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 62 genes and 8 molecular subtypes across 425 patients, 30 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',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • PTEN mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • ATM mutation correlated to 'CN_CNMF'.

  • PIK3CA mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • KDM6A mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • IDH1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • SMG7 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • EMG1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • MYOT mutation correlated to 'METHLYATION_CNMF'.

  • EDC4 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • CDK12 mutation correlated to 'CN_CNMF'.

  • DNMT3B mutation correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 62 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 30 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
FOXA1 25 (6%) 400 0.00012
(0.00595) 		1e-05
(0.000709) 		1e-05
(0.000709) 		3e-05
(0.00186) 		0.00579
(0.143) 		0.00665
(0.143) 		0.511
(1.00) 		0.593
(1.00)
SPOP 48 (11%) 377 1e-05
(0.000709) 		1e-05
(0.000709) 		1e-05
(0.000709) 		1e-05
(0.000709) 		0.68
(1.00) 		0.0372
(0.409) 		0.334
(0.858) 		0.193
(0.765)
TP53 43 (10%) 382 1e-05
(0.000709) 		0.00622
(0.143) 		0.00019
(0.00857) 		5e-05
(0.00276) 		0.773
(1.00) 		0.0571
(0.566) 		0.16
(0.727) 		0.041
(0.422)
KDM6A 9 (2%) 416 0.0105
(0.187) 		0.0869
(0.612) 		0.00158
(0.0603) 		0.0696
(0.589) 		0.54
(1.00) 		0.136
(0.7) 		0.149
(0.72) 		0.0111
(0.19)
IDH1 5 (1%) 420 0.00427
(0.118) 		0.0026
(0.0921) 		0.00658
(0.143) 		0.0294
(0.355) 		0.201
(0.765) 		0.078
(0.605) 		1
(1.00) 		0.0769
(0.605)
PIK3CA 11 (3%) 414 0.141
(0.712) 		0.00916
(0.168) 		0.156
(0.725) 		0.013
(0.215) 		0.23
(0.775) 		0.0322
(0.371) 		0.458
(0.944) 		0.221
(0.768)
PTEN 14 (3%) 411 0.557
(1.00) 		0.168
(0.739) 		0.0999
(0.649) 		0.00708
(0.146) 		0.657
(1.00) 		0.236
(0.775) 		0.527
(1.00) 		0.149
(0.72)
ATM 19 (4%) 406 0.00512
(0.134) 		0.167
(0.739) 		0.445
(0.94) 		0.0765
(0.605) 		0.0603
(0.575) 		0.278
(0.815) 		0.811
(1.00) 		0.387
(0.888)
SMG7 7 (2%) 418 0.874
(1.00) 		0.31
(0.834) 		0.0748
(0.605) 		0.00297
(0.0921) 		0.0727
(0.601) 		0.0913
