		0.933
(1.00) 		0.136
(0.527) 		0.411
(0.805) 		0.803
(1.00) 		0.312
(0.712) 		0.49
(0.86)
NBPF1 9 (2%) 489 0.967
(1.00) 		0.109
(0.51) 		0.854
(1.00) 		0.773
(0.995) 		0.433
(0.813) 		0.425
(0.81) 		0.56
(0.88) 		0.34
(0.731) 		0.619
(0.909) 		0.367
(0.77)
LMOD2 6 (1%) 492 0.472
(0.852) 		0.946
(1.00) 		0.671
(0.916) 		0.232
(0.658) 		0.395
(0.794) 		0.331
(0.728) 		0.296
(0.712) 		0.65
(0.914) 		0.946
(1.00) 		0.966
(1.00)
EHHADH 5 (1%) 493 0.641
(0.914) 		0.817
(1.00) 		0.153
(0.563) 		0.89
(1.00) 		0.648
(0.914) 		1
(1.00) 		0.47
(0.852) 		0.486
(0.86)
MED12 8 (2%) 490 1
(1.00) 		0.554
(0.88) 		0.984
(1.00) 		0.897
(1.00) 		0.964
(1.00) 		0.223
(0.658) 		0.847
(1.00) 		0.887
(1.00) 		0.574
(0.881) 		0.8
(1.00)
ZNF709 5 (1%) 493 0.923
(1.00) 		0.254
(0.673) 		0.115
(0.51) 		0.097
(0.489) 		0.648
(0.914) 		0.543
(0.88) 		0.12
(0.51) 		0.253
(0.673) 		0.33
(0.728) 		0.317
(0.713)
TCEB3 4 (1%) 494 0.838
(1.00) 		0.494
(0.86) 		0.293
(0.712) 		0.552
(0.88) 		0.206
(0.658) 		0.0342
(0.301) 		0.902
(1.00) 		0.174
(0.599) 		0.386
(0.791) 		0.28
(0.705)
MED15 7 (1%) 491 0.0844
(0.468) 		0.149
(0.554) 		0.397
(0.794) 		0.577
(0.882) 		0.837
(1.00) 		0.23
(0.658) 		0.788
(1.00) 		0.653
(0.915) 		0.813
(1.00) 		0.806
(1.00)
ERF 5 (1%) 493 1
(1.00) 		0.221
(0.658) 		0.573
(0.881) 		0.0601
(0.447) 		0.405
(0.803) 		0.63
(0.909) 		0.798
(1.00) 		0.127
(0.523) 		0.629
(0.909) 		0.699
(0.935)
MLLT10 5 (1%) 493 0.165
(0.585) 		0.45
(0.833) 		0.766
(0.992) 		0.66
(0.915) 		1
(1.00) 		0.627
(0.909) 		0.686
(0.924) 		0.591
(0.893)
FMN1 4 (1%) 494 0.539
(0.88) 		0.198
(0.644) 		0.569
(0.881) 		0.62
(0.909) 		0.227
(0.658) 		1
(1.00) 		0.821
(1.00) 		0.186
(0.62)
AKT1 3 (1%) 495 1
(1.00) 		0.0339
(0.301) 		0.367
(0.77) 		0.18
(0.615) 		0.649
(0.914) 		1
(1.00)
ATM 22 (4%) 476 0.0712
(0.447) 		0.257
(0.674) 		0.828
(1.00) 		0.827
(1.00) 		0.293
(0.712) 		0.0293
(0.274) 		0.296
(0.712) 		0.229
(0.658) 		0.663
(0.915) 		0.479
(0.86)
STRC 5 (1%) 493 0.64
(0.914) 		0.0484
(0.387) 		0.547
(0.88) 		0.248
(0.673) 		0.137
(0.527) 		0.0687
(0.447)
APC 10 (2%) 488 0.435
(0.813) 		0.23
(0.658) 		0.373
(0.778) 		1
(1.00) 		0.0712
(0.447) 		0.142
(0.54) 		0.319
(0.714) 		0.318
(0.713) 		0.526
(0.88) 		0.36
(0.765)
ZFP36L2 4 (1%) 494 0.542
(0.88) 		0.38
(0.787) 		0.092
(0.482) 		0.89
(1.00) 		0.23
(0.658) 		0.557
(0.88) 		1
(1.00) 		0.216
(0.658) 		0.5
(0.863) 		0.595
(0.896)
MYOT 5 (1%) 493 0.41
(0.805) 		0.0291
(0.274) 		0.606
(0.897) 		0.119
(0.51) 		0.0602
(0.447) 		0.301
(0.712) 		0.135
(0.527) 		0.128
(0.523) 		0.673
(0.916) 		0.423
(0.81)
KIRREL 6 (1%) 492 0.0997
(0.493) 		0.395
(0.794) 		0.866
(1.00) 		0.0852
(0.468) 		0.562
(0.88) 		0.509
(0.872) 		0.597
(0.896) 		0.606
(0.897) 		0.729
(0.961) 		0.883
(1.00)
PGBD2 3 (1%) 495 0.257
(0.674) 		0.186
(0.62) 		0.121
(0.51) 		0.251
(0.673) 		0.744
(0.971) 		0.215
(0.658) 		0.628
(0.909) 		0.599
(0.896)
LOC100132247 3 (1%) 495 0.309
(0.712) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.904
(1.00)
CDH16 4 (1%) 494 0.452
(0.833) 		0.417
(0.805) 		0.766
(0.992) 		0.132
(0.523) 		0.138
(0.527) 		0.454
(0.833) 		0.234
(0.66) 		0.221
(0.658) 		0.389
(0.793) 		0.554
(0.88)
'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
SPOP MUTATED 0 4 20 31
SPOP WILD-TYPE 108 87 78 164

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

'SPOP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
SPOP MUTATED 10 44 1 2
SPOP WILD-TYPE 151 96 125 69

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

'SPOP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0906 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
SPOP MUTATED 8 6 3 3 11 1
SPOP WILD-TYPE 98 45 42 50 47 38
'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
SPOP MUTATED 6 10 8 8
SPOP WILD-TYPE 69 104 85 62
'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
SPOP MUTATED 6 0 42 9
SPOP WILD-TYPE 90 142 109 99

Figure S3.  Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
SPOP MUTATED 10 47 0
SPOP WILD-TYPE 163 161 116

Figure S4.  Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
SPOP MUTATED 32 5 10 10
SPOP WILD-TYPE 181 66 114 76
'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
SPOP MUTATED 17 10 2 20 8
SPOP WILD-TYPE 131 88 57 113 48
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
SPOP MUTATED 4 13 5 13
SPOP WILD-TYPE 61 80 73 71
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.336 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
SPOP MUTATED 7 13 7 0 8
SPOP WILD-TYPE 68 75 62 23 57
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

Table S11.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
TP53 MUTATED 8 2 1 45
TP53 WILD-TYPE 100 89 97 150

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
TP53 MUTATED 11 11 24 11
TP53 WILD-TYPE 150 129 102 60

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.055

Table S13.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
TP53 MUTATED 5 7 3 8 3 11
TP53 WILD-TYPE 101 44 42 45 55 28

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

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0563 (Fisher's exact test), Q value = 0.43

Table S14.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
TP53 MUTATED 4 9 11 13
TP53 WILD-TYPE 71 105 82 57
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.061

Table S15.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
TP53 MUTATED 4 25 21 7
TP53 WILD-TYPE 92 117 130 101

Figure S8.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0024

Table S16.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
TP53 MUTATED 10 20 27
TP53 WILD-TYPE 163 188 89

Figure S9.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0711 (Fisher's exact test), Q value = 0.45

Table S17.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
TP53 MUTATED 33 4 10 10
TP53 WILD-TYPE 180 67 114 76
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00731 (Fisher's exact test), Q value = 0.13

Table S18.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
TP53 MUTATED 10 6 12 22 7
TP53 WILD-TYPE 138 92 47 111 49

Figure S10.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.21

Table S19.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
TP53 MUTATED 2 17 9 13
TP53 WILD-TYPE 63 76 69 71

Figure S11.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0611 (Fisher's exact test), Q value = 0.45

Table S20.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
TP53 MUTATED 9 18 6 0 8
TP53 WILD-TYPE 66 70 63 23 57
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
PTEN MUTATED 4 1 3 9
PTEN WILD-TYPE 104 90 95 186
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
PTEN MUTATED 3 5 6 3
PTEN WILD-TYPE 158 135 120 68
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
PTEN MUTATED 2 3 4 1 2 1
PTEN WILD-TYPE 104 48 41 52 56 38
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
PTEN MUTATED 2 7 2 2
PTEN WILD-TYPE 73 107 91 68
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.16