(0.612) 		1
(1.00) 		0.68
(1.00)
EMG1 4 (1%) 421 0.493
(0.974) 		0.274
(0.812) 		0.554
(1.00) 		0.235
(0.775) 		0.0373
(0.409) 		0.00286
(0.0921)
MYOT 4 (1%) 421 0.553
(1.00) 		0.00891
(0.168) 		0.213
(0.765) 		0.459
(0.944) 		0.462
(0.946) 		0.126
(0.688) 		0.211
(0.765) 		0.192
(0.765)
EDC4 3 (1%) 422 0.0701
(0.589) 		0.206
(0.765) 		1
(1.00) 		0.467
(0.954) 		0.512
(1.00) 		0.00388
(0.113) 		0.17
(0.739) 		0.641
(1.00)
CDK12 8 (2%) 417 0.00132
(0.0546) 		0.18
(0.765) 		0.668
(1.00) 		0.12
(0.67) 		0.398
(0.891) 		0.452
(0.943) 		0.318
(0.842) 		0.703
(1.00)
DNMT3B 4 (1%) 421 0.809
(1.00) 		0.00889
(0.168) 		0.215
(0.766) 		0.0877
(0.612) 		1
(1.00) 		0.856
(1.00) 		0.211
(0.765) 		0.469
(0.954)
CTNNB1 11 (3%) 414 0.158
(0.725) 		0.0304
(0.359) 		0.293
(0.822) 		0.219
(0.768) 		0.0998
(0.649) 		0.0172
(0.259) 		0.174
(0.748) 		0.0896
(0.612)
BRAF 8 (2%) 417 0.325
(0.852) 		0.0394
(0.415) 		0.202
(0.765) 		0.102
(0.649) 		1
(1.00) 		0.576
(1.00) 		0.652
(1.00) 		0.383
(0.886)
HRAS 5 (1%) 420 0.829
(1.00) 		0.535
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.411
(0.9) 		0.246
(0.788) 		0.752
(1.00)
ZMYM3 9 (2%) 416 0.719
(1.00) 		0.371
(0.884) 		0.145
(0.72) 		0.2
(0.765) 		0.202
(0.765) 		0.652
(1.00) 		0.157
(0.725) 		0.0913
(0.612)
EHHADH 5 (1%) 420 0.473
(0.957) 		0.868
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.291
(0.822)
TP53BP1 7 (2%) 418 0.129
(0.688) 		0.514
(1.00) 		0.895
(1.00) 		0.201
(0.765) 		1
(1.00) 		0.648
(1.00) 		0.525
(1.00) 		0.384
(0.886)
CNTNAP1 7 (2%) 418 0.206
(0.765) 		0.311
(0.834) 		0.35
(0.88) 		0.705
(1.00) 		0.715
(1.00) 		0.0254
(0.34)
BMP2K 6 (1%) 419 0.441
(0.936) 		0.693
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.699
(1.00) 		0.306
(0.834) 		0.535
(1.00)
RPTN 6 (1%) 419 0.089
(0.612) 		0.453
(0.943) 		1
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.0815
(0.612) 		0.417
(0.9) 		0.705
(1.00)
TCEB3 4 (1%) 421 0.807
(1.00) 		0.556
(1.00) 		0.271
(0.812) 		0.0417
(0.422) 		0.156
(0.725) 		0.195
(0.765) 		0.414
(0.9) 		0.571
(1.00)
NTM 6 (1%) 419 1
(1.00) 		0.876
(1.00) 		0.195
(0.765) 		0.58
(1.00) 		0.777
(1.00) 		0.728
(1.00) 		0.359
(0.884) 		0.755
(1.00)
MED12 7 (2%) 418 0.107
(0.651) 		0.799
(1.00) 		0.896
(1.00) 		0.235
(0.775) 		0.634
(1.00) 		0.957