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
PTEN MUTATED 1 9 7 0
PTEN WILD-TYPE 95 133 144 108

Figure S12.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.041

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
PTEN MUTATED 1 6 10
PTEN WILD-TYPE 172 202 106

Figure S13.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
PTEN MUTATED 10 2 2 3
PTEN WILD-TYPE 203 69 122 83
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
PTEN MUTATED 6 1 0 6 4
PTEN WILD-TYPE 142 97 59 127 52
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
PTEN MUTATED 1 5 3 4
PTEN WILD-TYPE 64 88 75 80
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
PTEN MUTATED 3 5 2 0 3
PTEN WILD-TYPE 72 83 67 23 62
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S31.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
NUDT11 MUTATED 1 2 4 4
NUDT11 WILD-TYPE 107 89 94 191
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
NUDT11 MUTATED 4 4 2 1
NUDT11 WILD-TYPE 157 136 124 70
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.51

Table S33.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
NUDT11 MUTATED 1 1 4 2 2 0
NUDT11 WILD-TYPE 105 50 41 51 56 39
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0884 (Fisher's exact test), Q value = 0.47

Table S34.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
NUDT11 MUTATED 0 6 1 3
NUDT11 WILD-TYPE 75 108 92 67
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
NUDT11 MUTATED 1 4 3 3
NUDT11 WILD-TYPE 95 138 148 105
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
NUDT11 MUTATED 4 4 3
NUDT11 WILD-TYPE 169 204 113
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.81

Table S37.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
NUDT11 MUTATED 3 1 5 2
NUDT11 WILD-TYPE 210 70 119 84
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 0.87

Table S38.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
NUDT11 MUTATED 6 2 0 2 1
NUDT11 WILD-TYPE 142 96 59 131 55
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.92

Table S39.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
NUDT11 MUTATED 0 1 2 2
NUDT11 WILD-TYPE 65 92 76 82
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.87

Table S40.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
NUDT11 MUTATED 3 1 1 0 0
NUDT11 WILD-TYPE 72 87 68 23 65
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0701 (Fisher's exact test), Q value = 0.45

Table S41.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
MLL2 MUTATED 3 2 8 16
MLL2 WILD-TYPE 105 89 90 179
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0962 (Fisher's exact test), Q value = 0.49

Table S42.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
MLL2 MUTATED 8 11 3 7
MLL2 WILD-TYPE 153 129 123 64
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.71

Table S43.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
MLL2 MUTATED 5 2 3 1 5 5
MLL2 WILD-TYPE 101 49 42 52 53 34
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S44.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
MLL2 MUTATED 2 7 6 6
MLL2 WILD-TYPE 73 107 87 64
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.26

Table S45.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
MLL2 MUTATED 7 2 13 7
MLL2 WILD-TYPE 89 140 138 101

Figure S14.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00848 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
MLL2 MUTATED 10 18 1
MLL2 WILD-TYPE 163 190 115

Figure S15.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.71

Table S47.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
MLL2 MUTATED 14 7 5 3
MLL2 WILD-TYPE 199 64 119 83
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.419 (Fisher's exact test), Q value = 0.8

Table S48.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
MLL2 MUTATED 7 9 5 6 2
MLL2 WILD-TYPE 141 89 54 127 54
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.1

Table S49.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
MLL2 MUTATED 0 12 5 3
MLL2 WILD-TYPE 65 81 73 81

Figure S16.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 0.73

Table S50.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
MLL2 MUTATED 4 9 5 0 2
MLL2 WILD-TYPE 71 79 64 23 63
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.62

Table S51.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
CTNNB1 MUTATED 2 1 6 4
CTNNB1 WILD-TYPE 106 90 92 191
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.14

Table S52.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
CTNNB1 MUTATED 0 6 3 4
CTNNB1 WILD-TYPE 161 134 123 67

Figure S17.  Get High-res Image Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.49

Table S53.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
CTNNB1 MUTATED 0 1 0 2 2 2
CTNNB1 WILD-TYPE 106 50 45 51 56 37
'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.16

Table S54.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
CTNNB1 MUTATED 0 1 1 5
CTNNB1 WILD-TYPE 75 113 92 65

Figure S18.  Get High-res Image Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0655 (Fisher's exact test), Q value = 0.45

Table S55.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
CTNNB1 MUTATED 1 5 7 0
CTNNB1 WILD-TYPE 95 137 144 108
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.66

Table S56.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
CTNNB1 MUTATED 2 6 5
CTNNB1 WILD-TYPE 171 202 111
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0651 (Fisher's exact test), Q value = 0.45

Table S57.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
CTNNB1 MUTATED 9 1 0 3
CTNNB1 WILD-TYPE 204 70 124 83
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00757 (Fisher's exact test), Q value = 0.13

Table S58.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
CTNNB1 MUTATED 1 0 1 8 3
CTNNB1 WILD-TYPE 147 98 58 125 53

Figure S19.  Get High-res Image Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.21

Table S59.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
CTNNB1 MUTATED 0 6 0 3
CTNNB1 WILD-TYPE 65 87 78 81

Figure S20.  Get High-res Image Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.51

Table S60.  Gene #6: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
CTNNB1 MUTATED 1 6 0 0 2
CTNNB1 WILD-TYPE 74 82 69 23 63
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0811 (Fisher's exact test), Q value = 0.47

Table S61.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
PIK3CA MUTATED 4 0 1 9
PIK3CA WILD-TYPE 104 91 97 186
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.16

Table S62.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
PIK3CA MUTATED 0 5 5 4
PIK3CA WILD-TYPE 161 135 121 67

Figure S21.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0637 (Fisher's exact test), Q value = 0.45

Table S63.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
PIK3CA MUTATED 0 1 1 3 0 1
PIK3CA WILD-TYPE 106 50 44 50 58 38
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 0.89

Table S64.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
PIK3CA MUTATED 0 2 2 2
PIK3CA WILD-TYPE 75 112 91 68
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.1

Table S65.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
PIK3CA MUTATED 0 5 9 0
PIK3CA WILD-TYPE 96 137 142 108

Figure S22.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00704 (Fisher's exact test), Q value = 0.13

Table S66.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
PIK3CA MUTATED 1 5 8
PIK3CA WILD-TYPE 172 203 108

Figure S23.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S67.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
PIK3CA MUTATED 9 1 0 4
PIK3CA WILD-TYPE 204 70 124 82

Figure S24.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.14

Table S68.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
PIK3CA MUTATED 1 0 3 7 3
PIK3CA WILD-TYPE 147 98 56 126 53

Figure S25.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.88

Table S69.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
PIK3CA MUTATED 1 3 2 5
PIK3CA WILD-TYPE 64 90 76 79
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.57

Table S70.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
PIK3CA MUTATED 0 6 2 1 2
PIK3CA WILD-TYPE 75 82 67 22 63
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.86

Table S71.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
KDM6A MUTATED 1 3 4 5
KDM6A WILD-TYPE 107 88 94 190
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.21

Table S72.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
KDM6A MUTATED 2 9 1 1
KDM6A WILD-TYPE 159 131 125 70

Figure S26.  Get High-res Image Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.86

Table S73.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
KDM6A MUTATED 2 2 2 0 2 0
KDM6A WILD-TYPE 104 49 43 53 56 39
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 0.94

Table S74.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
KDM6A MUTATED 1 2 2 3
KDM6A WILD-TYPE 74 112 91 67
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.14

Table S75.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
KDM6A MUTATED 4 1 8 0
KDM6A WILD-TYPE 92 141 143 108

Figure S27.  Get High-res Image Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00876 (Fisher's exact test), Q value = 0.14

Table S76.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
KDM6A MUTATED 1 11 1
KDM6A WILD-TYPE 172 197 115

Figure S28.  Get High-res Image Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0804 (Fisher's exact test), Q value = 0.47

Table S77.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
KDM6A MUTATED 7 2 0 4
KDM6A WILD-TYPE 206 69 124 82
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 0.68

Table S78.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
KDM6A MUTATED 2 6 1 3 1
KDM6A WILD-TYPE 146 92 58 130 55
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.71

Table S79.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
KDM6A MUTATED 0 3 1 4
KDM6A WILD-TYPE 65 90 77 80
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 0.81

Table S80.  Gene #8: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
KDM6A MUTATED 0 3 3 0 2
KDM6A WILD-TYPE 75 85 66 23 63
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.041

Table S81.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
FOXA1 MUTATED 1 1 11 14
FOXA1 WILD-TYPE 107 90 87 181

Figure S29.  Get High-res Image Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

Table S82.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
FOXA1 MUTATED 2 22 1 3
FOXA1 WILD-TYPE 159 118 125 68

Figure S30.  Get High-res Image Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.13

Table S83.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
FOXA1 MUTATED 3 2 2 4 10 0
FOXA1 WILD-TYPE 103 49 43 49 48 39

Figure S31.  Get High-res Image Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0785 (Fisher's exact test), Q value = 0.47

Table S84.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
FOXA1 MUTATED 2 6 4 9
FOXA1 WILD-TYPE 73 108 89 61
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

Table S85.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
FOXA1 MUTATED 3 0 24 1
FOXA1 WILD-TYPE 93 142 127 107

Figure S32.  Get High-res Image Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00055

Table S86.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
FOXA1 MUTATED 3 24 1
FOXA1 WILD-TYPE 170 184 115

Figure S33.  Get High-res Image Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0977 (Fisher's exact test), Q value = 0.49

Table S87.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
FOXA1 MUTATED 18 2 3 5
FOXA1 WILD-TYPE 195 69 121 81
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 0.13

Table S88.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
FOXA1 MUTATED 2 9 1 12 4
FOXA1 WILD-TYPE 146 89 58 121 52

Figure S34.  Get High-res Image Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.63

Table S89.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
FOXA1 MUTATED 2 4 1 7
FOXA1 WILD-TYPE 63 89 77 77
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.67

Table S90.  Gene #9: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
FOXA1 MUTATED 1 6 2 0 5
FOXA1 WILD-TYPE 74 82 67 23 60
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.34

Table S91.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
MLL3 MUTATED 4 1 7 17
MLL3 WILD-TYPE 104 90 91 178

Figure S35.  Get High-res Image Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.71

Table S92.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
MLL3 MUTATED 5 10 9 5
MLL3 WILD-TYPE 156 130 117 66
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
MLL3 MUTATED 6 3 2 4 2 4
MLL3 WILD-TYPE 100 48 43 49 56 35
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00732 (Fisher's exact test), Q value = 0.13

Table S94.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
MLL3 MUTATED 1 3 11 6
MLL3 WILD-TYPE 74 111 82 64

Figure S36.  Get High-res Image Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.754 (Fisher's exact test), Q value = 0.98

Table S95.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
MLL3 MUTATED 4 9 11 5
MLL3 WILD-TYPE 92 133 140 103
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.71 (Fisher's exact test), Q value = 0.94

Table S96.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
MLL3 MUTATED 8 14 7
MLL3 WILD-TYPE 165 194 109
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.67

Table S97.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
MLL3 MUTATED 18 3 4 4
MLL3 WILD-TYPE 195 68 120 82
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.79

Table S98.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
MLL3 MUTATED 7 6 6 9 1
MLL3 WILD-TYPE 141 92 53 124 55
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.71

Table S99.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
MLL3 MUTATED 3 10 3 5
MLL3 WILD-TYPE 62 83 75 79
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.2

Table S100.  Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
MLL3 MUTATED 2 13 2 1 3
MLL3 WILD-TYPE 73 75 67 22 62

Figure S37.  Get High-res Image Gene #10: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GAGE2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.88

Table S101.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
GAGE2A MUTATED 1 2 0 2
GAGE2A WILD-TYPE 107 89 98 193
'GAGE2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 0.91

Table S102.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
GAGE2A MUTATED 3 1 1 0
GAGE2A WILD-TYPE 158 139 125 71
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.92

Table S103.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
GAGE2A MUTATED 0 1 2 2
GAGE2A WILD-TYPE 96 141 149 106
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.83

Table S104.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
GAGE2A MUTATED 3 1 1
GAGE2A WILD-TYPE 170 207 115
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S105.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
GAGE2A MUTATED 2 0 2 1
GAGE2A WILD-TYPE 211 71 122 85
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 0.89

Table S106.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
GAGE2A MUTATED 3 0 0 2 0
GAGE2A WILD-TYPE 145 98 59 131 56
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.52

Table S107.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
GAGE2A MUTATED 2 0 0 1
GAGE2A WILD-TYPE 63 93 78 83
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.71

Table S108.  Gene #11: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
GAGE2A MUTATED 1 1 0 1 0
GAGE2A WILD-TYPE 74 87 69 22 65
'TNRC18 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.73

Table S109.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
TNRC18 MUTATED 1 0 2 6
TNRC18 WILD-TYPE 107 91 96 189
'TNRC18 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.68

Table S110.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
TNRC18 MUTATED 1 3 2 3
TNRC18 WILD-TYPE 160 137 124 68
'TNRC18 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.88

Table S111.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
TNRC18 MUTATED 2 0 1 0 0 1
TNRC18 WILD-TYPE 104 51 44 53 58 38
'TNRC18 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.71

Table S112.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
TNRC18 MUTATED 1 3 0 0
TNRC18 WILD-TYPE 74 111 93 70
'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 0.91

Table S113.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
TNRC18 MUTATED 3 2 3 1
TNRC18 WILD-TYPE 93 140 148 107
'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.88

Table S114.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
TNRC18 MUTATED 2 4 3
TNRC18 WILD-TYPE 171 204 113
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.8

Table S115.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
TNRC18 MUTATED 6 0 1 2
TNRC18 WILD-TYPE 207 71 123 84
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.66

Table S116.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
TNRC18 MUTATED 1 1 2 5 0
TNRC18 WILD-TYPE 147 97 57 128 56
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S117.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
TNRC18 MUTATED 0 3 2 3
TNRC18 WILD-TYPE 65 90 76 81
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S118.  Gene #12: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
TNRC18 MUTATED 1 3 2 0 2
TNRC18 WILD-TYPE 74 85 67 23 63
'AGAP6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S119.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
AGAP6 MUTATED 1 1 1 2
AGAP6 WILD-TYPE 107 90 97 193
'AGAP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.659 (Fisher's exact test), Q value = 0.91

Table S120.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
AGAP6 MUTATED 3 1 1 0
AGAP6 WILD-TYPE 158 139 125 71
'AGAP6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.86

Table S121.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
AGAP6 MUTATED 1 0 0 2 1 0
AGAP6 WILD-TYPE 105 51 45 51 57 39
'AGAP6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.67

Table S122.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
AGAP6 MUTATED 1 0 1 2
AGAP6 WILD-TYPE 74 114 92 68
'AGAP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.66

Table S123.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
AGAP6 MUTATED 2 1 0 2
AGAP6 WILD-TYPE 94 141 151 106
'AGAP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.83

Table S124.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
AGAP6 MUTATED 3 1 1
AGAP6 WILD-TYPE 170 207 115
'AGAP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 0.97

Table S125.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
AGAP6 MUTATED 2 1 2 0
AGAP6 WILD-TYPE 211 70 122 86
'AGAP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.71

Table S126.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
AGAP6 MUTATED 1 2 1 0 1
AGAP6 WILD-TYPE 147 96 58 133 55
'AGAP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.8

Table S127.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
AGAP6 MUTATED 2 1 1 0
AGAP6 WILD-TYPE 63 92 77 84
'AGAP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S128.  Gene #13: 'AGAP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
AGAP6 MUTATED 1 1 1 0 1
AGAP6 WILD-TYPE 74 87 68 23 64
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S129.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
IDH1 MUTATED 1 1 2 2
IDH1 WILD-TYPE 107 90 96 193
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.16

Table S130.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
IDH1 MUTATED 0 5 0 1
IDH1 WILD-TYPE 161 135 126 70

Figure S38.  Get High-res Image Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.8

Table S131.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
IDH1 MUTATED 1 1 0 2 0 0
IDH1 WILD-TYPE 105 50 45 51 58 39
'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.73

Table S132.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
IDH1 MUTATED 2 0 1 1
IDH1 WILD-TYPE 73 114 92 69
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0721 (Fisher's exact test), Q value = 0.45

Table S133.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
IDH1 MUTATED 2 0 4 0
IDH1 WILD-TYPE 94 142 147 108
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.14

Table S134.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
IDH1 MUTATED 0 6 0
IDH1 WILD-TYPE 173 202 116