(1.00) 		0.212
(0.765) 		0.796
(1.00)
MED15 6 (1%) 419 0.44
(0.936) 		0.0872
(0.612) 		0.877
(1.00) 		0.293
(0.822) 		0.878
(1.00) 		0.698
(1.00) 		0.933
(1.00) 		0.554
(1.00)
ERN1 3 (1%) 422 0.225
(0.771) 		0.0288
(0.355) 		0.406
(0.895) 		0.79
(1.00) 		0.778
(1.00) 		0.915
(1.00)
LMOD2 5 (1%) 420 1
(1.00) 		1
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.743
(1.00) 		0.738
(1.00) 		0.6
(1.00) 		0.653
(1.00)
FAM111A 3 (1%) 422 1
(1.00) 		0.529
(1.00) 		0.109
(0.651) 		0.257
(0.812) 		0.779
(1.00) 		0.106
(0.651)
ZNF709 5 (1%) 420 0.226
(0.771) 		1
(1.00) 		0.281
(0.82) 		0.639
(1.00) 		0.862
(1.00) 		0.263
(0.812) 		0.637
(1.00) 		0.704
(1.00)
MLLT10 4 (1%) 421 0.808
(1.00) 		0.165
(0.739) 		1
(1.00) 		0.683
(1.00) 		0.269
(0.812) 		0.648
(1.00)
TNRC18 6 (1%) 419 0.851
(1.00) 		0.873
(1.00) 		0.689
(1.00) 		0.394
(0.891) 		0.683
(1.00) 		0.554
(1.00) 		0.721
(1.00) 		0.75
(1.00)
GAGE2D 3 (1%) 422 0.754
(1.00) 		0.0675
(0.587) 		0.0269
(0.342) 		0.0614
(0.575) 		0.64
(1.00) 		0.372
(0.884)
LAMA3 7 (2%) 418 0.367
(0.884) 		0.267
(0.812) 		0.35
(0.88) 		0.702
(1.00) 		1
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.645
(1.00)
RPL11 4 (1%) 421 0.632
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.819
(1.00)
ZFHX3 13 (3%) 412 0.114
(0.657) 		0.221
(0.768) 		0.128
(0.688) 		0.108
(0.651) 		0.288
(0.822) 		0.492
(0.974) 		0.317
(0.842) 		0.99
(1.00)
MUC17 25 (6%) 400 0.136
(0.7) 		0.117
(0.662) 		0.084
(0.612) 		0.341
(0.867) 		0.0825
(0.612) 		0.795
(1.00) 		0.955
(1.00) 		0.286
(0.822)
CDKN1B 5 (1%) 420 1
(1.00) 		0.866
(1.00) 		0.384
(0.886) 		0.15
(0.72) 		0.275
(0.812) 		0.102
(0.649) 		0.7
(1.00) 		0.369
(0.884)
POM121 3 (1%) 422 0.755
(1.00) 		0.412
(0.9) 		0.403
(0.895) 		0.621
(1.00) 		0.2
(0.765) 		0.617
(1.00)
ESCO1 4 (1%) 421 0.636
(1.00) 		0.842
(1.00) 		0.113
(0.657) 		0.132
(0.699) 		0.268
(0.812) 		0.433
(0.929)
L1CAM 7 (2%) 418 0.578
(1.00) 		0.0264
(0.342) 		0.404
(0.895) 		0.201
(0.765) 		1
(1.00) 		0.0202
(0.295) 		0.245
(0.788) 		0.254
(0.807)
FAM47C 9 (2%) 416 0.128
(0.688) 		0.481
(0.964) 		0.837
(1.00) 		0.58
(1.00) 		0.538
(1.00) 		0.39
(0.891) 		0.87
(1.00) 		0.375
(0.884)
CR1L 5 (1%) 420 0.691
(1.00) 		0.455
(0.944) 		0.63
(1.00) 		0.151
(0.722) 		0.633
(1.00) 		0.928
(1.00)