Figure S39.  Get High-res Image Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.71

Table S135.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
IDH1 MUTATED 3 2 0 1
IDH1 WILD-TYPE 210 69 124 85
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.51

Table S136.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
IDH1 MUTATED 0 3 0 3 0
IDH1 WILD-TYPE 148 95 59 130 56
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 0.96

Table S137.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
IDH1 MUTATED 0 2 2 1
IDH1 WILD-TYPE 65 91 76 83
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.66

Table S138.  Gene #14: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
IDH1 MUTATED 0 2 3 0 0
IDH1 WILD-TYPE 75 86 66 23 65
'GATA6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S139.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
GATA6 MUTATED 1 1 1 1
GATA6 WILD-TYPE 107 90 97 194
'GATA6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S140.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
GATA6 MUTATED 1 2 0 1
GATA6 WILD-TYPE 160 138 126 70
'GATA6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 0.91

Table S141.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
GATA6 MUTATED 0 1 1 2
GATA6 WILD-TYPE 96 141 150 106
'GATA6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S142.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
GATA6 MUTATED 2 1 1
GATA6 WILD-TYPE 171 207 115
'GATA6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S143.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
GATA6 MUTATED 2 0 1 1
GATA6 WILD-TYPE 211 71 123 85
'GATA6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.689 (Fisher's exact test), Q value = 0.92

Table S144.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
GATA6 MUTATED 2 0 0 1 1
GATA6 WILD-TYPE 146 98 59 132 55
'GATA6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 0.91

Table S145.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
GATA6 MUTATED 1 1 0 2
GATA6 WILD-TYPE 64 92 78 82
'GATA6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'GATA6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
GATA6 MUTATED 1 2 0 0 1
GATA6 WILD-TYPE 74 86 69 23 64
'SMG7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.3

Table S147.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
SMG7 MUTATED 0 1 5 2
SMG7 WILD-TYPE 108 90 93 193

Figure S40.  Get High-res Image Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SMG7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0741 (Fisher's exact test), Q value = 0.45

Table S148.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
SMG7 MUTATED 0 5 2 1
SMG7 WILD-TYPE 161 135 124 70
'SMG7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.88

Table S149.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
SMG7 MUTATED 2 0 0 1 1 2
SMG7 WILD-TYPE 104 51 45 52 57 37
'SMG7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 0.96

Table S150.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
SMG7 MUTATED 1 1 3 1
SMG7 WILD-TYPE 74 113 90 69
'SMG7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.16

Table S151.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
SMG7 MUTATED 2 0 6 0
SMG7 WILD-TYPE 94 142 145 108

Figure S41.  Get High-res Image Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SMG7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.06

Table S152.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
SMG7 MUTATED 0 8 0
SMG7 WILD-TYPE 173 200 116

Figure S42.  Get High-res Image Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SMG7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.71

Table S153.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
SMG7 MUTATED 5 1 0 2
SMG7 WILD-TYPE 208 70 124 84
'SMG7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0871 (Fisher's exact test), Q value = 0.47

Table S154.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
SMG7 MUTATED 0 2 0 4 2
SMG7 WILD-TYPE 148 96 59 129 54
'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S155.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
SMG7 MUTATED 1 2 1 1
SMG7 WILD-TYPE 64 91 77 83
'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.66

Table S156.  Gene #16: 'SMG7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
SMG7 MUTATED 0 3 0 0 2
SMG7 WILD-TYPE 75 85 69 23 63
'CNTNAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 0.66

Table S157.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
CNTNAP1 MUTATED 0 1 1 6
CNTNAP1 WILD-TYPE 108 90 97 189
'CNTNAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.59

Table S158.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
CNTNAP1 MUTATED 1 5 1 2
CNTNAP1 WILD-TYPE 160 135 125 69
'CNTNAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S159.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
CNTNAP1 MUTATED 1 1 0 1 0 0
CNTNAP1 WILD-TYPE 105 50 45 52 58 39
'CNTNAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S160.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
CNTNAP1 MUTATED 1 1 1 0
CNTNAP1 WILD-TYPE 74 113 92 70
'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 0.88

Table S161.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
CNTNAP1 MUTATED 1 1 4 3
CNTNAP1 WILD-TYPE 95 141 147 105
'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.701 (Fisher's exact test), Q value = 0.93

Table S162.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
CNTNAP1 MUTATED 2 5 2
CNTNAP1 WILD-TYPE 171 203 114
'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S163.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
CNTNAP1 MUTATED 4 1 3 1
CNTNAP1 WILD-TYPE 209 70 121 85
'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0687 (Fisher's exact test), Q value = 0.45

Table S164.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
CNTNAP1 MUTATED 0 1 1 5 2
CNTNAP1 WILD-TYPE 148 97 58 128 54
'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
CNTNAP1 MUTATED 0 1 1 2
CNTNAP1 WILD-TYPE 65 92 77 82
'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.91

Table S166.  Gene #17: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
CNTNAP1 MUTATED 0 1 1 0 2
CNTNAP1 WILD-TYPE 75 87 68 23 63
'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.71

Table S167.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
CDKN1B MUTATED 1 0 3 2
CDKN1B WILD-TYPE 107 91 95 193
'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.51

Table S168.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
CDKN1B MUTATED 0 3 1 2
CDKN1B WILD-TYPE 161 137 125 69
'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.5

Table S169.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
CDKN1B MUTATED 0 0 1 1 2 2
CDKN1B WILD-TYPE 106 51 44 52 56 37
'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.2

Table S170.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
CDKN1B MUTATED 0 2 0 4
CDKN1B WILD-TYPE 75 112 93 66

Figure S43.  Get High-res Image Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.88

Table S171.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
CDKN1B MUTATED 2 2 2 0
CDKN1B WILD-TYPE 94 140 149 108
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0958 (Fisher's exact test), Q value = 0.49

Table S172.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
CDKN1B MUTATED 0 5 1
CDKN1B WILD-TYPE 173 203 115
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.71

Table S173.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
CDKN1B MUTATED 3 2 0 1
CDKN1B WILD-TYPE 210 69 124 85
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.51

Table S174.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
CDKN1B MUTATED 0 3 0 3 0
CDKN1B WILD-TYPE 148 95 59 130 56
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.71

Table S175.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
CDKN1B MUTATED 0 3 0 1
CDKN1B WILD-TYPE 65 90 78 83
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S176.  Gene #18: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
CDKN1B MUTATED 0 2 1 0 1
CDKN1B WILD-TYPE 75 86 68 23 64
'EOMES MUTATION STATUS' versus 'CN_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
EOMES MUTATED 2 2 0 1
EOMES WILD-TYPE 106 89 98 194
'EOMES MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
EOMES MUTATED 3 2 0 0
EOMES WILD-TYPE 158 138 126 71
'EOMES MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
EOMES MUTATED 1 1 0 1 0 1
EOMES WILD-TYPE 105 50 45 52 58 38
'EOMES MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
EOMES MUTATED 1 0 3 0
EOMES WILD-TYPE 74 114 90 70
'EOMES MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
EOMES MUTATED 1 2 1 1
EOMES WILD-TYPE 95 140 150 107
'EOMES MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
EOMES MUTATED 4 1 0
EOMES WILD-TYPE 169 207 116
'EOMES MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
EOMES MUTATED 2 2 1 0
EOMES WILD-TYPE 211 69 123 86
'EOMES MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
EOMES MUTATED 2 2 0 1 0
EOMES WILD-TYPE 146 96 59 132 56
'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
EOMES MUTATED 0 2 2 0
EOMES WILD-TYPE 65 91 76 84
'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
EOMES MUTATED 1 1 1 1 0
EOMES WILD-TYPE 74 87 68 22 65
'NBPF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.967 (Fisher's exact test), Q value = 1

Table S187.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
NBPF1 MUTATED 2 2 2 3
NBPF1 WILD-TYPE 106 89 96 192
'NBPF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.51

Table S188.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
NBPF1 MUTATED 2 5 0 2
NBPF1 WILD-TYPE 159 135 126 69
'NBPF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S189.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
NBPF1 MUTATED 2 1 0 1 0 1
NBPF1 WILD-TYPE 104 50 45 52 58 38
'NBPF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 0.99

Table S190.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
NBPF1 MUTATED 0 2 2 1
NBPF1 WILD-TYPE 75 112 91 69
'NBPF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.81

Table S191.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
NBPF1 MUTATED 3 1 4 1
NBPF1 WILD-TYPE 93 141 147 107
'NBPF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.81

Table S192.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
NBPF1 MUTATED 2 6 1
NBPF1 WILD-TYPE 171 202 115
'NBPF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.88

Table S193.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
NBPF1 MUTATED 4 1 1 3
NBPF1 WILD-TYPE 209 70 123 83
'NBPF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.34 (Fisher's exact test), Q value = 0.73

Table S194.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
NBPF1 MUTATED 1 2 0 4 2
NBPF1 WILD-TYPE 147 96 59 129 54
'NBPF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 0.91

Table S195.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
NBPF1 MUTATED 0 3 2 2
NBPF1 WILD-TYPE 65 90 76 82
'NBPF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.77

Table S196.  Gene #20: 'NBPF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
NBPF1 MUTATED 0 4 2 0 1
NBPF1 WILD-TYPE 75 84 67 23 64
'LMOD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S197.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
LMOD2 MUTATED 2 2 1 1
LMOD2 WILD-TYPE 106 89 97 194
'LMOD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S198.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
LMOD2 MUTATED 2 1 2 1
LMOD2 WILD-TYPE 159 139 124 70
'LMOD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 0.92

Table S199.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
LMOD2 MUTATED 3 1 0 0 2 0
LMOD2 WILD-TYPE 103 50 45 53 56 39
'LMOD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.66

Table S200.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
LMOD2 MUTATED 2 0 2 2
LMOD2 WILD-TYPE 73 114 91 68
'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.79

Table S201.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
LMOD2 MUTATED 2 3 1 0
LMOD2 WILD-TYPE 94 139 150 108
'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 0.73

Table S202.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
LMOD2 MUTATED 1 2 3
LMOD2 WILD-TYPE 172 206 113
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.71

Table S203.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
LMOD2 MUTATED 1 2 2 1
LMOD2 WILD-TYPE 212 69 122 85
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.65 (Fisher's exact test), Q value = 0.91

Table S204.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
LMOD2 MUTATED 1 2 1 1 1
LMOD2 WILD-TYPE 147 96 58 132 55
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S205.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
LMOD2 MUTATED 1 2 2 1
LMOD2 WILD-TYPE 64 91 76 83
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S206.  Gene #21: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
LMOD2 MUTATED 1 2 2 0 1
LMOD2 WILD-TYPE 74 86 67 23 64
'EHHADH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 0.91

Table S207.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
EHHADH MUTATED 1 0 2 2
EHHADH WILD-TYPE 107 91 96 193
'EHHADH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S208.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
EHHADH MUTATED 1 2 1 1
EHHADH WILD-TYPE 160 138 125 70
'EHHADH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.56

Table S209.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
EHHADH MUTATED 1 0 0 0 0 2
EHHADH WILD-TYPE 105 51 45 53 58 37
'EHHADH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S210.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
EHHADH MUTATED 0 1 1 1
EHHADH WILD-TYPE 75 113 92 69
'EHHADH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 0.91

Table S211.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
EHHADH MUTATED 0 2 1 2
EHHADH WILD-TYPE 96 140 150 106
'EHHADH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S212.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
EHHADH MUTATED 2 2 1
EHHADH WILD-TYPE 171 206 115
'EHHADH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.85

Table S213.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
EHHADH MUTATED 4 0 0 1
EHHADH WILD-TYPE 209 71 124 85
'EHHADH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 0.86

Table S214.  Gene #22: 'EHHADH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
EHHADH MUTATED 1 0 1 3 0
EHHADH WILD-TYPE 147 98 58 130 56
'MED12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S215.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
MED12 MUTATED 2 1 2 3
MED12 WILD-TYPE 106 90 96 192
'MED12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.88

Table S216.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
MED12 MUTATED 2 4 2 0
MED12 WILD-TYPE 159 136 124 71
'MED12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.984 (Fisher's exact test), Q value = 1

Table S217.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
MED12 MUTATED 2 1 0 1 1 1
MED12 WILD-TYPE 104 50 45 52 57 38
'MED12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S218.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
MED12 MUTATED 2 2 1 1
MED12 WILD-TYPE 73 112 92 69
'MED12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S219.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
MED12 MUTATED 2 2 2 2
MED12 WILD-TYPE 94 140 149 106
'MED12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.66

Table S220.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
MED12 MUTATED 1 6 1
MED12 WILD-TYPE 172 202 115
'MED12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S221.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
MED12 MUTATED 5 1 1 1
MED12 WILD-TYPE 208 70 123 85
'MED12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
MED12 MUTATED 3 1 0 3 1
MED12 WILD-TYPE 145 97 59 130 55
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.88

Table S223.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
MED12 MUTATED 1 1 2 0
MED12 WILD-TYPE 64 92 76 84
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'MED12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
MED12 MUTATED 2 1 1 0 0
MED12 WILD-TYPE 73 87 68 23 65
'ZNF709 MUTATION STATUS' versus 'CN_CNMF'

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

Table S225.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
ZNF709 MUTATED 1 0 1 3
ZNF709 WILD-TYPE 107 91 97 192
'ZNF709 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 0.67

Table S226.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
ZNF709 MUTATED 2 0 1 2
ZNF709 WILD-TYPE 159 140 125 69
'ZNF709 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.51

Table S227.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
ZNF709 MUTATED 0 1 0 2 0 1
ZNF709 WILD-TYPE 106 50 45 51 58 38
'ZNF709 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.097 (Fisher's exact test), Q value = 0.49

Table S228.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
ZNF709 MUTATED 0 0 3 1
ZNF709 WILD-TYPE 75 114 90 69
'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 0.91

Table S229.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
ZNF709 MUTATED 0 2 1 2
ZNF709 WILD-TYPE 96 140 150 106
'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S230.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
ZNF709 MUTATED 2 1 2
ZNF709 WILD-TYPE 171 207 114
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.51

Table S231.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
ZNF709 MUTATED 1 0 1 3
ZNF709 WILD-TYPE 212 71 123 83
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.67

Table S232.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
ZNF709 MUTATED 1 0 0 2 2
ZNF709 WILD-TYPE 147 98 59 131 54
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 0.73

Table S233.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
ZNF709 MUTATED 1 1 0 3
ZNF709 WILD-TYPE 64 92 78 81
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.71

Table S234.  Gene #24: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
ZNF709 MUTATED 1 1 0 0 3
ZNF709 WILD-TYPE 74 87 69 23 62
'TCEB3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S235.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
TCEB3 MUTATED 1 1 0 2
TCEB3 WILD-TYPE 107 90 98 193
'TCEB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.86

Table S236.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
TCEB3 MUTATED 2 0 2 0
TCEB3 WILD-TYPE 159 140 124 71
'TCEB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.71

Table S237.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
TCEB3 MUTATED 0 0 0 1 1 1
TCEB3 WILD-TYPE 106 51 45 52 57 38
'TCEB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 0.88

Table S238.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
TCEB3 MUTATED 0 1 2 0
TCEB3 WILD-TYPE 75 113 91 70
'TCEB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.66

Table S239.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
TCEB3 MUTATED 0 2 0 2
TCEB3 WILD-TYPE 96 140 151 106
'TCEB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.3

Table S240.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
TCEB3 MUTATED 1 0 3
TCEB3 WILD-TYPE 172 208 113

Figure S44.  Get High-res Image Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S241.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
TCEB3 MUTATED 2 1 1 0
TCEB3 WILD-TYPE 211 70 123 86
'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.6

Table S242.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
TCEB3 MUTATED 1 1 2 0 0
TCEB3 WILD-TYPE 147 97 57 133 56
'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.79

Table S243.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
TCEB3 MUTATED 1 2 0 0
TCEB3 WILD-TYPE 64 91 78 84
'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.71

Table S244.  Gene #25: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
TCEB3 MUTATED 1 1 0 1 0
TCEB3 WILD-TYPE 74 87 69 22 65
'MED15 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0844 (Fisher's exact test), Q value = 0.47

Table S245.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
MED15 MUTATED 3 0 3 1
MED15 WILD-TYPE 105 91 95 194
'MED15 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.55

Table S246.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
MED15 MUTATED 0 4 2 1
MED15 WILD-TYPE 161 136 124 70
'MED15 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.79

Table S247.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
MED15 MUTATED 1 2 0 1 0 1
MED15 WILD-TYPE 105 49 45 52 58 38
'MED15 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.577 (Fisher's exact test), Q value = 0.88