FAM120B 3 (1%) 422 0.227
(0.771) 		1
(1.00) 		0.645
(1.00) 		0.788
(1.00) 		0.293
(0.822) 		0.0165
(0.256)
KIRREL 5 (1%) 420 1
(1.00) 		0.742
(1.00) 		0.449
(0.943) 		0.375
(0.884) 		1
(1.00) 		0.693
(1.00) 		0.782
(1.00) 		1
(1.00)
TCERG1 4 (1%) 421 1
(1.00) 		0.331
(0.858) 		0.272
(0.812) 		0.56
(1.00) 		0.837
(1.00) 		0.308
(0.834) 		0.913
(1.00) 		0.0164
(0.256)
SLC16A6 4 (1%) 421 0.808
(1.00) 		0.273
(0.812) 		0.399
(0.891) 		0.065
(0.587) 		0.0379
(0.409) 		0.355
(0.884) 		0.697
(1.00) 		0.679
(1.00)
NKX3-1 5 (1%) 420 0.375
(0.884) 		0.629
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.137
(0.7) 		0.508
(1)
RNF17 3 (1%) 422 0.756
(1.00) 		0.777
(1.00) 		0.11
(0.651) 		0.185
(0.765) 		0.639
(1.00) 		0.524
(1.00)
KYNU 3 (1%) 422 0.557
(1.00) 		0.416
(0.9) 		0.203
(0.765) 		0.788
(1.00) 		1
(1.00) 		0.442
(0.936)
LARP1 4 (1%) 421 0.632
(1.00) 		0.842
(1.00) 		0.27
(0.812) 		0.834
(1.00) 		1
(1.00) 		0.678
(1.00)
ACPT 3 (1%) 422 0.372
(0.884) 		0.652
(1.00) 		0.303
(0.832) 		0.351
(0.88) 		0.398
(0.891) 		0.522
(1.00) 		0.479
(0.964) 		0.876
(1.00)
AP4B1 5 (1%) 420 0.369
(0.884) 		0.242
(0.785) 		0.331
(0.858) 		0.85
(1.00) 		1
(1.00) 		0.674
(1.00)
RAG1 9 (2%) 416 0.802
(1.00) 		0.482
(0.964) 		0.533
(1.00) 		0.912
(1.00) 		0.272
(0.812) 		0.613
(1.00) 		0.21
(0.765) 		0.302
(0.832)
APC 9 (2%) 416 0.0654
(0.587) 		0.202
(0.765) 		0.485
(0.966) 		0.239
(0.779) 		0.0234
(0.331) 		0.341
(0.867) 		0.169
(0.739) 		0.718
(1.00)
MSLNL 4 (1%) 421 0.807
(1.00) 		0.117
(0.662) 		0.84
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.232
(0.775)
GAB2 5 (1%) 420 1
(1.00) 		0.867
(1.00) 		1
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.291
(0.822) 		0.65
(1.00) 		0.679
(1.00)
NCKAP1L 5 (1%) 420 0.688
(1.00) 		0.109
(0.651) 		0.381
(0.886) 		0.22
(0.768) 		1
(1.00) 		0.652
(1.00)
PRTFDC1 3 (1%) 422 0.754
(1.00) 		1
(1.00) 		1
(1.00) 		0.0606
(0.575) 		0.0241
(0.331) 		0.304
(0.832)
PCSK5 6 (1%) 419 0.369
(0.884) 		0.0671
(0.587) 		0.332
(0.858) 		0.143
(0.717) 		0.68
(1.00) 		0.972
(1.00)
ITGA2B 4 (1%) 421 0.376
(0.884) 		1
(1.00) 		0.397
(0.891) 		0.295
(0.822) 		0.211
(0.765) 		0.319
(0.842) 		0.877
(1.00) 		0.677
(1.00)
'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
SPOP MUTATED 6 13 27
SPOP WILD-TYPE 240 87 47