Table S248.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
MED15 MUTATED 0 2 1 2
MED15 WILD-TYPE 75 112 92 68
'MED15 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S249.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
MED15 MUTATED 1 1 3 2
MED15 WILD-TYPE 95 141 148 106
'MED15 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.66

Table S250.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
MED15 MUTATED 2 5 0
MED15 WILD-TYPE 171 203 116
'MED15 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S251.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
MED15 MUTATED 2 1 2 2
MED15 WILD-TYPE 211 70 122 84
'MED15 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.91

Table S252.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
MED15 MUTATED 2 1 0 2 2
MED15 WILD-TYPE 146 97 59 131 54
'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S253.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
MED15 MUTATED 1 3 1 1
MED15 WILD-TYPE 64 90 77 83
'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S254.  Gene #26: 'MED15 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
MED15 MUTATED 1 2 1 1 1
MED15 WILD-TYPE 74 86 68 22 64
'ERF MUTATION STATUS' versus 'CN_CNMF'

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

Table S255.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
ERF MUTATED 1 0 1 2
ERF WILD-TYPE 107 91 97 193
'ERF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.66

Table S256.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
ERF MUTATED 1 2 0 2
ERF WILD-TYPE 160 138 126 69
'ERF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.88

Table S257.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
ERF MUTATED 1 0 0 1 0 1
ERF WILD-TYPE 105 51 45 52 58 38
'ERF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0601 (Fisher's exact test), Q value = 0.45

Table S258.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
ERF MUTATED 1 0 0 2
ERF WILD-TYPE 74 114 93 68
'ERF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 0.8

Table S259.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
ERF MUTATED 1 0 3 1
ERF WILD-TYPE 95 142 148 107
'ERF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 0.91

Table S260.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
ERF MUTATED 2 3 0
ERF WILD-TYPE 171 205 116
'ERF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S261.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
ERF MUTATED 3 1 1 0
ERF WILD-TYPE 210 70 123 86
'ERF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.52

Table S262.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
ERF MUTATED 0 1 0 4 0
ERF WILD-TYPE 148 97 59 129 56
'ERF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 0.91

Table S263.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
ERF MUTATED 0 2 0 1
ERF WILD-TYPE 65 91 78 83
'ERF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 0.93

Table S264.  Gene #27: 'ERF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
ERF MUTATED 1 2 0 0 0
ERF WILD-TYPE 74 86 69 23 65
'ERN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.77

Table S265.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
ERN1 MUTATED 0 0 2 2
ERN1 WILD-TYPE 108 91 96 193
'ERN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.21

Table S266.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
ERN1 MUTATED 0 4 0 0
ERN1 WILD-TYPE 161 136 126 71

Figure S45.  Get High-res Image Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ERN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.66

Table S267.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
ERN1 MUTATED 0 0 3 1
ERN1 WILD-TYPE 96 142 148 107
'ERN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.88

Table S268.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
ERN1 MUTATED 1 3 0
ERN1 WILD-TYPE 172 205 116
'ERN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.71

Table S269.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
ERN1 MUTATED 4 0 0 0
ERN1 WILD-TYPE 209 71 124 86
'ERN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S270.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
ERN1 MUTATED 2 0 0 2 0
ERN1 WILD-TYPE 146 98 59 131 56
'ERN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0642 (Fisher's exact test), Q value = 0.45

Table S271.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
ERN1 MUTATED 0 3 0 0
ERN1 WILD-TYPE 65 90 78 84
'ERN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.52

Table S272.  Gene #28: 'ERN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
ERN1 MUTATED 0 3 0 0 0
ERN1 WILD-TYPE 75 85 69 23 65
'MLLT10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.59

Table S273.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
MLLT10 MUTATED 1 0 3 1
MLLT10 WILD-TYPE 107 91 95 194
'MLLT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.83

Table S274.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
MLLT10 MUTATED 3 1 0 1
MLLT10 WILD-TYPE 158 139 126 70
'MLLT10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 0.99

Table S275.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
MLLT10 MUTATED 1 0 0 1 1 1
MLLT10 WILD-TYPE 105 51 45 52 57 38
'MLLT10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.66 (Fisher's exact test), Q value = 0.91

Table S276.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
MLLT10 MUTATED 1 2 0 1
MLLT10 WILD-TYPE 74 112 93 69
'MLLT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S277.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
MLLT10 MUTATED 1 1 2 1
MLLT10 WILD-TYPE 95 141 149 107
'MLLT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 0.91

Table S278.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
MLLT10 MUTATED 2 3 0
MLLT10 WILD-TYPE 171 205 116
'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.92

Table S279.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
MLLT10 MUTATED 3 0 2 0
MLLT10 WILD-TYPE 210 71 122 86
'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 0.89

Table S280.  Gene #29: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
MLLT10 MUTATED 3 0 0 2 0
MLLT10 WILD-TYPE 145 98 59 131 56
'ZFHX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.79

Table S281.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
ZFHX3 MUTATED 3 2 6 5
ZFHX3 WILD-TYPE 105 89 92 190
'ZFHX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.59

Table S282.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
ZFHX3 MUTATED 3 8 2 3
ZFHX3 WILD-TYPE 158 132 124 68
'ZFHX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0815 (Fisher's exact test), Q value = 0.47

Table S283.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
ZFHX3 MUTATED 1 0 2 3 1 3
ZFHX3 WILD-TYPE 105 51 43 50 57 36
'ZFHX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 0.99

Table S284.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
ZFHX3 MUTATED 1 3 3 3
ZFHX3 WILD-TYPE 74 111 90 67
'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.64

Table S285.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
ZFHX3 MUTATED 4 3 8 1
ZFHX3 WILD-TYPE 92 139 143 107
'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 0.51

Table S286.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
ZFHX3 MUTATED 3 11 2
ZFHX3 WILD-TYPE 170 197 114
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.21

Table S287.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
ZFHX3 MUTATED 11 1 0 4
ZFHX3 WILD-TYPE 202 70 124 82

Figure S46.  Get High-res Image Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.71

Table S288.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
ZFHX3 MUTATED 3 2 1 6 4
ZFHX3 WILD-TYPE 145 96 58 127 52
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.79

Table S289.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
ZFHX3 MUTATED 0 4 3 3
ZFHX3 WILD-TYPE 65 89 75 81
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S290.  Gene #30: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
ZFHX3 MUTATED 2 4 2 0 2
ZFHX3 WILD-TYPE 73 84 67 23 63
'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.73

Table S291.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
ZMYM3 MUTATED 3 0 2 7
ZMYM3 WILD-TYPE 105 91 96 188
'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.041

Table S292.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
ZMYM3 MUTATED 1 2 2 7
ZMYM3 WILD-TYPE 160 138 124 64

Figure S47.  Get High-res Image Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZMYM3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.83

Table S293.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
ZMYM3 MUTATED 3 1 0 2 1 3
ZMYM3 WILD-TYPE 103 50 45 51 57 36
'ZMYM3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0513 (Fisher's exact test), Q value = 0.4

Table S294.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
ZMYM3 MUTATED 3 0 5 2
ZMYM3 WILD-TYPE 72 114 88 68
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0843 (Fisher's exact test), Q value = 0.47

Table S295.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
ZMYM3 MUTATED 0 4 7 1
ZMYM3 WILD-TYPE 96 138 144 107
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.55

Table S296.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
ZMYM3 MUTATED 1 7 4
ZMYM3 WILD-TYPE 172 201 112
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.37

Table S297.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
ZMYM3 MUTATED 10 1 1 0
ZMYM3 WILD-TYPE 203 70 123 86

Figure S48.  Get High-res Image Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 0.91

Table S298.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
ZMYM3 MUTATED 3 2 2 5 0
ZMYM3 WILD-TYPE 145 96 57 128 56
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.67

Table S299.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
ZMYM3 MUTATED 1 6 2 1
ZMYM3 WILD-TYPE 64 87 76 83
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 0.67

Table S300.  Gene #31: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
ZMYM3 MUTATED 4 4 1 1 0
ZMYM3 WILD-TYPE 71 84 68 22 65
'FMN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.88

Table S301.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
FMN1 MUTATED 2 0 1 1
FMN1 WILD-TYPE 106 91 97 194
'FMN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.64

Table S302.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
FMN1 MUTATED 1 1 0 2
FMN1 WILD-TYPE 160 139 126 69
'FMN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.88

Table S303.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
FMN1 MUTATED 1 0 0 1 0 1
FMN1 WILD-TYPE 105 51 45 52 58 38
'FMN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 0.91

Table S304.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
FMN1 MUTATED 1 0 1 1
FMN1 WILD-TYPE 74 114 92 69
'FMN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.66

Table S305.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
FMN1 MUTATED 0 0 3 1
FMN1 WILD-TYPE 96 142 148 107
'FMN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S306.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
FMN1 MUTATED 1 2 1
FMN1 WILD-TYPE 172 206 115
'FMN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S307.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
FMN1 MUTATED 3 0 1 0
FMN1 WILD-TYPE 210 71 123 86
'FMN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 0.62

Table S308.  Gene #32: 'FMN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
FMN1 MUTATED 0 0 1 2 1
FMN1 WILD-TYPE 148 98 58 131 55
'AKT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S309.  Gene #33: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
AKT1 MUTATED 1 0 1 1
AKT1 WILD-TYPE 107 91 97 194
'AKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.3

Table S310.  Gene #33: 'AKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
AKT1 MUTATED 0 0 3 0
AKT1 WILD-TYPE 161 140 123 71

Figure S49.  Get High-res Image Gene #33: 'AKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'AKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.77

Table S311.  Gene #33: 'AKT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
AKT1 MUTATED 0 2 0 1
AKT1 WILD-TYPE 96 140 151 107
'AKT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.61

Table S312.  Gene #33: 'AKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
AKT1 MUTATED 0 1 2
AKT1 WILD-TYPE 173 207 114
'AKT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 0.91

Table S313.  Gene #33: 'AKT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
AKT1 MUTATED 1 1 1 0
AKT1 WILD-TYPE 212 70 123 86
'AKT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S314.  Gene #33: 'AKT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
AKT1 MUTATED 1 1 0 1 0
AKT1 WILD-TYPE 147 97 59 132 56
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0712 (Fisher's exact test), Q value = 0.45

Table S315.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
ATM MUTATED 2 2 3 15
ATM WILD-TYPE 106 89 95 180
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.67

Table S316.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
ATM MUTATED 4 10 6 2
ATM WILD-TYPE 157 130 120 69
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S317.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
ATM MUTATED 3 3 2 3 4 2
ATM WILD-TYPE 103 48 43 50 54 37
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S318.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
ATM MUTATED 3 5 4 5
ATM WILD-TYPE 72 109 89 65
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.71

Table S319.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
ATM MUTATED 3 4 11 4
ATM WILD-TYPE 93 138 140 104
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.27

Table S320.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
ATM MUTATED 3 15 4
ATM WILD-TYPE 170 193 112

Figure S50.  Get High-res Image Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.71

Table S321.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
ATM MUTATED 10 6 4 2
ATM WILD-TYPE 203 65 120 84
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.66

Table S322.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
ATM MUTATED 3 8 2 6 3
ATM WILD-TYPE 145 90 57 127 53
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 0.91

Table S323.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
ATM MUTATED 2 4 6 4
ATM WILD-TYPE 63 89 72 80
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.86

Table S324.  Gene #34: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
ATM MUTATED 2 3 6 1 4
ATM WILD-TYPE 73 85 63 22 61
'STRC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 0.91

Table S325.  Gene #35: 'STRC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
STRC MUTATED 1 0 2 2
STRC WILD-TYPE 107 91 96 193
'STRC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.39

Table S326.  Gene #35: 'STRC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
STRC MUTATED 0 1 4 0
STRC WILD-TYPE 161 139 122 71

Figure S51.  Get High-res Image Gene #35: 'STRC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'STRC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 0.88

Table S327.  Gene #35: 'STRC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
STRC MUTATED 0 3 1 1
STRC WILD-TYPE 96 139 150 107
'STRC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.67

Table S328.  Gene #35: 'STRC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
STRC MUTATED 0 3 2
STRC WILD-TYPE 173 205 114
'STRC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.53

Table S329.  Gene #35: 'STRC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
STRC MUTATED 5 0 0 0
STRC WILD-TYPE 208 71 124 86
'STRC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0687 (Fisher's exact test), Q value = 0.45

Table S330.  Gene #35: 'STRC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
STRC MUTATED 0 0 2 2 1
STRC WILD-TYPE 148 98 57 131 55
'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 0.81

Table S331.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
APC MUTATED 2 0 2 6
APC WILD-TYPE 106 91 96 189
'APC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.66

Table S332.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
APC MUTATED 1 4 2 3
APC WILD-TYPE 160 136 124 68
'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.78

Table S333.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
APC MUTATED 1 0 0 0 2 1
APC WILD-TYPE 105 51 45 53 56 38
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S334.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
APC MUTATED 1 1 1 1
APC WILD-TYPE 74 113 92 69
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0712 (Fisher's exact test), Q value = 0.45

Table S335.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
APC MUTATED 0 2 7 1
APC WILD-TYPE 96 140 144 107
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.54

Table S336.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
APC MUTATED 1 7 2
APC WILD-TYPE 172 201 114
'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.71

Table S337.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
APC MUTATED 7 0 1 2
APC WILD-TYPE 206 71 123 84
'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.71

Table S338.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
APC MUTATED 1 1 2 4 2
APC WILD-TYPE 147 97 57 129 54
'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.88

Table S339.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
APC MUTATED 1 3 0 1
APC WILD-TYPE 64 90 78 83
'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 0.77

Table S340.  Gene #36: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
APC MUTATED 2 3 0 0 0
APC WILD-TYPE 73 85 69 23 65
'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 0.88

Table S341.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
ZFP36L2 MUTATED 2 0 1 1
ZFP36L2 WILD-TYPE 106 91 97 194
'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.79

Table S342.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
ZFP36L2 MUTATED 0 2 1 1
ZFP36L2 WILD-TYPE 161 138 125 70
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.092 (Fisher's exact test), Q value = 0.48

Table S343.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
ZFP36L2 MUTATED 0 0 1 2 0 0
ZFP36L2 WILD-TYPE 106 51 44 51 58 39
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S344.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
ZFP36L2 MUTATED 0 1 1 1
ZFP36L2 WILD-TYPE 75 113 92 69
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.66

Table S345.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
ZFP36L2 MUTATED 0 0 3 1
ZFP36L2 WILD-TYPE 96 142 148 107
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 0.88

Table S346.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
ZFP36L2 MUTATED 1 3 0
ZFP36L2 WILD-TYPE 172 205 116
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S347.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
ZFP36L2 MUTATED 2 0 1 0
ZFP36L2 WILD-TYPE 211 71 123 86
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test), Q value = 0.66

Table S348.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
ZFP36L2 MUTATED 0 0 0 2 1
ZFP36L2 WILD-TYPE 148 98 59 131 55
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.86

Table S349.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
ZFP36L2 MUTATED 0 1 0 2
ZFP36L2 WILD-TYPE 65 92 78 82
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 0.9

Table S350.  Gene #37: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
ZFP36L2 MUTATED 0 2 0 0 1
ZFP36L2 WILD-TYPE 75 86 69 23 64
'MYOT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 0.8

Table S351.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
MYOT MUTATED 1 0 2 1
MYOT WILD-TYPE 107 91 96 194
'MYOT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.27

Table S352.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
MYOT MUTATED 0 4 0 1
MYOT WILD-TYPE 161 136 126 70

Figure S52.  Get High-res Image Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MYOT MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.9

Table S353.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
MYOT MUTATED 1 0 0 0 1 1
MYOT WILD-TYPE 105 51 45 53 57 38
'MYOT MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.51

Table S354.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
MYOT MUTATED 0 0 1 2
MYOT WILD-TYPE 75 114 92 68
'MYOT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0602 (Fisher's exact test), Q value = 0.45

Table S355.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
MYOT MUTATED 1 0 4 0
MYOT WILD-TYPE 95 142 147 108
'MYOT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.71

Table S356.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
MYOT MUTATED 1 4 0
MYOT WILD-TYPE 172 204 116
'MYOT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.53

Table S357.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
MYOT MUTATED 5 0 0 0
MYOT WILD-TYPE 208 71 124 86
'MYOT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.52

Table S358.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
MYOT MUTATED 0 1 0 4 0
MYOT WILD-TYPE 148 97 59 129 56
'MYOT MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 0.92

Table S359.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
MYOT MUTATED 1 2 1 0
MYOT WILD-TYPE 64 91 77 84
'MYOT MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 0.81