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 = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
SPOP MUTATED 8 39 1
SPOP WILD-TYPE 134 93 150

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

'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
SPOP MUTATED 8 40 0
SPOP WILD-TYPE 120 103 153

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

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
SPOP MUTATED 7 41 0
SPOP WILD-TYPE 146 126 104

Figure S4.  Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
SPOP MUTATED 14 14 20
SPOP WILD-TYPE 130 109 134
'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
SPOP MUTATED 13 9 1 17 8
SPOP WILD-TYPE 123 72 51 79 48

Figure S5.  Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
SPOP MUTATED 4 11 3 11
SPOP WILD-TYPE 55 63 42 69
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
SPOP MUTATED 6 5 1 10 0 7
SPOP WILD-TYPE 58 24 20 50 25 52
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

Table S9.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
TP53 MUTATED 12 29 2
TP53 WILD-TYPE 234 71 72

Figure S6.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
TP53 MUTATED 10 8 25
TP53 WILD-TYPE 132 124 126

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0086

Table S11.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
TP53 MUTATED 6 9 28
TP53 WILD-TYPE 122 134 125

Figure S8.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0028

Table S12.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
TP53 MUTATED 9 10 24
TP53 WILD-TYPE 144 157 80

Figure S9.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
TP53 MUTATED 14 11 18
TP53 WILD-TYPE 130 112 136
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0571 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
TP53 MUTATED 10 4 10 12 7
TP53 WILD-TYPE 126 77 42 84 49
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
TP53 MUTATED 2 10 6 10
TP53 WILD-TYPE 57 64 39 70
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.42

Table S16.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
TP53 MUTATED 6 1 6 8 0 7
TP53 WILD-TYPE 58 28 15 52 25 52

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

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
PTEN MUTATED 7 5 2
PTEN WILD-TYPE 239 95 72
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.74

Table S18.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
PTEN MUTATED 2 4 8
PTEN WILD-TYPE 140 128 143
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0999 (Fisher's exact test), Q value = 0.65

Table S19.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
PTEN MUTATED 1 5 8
PTEN WILD-TYPE 127 138 145
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00708 (Fisher's exact test), Q value = 0.15

Table S20.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
PTEN MUTATED 1 5 8
PTEN WILD-TYPE 152 162 96

Figure S11.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
PTEN MUTATED 4 3 7
PTEN WILD-TYPE 140 120 147
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 0.77

Table S22.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
PTEN MUTATED 5 1 0 4 4
PTEN WILD-TYPE 131 80 52 92 52
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
PTEN MUTATED 1 5 1 3
PTEN WILD-TYPE 58 69 44 77
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.72

Table S24.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
PTEN MUTATED 1 0 0 6 0 3
PTEN WILD-TYPE 63 29 21 54 25 56
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.73

Table S25.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
CTNNB1 MUTATED 4 3 4
CTNNB1 WILD-TYPE 242 97 70
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.36

Table S26.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
CTNNB1 MUTATED 0 5 6
CTNNB1 WILD-TYPE 142 127 145

Figure S12.  Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.82

Table S27.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
CTNNB1 MUTATED 1 5 5
CTNNB1 WILD-TYPE 127 138 148
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.77

Table S28.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
CTNNB1 MUTATED 2 4 5
CTNNB1 WILD-TYPE 151 163 99
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0998 (Fisher's exact test), Q value = 0.65

Table S29.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
CTNNB1 MUTATED 1 3 7
CTNNB1 WILD-TYPE 143 120 147
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.26

Table S30.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
CTNNB1 MUTATED 1 0 1 6 3
CTNNB1 WILD-TYPE 135 81 51 90 53

Figure S13.  Get High-res Image Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.75

Table S31.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
CTNNB1 MUTATED 0 4 0 3
CTNNB1 WILD-TYPE 59 70 45 77
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0896 (Fisher's exact test), Q value = 0.61

Table S32.  Gene #4: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
CTNNB1 MUTATED 0 0 0 5 0 2
CTNNB1 WILD-TYPE 64 29 21 55 25 57
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.006

Table S33.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
FOXA1 MUTATED 5 9 10
FOXA1 WILD-TYPE 241 91 64

Figure S14.  Get High-res Image Gene #5: '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 = 0.00071

Table S34.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
FOXA1 MUTATED 2 22 1
FOXA1 WILD-TYPE 140 110 150

Figure S15.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

Table S35.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
FOXA1 MUTATED 4 20 1
FOXA1 WILD-TYPE 124 123 152

Figure S16.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0019

Table S36.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
FOXA1 MUTATED 3 21 1
FOXA1 WILD-TYPE 150 146 103

Figure S17.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00579 (Fisher's exact test), Q value = 0.14

Table S37.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
FOXA1 MUTATED 4 4 17
FOXA1 WILD-TYPE 140 119 137

Figure S18.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00665 (Fisher's exact test), Q value = 0.14

Table S38.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
FOXA1 MUTATED 2 7 1 11 4
FOXA1 WILD-TYPE 134 74 51 85 52

Figure S19.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
FOXA1 MUTATED 2 2 1 6
FOXA1 WILD-TYPE 57 72 44 74
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
FOXA1 MUTATED 2 1 0 3 0 5
FOXA1 WILD-TYPE 62 28 21 57 25 54
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.13

Table S41.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ATM MUTATED 5 10 4
ATM WILD-TYPE 241 90 70

Figure S20.  Get High-res Image Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.74

Table S42.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ATM MUTATED 3 9 7
ATM WILD-TYPE 139 123 144
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.94

Table S43.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ATM MUTATED 4 9 6
ATM WILD-TYPE 124 134 147
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0765 (Fisher's exact test), Q value = 0.6

Table S44.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ATM MUTATED 3 12 4
ATM WILD-TYPE 150 155 100
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0603 (Fisher's exact test), Q value = 0.57

Table S45.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ATM MUTATED 2 8 9
ATM WILD-TYPE 142 115 145
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 0.82

Table S46.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ATM MUTATED 3 7 2 4 3
ATM WILD-TYPE 133 74 50 92 53
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
ATM MUTATED 2 3 3 5
ATM WILD-TYPE 57 71 42 75
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.89

Table S48.  Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
ATM MUTATED 1 3 2 3 1 3
ATM WILD-TYPE 63 26 19 57 24 56
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.71

Table S49.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
PIK3CA MUTATED 6 5 0
PIK3CA WILD-TYPE 240 95 74
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00916 (Fisher's exact test), Q value = 0.17

Table S50.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
PIK3CA MUTATED 0 3 8
PIK3CA WILD-TYPE 142 129 143

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

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.73

Table S51.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
PIK3CA MUTATED 1 3 7
PIK3CA WILD-TYPE 127 140 146
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.21

Table S52.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
PIK3CA MUTATED 1 3 7
PIK3CA WILD-TYPE 152 164 97

Figure S22.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.77

Table S53.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
PIK3CA MUTATED 2 2 7
PIK3CA WILD-TYPE 142 121 147
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.37

Table S54.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
PIK3CA MUTATED 1 0 2 5 3
PIK3CA WILD-TYPE 135 81 50 91 53

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

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.94

Table S55.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
PIK3CA MUTATED 1 3 0 4
PIK3CA WILD-TYPE 58 71 45 76
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.77

Table S56.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
PIK3CA MUTATED 0 0 1 4 1 2
PIK3CA WILD-TYPE 64 29 20 56 24 57
'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.85

Table S57.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
BRAF MUTATED 4 1 3
BRAF WILD-TYPE 242 99 71
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.42

Table S58.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
BRAF MUTATED 3 5 0
BRAF WILD-TYPE 139 127 151

Figure S24.  Get High-res Image Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.77

Table S59.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
BRAF MUTATED 2 5 1
BRAF WILD-TYPE 126 138 152
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 0.65

Table S60.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
BRAF MUTATED 2 6 0
BRAF WILD-TYPE 151 161 104
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
BRAF MUTATED 3 2 3
BRAF WILD-TYPE 141 121 151
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
BRAF MUTATED 4 1 0 3 0
BRAF WILD-TYPE 132 80 52 93 56
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
BRAF MUTATED 0 2 1 1
BRAF WILD-TYPE 59 72 44 79
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.89

Table S64.  Gene #8: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
BRAF MUTATED 0 0 1 2 0 1
BRAF WILD-TYPE 64 29 20 58 25 58
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
HRAS MUTATED 4 1 0
HRAS WILD-TYPE 242 99 74
'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
HRAS MUTATED 3 1 1
HRAS WILD-TYPE 139 131 150
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
HRAS MUTATED 2 2 1
HRAS WILD-TYPE 126 141 152
'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S68.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
HRAS MUTATED 2 2 1
HRAS WILD-TYPE 151 165 103
'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
HRAS MUTATED 2 2 1
HRAS WILD-TYPE 142 121 153
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 0.9

Table S70.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
HRAS MUTATED 2 0 0 3 0
HRAS WILD-TYPE 134 81 52 93 56
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.79