Table S360.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
MYOT MUTATED 0 2 2 0 0
MYOT WILD-TYPE 75 86 67 23 65
'KIRREL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0997 (Fisher's exact test), Q value = 0.49

Table S361.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
KIRREL MUTATED 0 2 3 1
KIRREL WILD-TYPE 108 89 95 194
'KIRREL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.79

Table S362.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
KIRREL MUTATED 2 3 0 1
KIRREL WILD-TYPE 159 137 126 70
'KIRREL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S363.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
KIRREL MUTATED 2 0 0 1 0 0
KIRREL WILD-TYPE 104 51 45 52 58 39
'KIRREL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0852 (Fisher's exact test), Q value = 0.47

Table S364.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
KIRREL MUTATED 2 0 0 1
KIRREL WILD-TYPE 73 114 93 69
'KIRREL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.88

Table S365.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
KIRREL MUTATED 2 2 2 0
KIRREL WILD-TYPE 94 140 149 108
'KIRREL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S366.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
KIRREL MUTATED 3 3 0
KIRREL WILD-TYPE 170 205 116
'KIRREL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 0.9

Table S367.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
KIRREL MUTATED 2 0 2 2
KIRREL WILD-TYPE 211 71 122 84
'KIRREL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 0.9

Table S368.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
KIRREL MUTATED 3 0 0 2 1
KIRREL WILD-TYPE 145 98 59 131 55
'KIRREL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 0.96

Table S369.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
KIRREL MUTATED 1 2 0 1
KIRREL WILD-TYPE 64 91 78 83
'KIRREL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S370.  Gene #39: 'KIRREL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
KIRREL MUTATED 1 2 0 0 1
KIRREL WILD-TYPE 74 86 69 23 64
'PGBD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.67

Table S371.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
PGBD2 MUTATED 0 0 2 1
PGBD2 WILD-TYPE 108 91 96 194
'PGBD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 0.62

Table S372.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
PGBD2 MUTATED 0 2 0 1
PGBD2 WILD-TYPE 161 138 126 70
'PGBD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.51

Table S373.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
PGBD2 MUTATED 0 0 3 0
PGBD2 WILD-TYPE 96 142 148 108
'PGBD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.67

Table S374.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
PGBD2 MUTATED 0 3 0
PGBD2 WILD-TYPE 173 205 116
'PGBD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 0.97

Table S375.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
PGBD2 MUTATED 2 0 0 1
PGBD2 WILD-TYPE 211 71 124 85
'PGBD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.66

Table S376.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
PGBD2 MUTATED 0 0 0 2 1
PGBD2 WILD-TYPE 148 98 59 131 55
'PGBD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 0.91

Table S377.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
PGBD2 MUTATED 0 2 0 1
PGBD2 WILD-TYPE 65 91 78 83
'PGBD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 0.9

Table S378.  Gene #40: 'PGBD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
PGBD2 MUTATED 0 2 0 0 1
PGBD2 WILD-TYPE 75 86 69 23 64
'LOC100132247 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.71

Table S379.  Gene #41: 'LOC100132247 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
LOC100132247 MUTATED 1 1 1 0
LOC100132247 WILD-TYPE 107 90 97 195
'LOC100132247 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S380.  Gene #41: 'LOC100132247 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
LOC100132247 MUTATED 1 1 1 0
LOC100132247 WILD-TYPE 160 139 125 71
'LOC100132247 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S381.  Gene #41: 'LOC100132247 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
LOC100132247 MUTATED 0 1 1 1
LOC100132247 WILD-TYPE 96 141 150 107
'LOC100132247 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S382.  Gene #41: 'LOC100132247 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
LOC100132247 MUTATED 1 1 1
LOC100132247 WILD-TYPE 172 207 115
'LOC100132247 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S383.  Gene #41: 'LOC100132247 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
LOC100132247 MUTATED 2 0 1 0
LOC100132247 WILD-TYPE 211 71 123 86
'LOC100132247 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S384.  Gene #41: 'LOC100132247 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
LOC100132247 MUTATED 2 0 0 1 0
LOC100132247 WILD-TYPE 146 98 59 132 56
'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 0.86

Table S385.  Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
EMG1 MUTATED 2 0 0 2
EMG1 WILD-TYPE 106 91 98 193
'EMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.51

Table S386.  Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
EMG1 MUTATED 0 1 3 0
EMG1 WILD-TYPE 161 139 123 71
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 0.8

Table S387.  Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
EMG1 MUTATED 0 1 3 0
EMG1 WILD-TYPE 96 141 148 108
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.66

Table S388.  Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
EMG1 MUTATED 0 2 2
EMG1 WILD-TYPE 173 206 114
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.37

Table S389.  Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
EMG1 MUTATED 1 0 0 3
EMG1 WILD-TYPE 212 71 124 83

Figure S53.  Get High-res Image Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.041

Table S390.  Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
EMG1 MUTATED 0 0 1 0 3
EMG1 WILD-TYPE 148 98 58 133 53

Figure S54.  Get High-res Image Gene #42: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CDH16 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.83

Table S391.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
CDH16 MUTATED 2 1 0 1
CDH16 WILD-TYPE 106 90 98 194
'CDH16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.8

Table S392.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
CDH16 MUTATED 1 0 2 1
CDH16 WILD-TYPE 160 140 124 70
'CDH16 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 0.99

Table S393.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
CDH16 MUTATED 1 0 0 1 1 1
CDH16 WILD-TYPE 105 51 45 52 57 38
'CDH16 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.52

Table S394.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
CDH16 MUTATED 0 0 2 2
CDH16 WILD-TYPE 75 114 91 68
'CDH16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.53

Table S395.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
CDH16 MUTATED 0 3 0 1
CDH16 WILD-TYPE 96 139 151 107
'CDH16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.83

Table S396.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
CDH16 MUTATED 1 1 2
CDH16 WILD-TYPE 172 207 114
'CDH16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 0.66

Table S397.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
CDH16 MUTATED 1 0 3 0
CDH16 WILD-TYPE 212 71 121 86
'CDH16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.66

Table S398.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
CDH16 MUTATED 3 0 1 0 0
CDH16 WILD-TYPE 145 98 58 133 56
'CDH16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.79

Table S399.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
CDH16 MUTATED 1 2 0 0
CDH16 WILD-TYPE 64 91 78 84
'CDH16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.554 (Fisher's exact test), Q value = 0.88

Table S400.  Gene #43: 'CDH16 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
CDH16 MUTATED 2 1 0 0 0
CDH16 WILD-TYPE 73 87 69 23 65
'KRT25 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 0.9

Table S401.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
KRT25 MUTATED 0 1 2 3
KRT25 WILD-TYPE 108 90 96 192
'KRT25 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0803 (Fisher's exact test), Q value = 0.47

Table S402.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 140 126 71
KRT25 MUTATED 1 0 4 1
KRT25 WILD-TYPE 160 140 122 70
'KRT25 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S403.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 106 51 45 53 58 39
KRT25 MUTATED 1 0 1 1 1 1
KRT25 WILD-TYPE 105 51 44 52 57 38
'KRT25 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 0.88

Table S404.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 75 114 93 70
KRT25 MUTATED 0 2 1 2
KRT25 WILD-TYPE 75 112 92 68
'KRT25 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.56

Table S405.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 142 151 108
KRT25 MUTATED 0 4 2 0
KRT25 WILD-TYPE 96 138 149 108
'KRT25 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S406.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 208 116
KRT25 MUTATED 2 2 2
KRT25 WILD-TYPE 171 206 114
'KRT25 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.68

Table S407.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 71 124 86
KRT25 MUTATED 4 0 0 2
KRT25 WILD-TYPE 209 71 124 84
'KRT25 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.057

Table S408.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 148 98 59 133 56
KRT25 MUTATED 0 0 4 2 0
KRT25 WILD-TYPE 148 98 55 131 56

Figure S55.  Get High-res Image Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KRT25 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 0.91

Table S409.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 93 78 84
KRT25 MUTATED 1 2 0 2
KRT25 WILD-TYPE 64 91 78 82
'KRT25 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.59

Table S410.  Gene #44: 'KRT25 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 88 69 23 65
KRT25 MUTATED 0 3 0 1 1
KRT25 WILD-TYPE 75 85 69 22 64
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/PRAD-TP/22592902/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/22553796/PRAD-TP.transferedmergedcluster.txt

  • Number of patients = 498

  • Number of significantly mutated genes = 44

  • 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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