Table S71.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
HRAS MUTATED 1 0 2 1
HRAS WILD-TYPE 58 74 43 79
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
HRAS MUTATED 2 0 0 0 0 2
HRAS WILD-TYPE 62 29 21 60 25 57
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.19

Table S73.  Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
KDM6A MUTATED 2 2 5
KDM6A WILD-TYPE 244 98 69

Figure S25.  Get High-res Image Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0869 (Fisher's exact test), Q value = 0.61

Table S74.  Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
KDM6A MUTATED 2 6 1
KDM6A WILD-TYPE 140 126 150
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.06

Table S75.  Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
KDM6A MUTATED 0 8 1
KDM6A WILD-TYPE 128 135 152

Figure S26.  Get High-res Image Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0696 (Fisher's exact test), Q value = 0.59

Table S76.  Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
KDM6A MUTATED 1 7 1
KDM6A WILD-TYPE 152 160 103
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S77.  Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
KDM6A MUTATED 3 4 2
KDM6A WILD-TYPE 141 119 152
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.7

Table S78.  Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
KDM6A MUTATED 2 5 0 1 1
KDM6A WILD-TYPE 134 76 52 95 55
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.72

Table S79.  Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
KDM6A MUTATED 0 0 1 3
KDM6A WILD-TYPE 59 74 44 77
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
KDM6A MUTATED 0 3 0 0 0 1
KDM6A WILD-TYPE 64 26 21 60 25 58

Figure S27.  Get High-res Image Gene #10: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00427 (Fisher's exact test), Q value = 0.12

Table S81.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
IDH1 MUTATED 1 0 4
IDH1 WILD-TYPE 245 100 70

Figure S28.  Get High-res Image Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0026 (Fisher's exact test), Q value = 0.092

Table S82.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
IDH1 MUTATED 0 5 0
IDH1 WILD-TYPE 142 127 151

Figure S29.  Get High-res Image Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.14

Table S83.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
IDH1 MUTATED 0 5 0
IDH1 WILD-TYPE 128 138 153

Figure S30.  Get High-res Image Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.36

Table S84.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
IDH1 MUTATED 0 5 0
IDH1 WILD-TYPE 153 162 104

Figure S31.  Get High-res Image Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.77

Table S85.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
IDH1 MUTATED 0 3 2
IDH1 WILD-TYPE 144 120 152
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.078 (Fisher's exact test), Q value = 0.6

Table S86.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
IDH1 MUTATED 0 3 0 2 0
IDH1 WILD-TYPE 136 78 52 94 56
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S87.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
IDH1 MUTATED 1 1 1 1
IDH1 WILD-TYPE 58 73 44 79
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0769 (Fisher's exact test), Q value = 0.6

Table S88.  Gene #11: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
IDH1 MUTATED 0 2 0 1 1 0
IDH1 WILD-TYPE 64 27 21 59 24 59
'SMG7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S89.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
SMG7 MUTATED 5 1 1
SMG7 WILD-TYPE 241 99 73
'SMG7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.83

Table S90.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
SMG7 MUTATED 1 4 2
SMG7 WILD-TYPE 141 128 149
'SMG7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0748 (Fisher's exact test), Q value = 0.6

Table S91.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
SMG7 MUTATED 0 5 2
SMG7 WILD-TYPE 128 138 151
'SMG7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00297 (Fisher's exact test), Q value = 0.092

Table S92.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
SMG7 MUTATED 0 7 0
SMG7 WILD-TYPE 153 160 104

Figure S32.  Get High-res Image Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'SMG7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0727 (Fisher's exact test), Q value = 0.6

Table S93.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
SMG7 MUTATED 0 2 5
SMG7 WILD-TYPE 144 121 149
'SMG7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0913 (Fisher's exact test), Q value = 0.61

Table S94.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
SMG7 MUTATED 0 2 0 3 2
SMG7 WILD-TYPE 136 79 52 93 54
'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S95.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
SMG7 MUTATED 1 1 1 1
SMG7 WILD-TYPE 58 73 44 79
'SMG7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S96.  Gene #12: 'SMG7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
SMG7 MUTATED 0 1 0 2 0 1
SMG7 WILD-TYPE 64 28 21 58 25 58
'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S97.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ZMYM3 MUTATED 6 1 2
ZMYM3 WILD-TYPE 240 99 72
'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.88

Table S98.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ZMYM3 MUTATED 1 4 4
ZMYM3 WILD-TYPE 141 128 147
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.72

Table S99.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ZMYM3 MUTATED 2 1 6
ZMYM3 WILD-TYPE 126 142 147
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.77

Table S100.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ZMYM3 MUTATED 1 4 4
ZMYM3 WILD-TYPE 152 163 100
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.77

Table S101.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ZMYM3 MUTATED 2 1 6
ZMYM3 WILD-TYPE 142 122 148
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S102.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ZMYM3 MUTATED 3 1 2 3 0
ZMYM3 WILD-TYPE 133 80 50 93 56
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.73

Table S103.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
ZMYM3 MUTATED 2 4 1 0
ZMYM3 WILD-TYPE 57 70 44 80
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0913 (Fisher's exact test), Q value = 0.61

Table S104.  Gene #13: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
ZMYM3 MUTATED 1 0 0 4 2 0
ZMYM3 WILD-TYPE 63 29 21 56 23 59
'EHHADH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 0.96

Table S105.  Gene #14: 'EHHADH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
EHHADH MUTATED 4 0 1
EHHADH WILD-TYPE 242 100 73
'EHHADH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S106.  Gene #14: 'EHHADH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
EHHADH MUTATED 1 2 2
EHHADH WILD-TYPE 141 130 149
'EHHADH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S107.  Gene #14: 'EHHADH MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
EHHADH MUTATED 2 1 2
EHHADH WILD-TYPE 126 142 151
'EHHADH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S108.  Gene #14: 'EHHADH MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
EHHADH MUTATED 2 2 1
EHHADH WILD-TYPE 151 165 103
'EHHADH MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S109.  Gene #14: 'EHHADH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
EHHADH MUTATED 1 1 3
EHHADH WILD-TYPE 143 122 151
'EHHADH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 0.82

Table S110.  Gene #14: 'EHHADH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
EHHADH MUTATED 1 0 1 3 0
EHHADH WILD-TYPE 135 81 51 93 56
'TP53BP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.69

Table S111.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
TP53BP1 MUTATED 2 2 3
TP53BP1 WILD-TYPE 244 98 71
'TP53BP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S112.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
TP53BP1 MUTATED 3 3 1
TP53BP1 WILD-TYPE 139 129 150
'TP53BP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S113.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
TP53BP1 MUTATED 2 3 2
TP53BP1 WILD-TYPE 126 140 151
'TP53BP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.77

Table S114.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
TP53BP1 MUTATED 2 5 0
TP53BP1 WILD-TYPE 151 162 104
'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S115.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
TP53BP1 MUTATED 2 2 3
TP53BP1 WILD-TYPE 142 121 151
'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S116.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
TP53BP1 MUTATED 2 2 0 3 0
TP53BP1 WILD-TYPE 134 79 52 93 56
'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 1

Table S117.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
TP53BP1 MUTATED 0 3 1 2
TP53BP1 WILD-TYPE 59 71 44 78
'TP53BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.89

Table S118.  Gene #15: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
TP53BP1 MUTATED 2 2 0 2 0 0
TP53BP1 WILD-TYPE 62 27 21 58 25 59
'CNTNAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.77

Table S119.  Gene #16: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
CNTNAP1 MUTATED 2 3 1
CNTNAP1 WILD-TYPE 244 97 73
'CNTNAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.83

Table S120.  Gene #16: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
CNTNAP1 MUTATED 1 4 2
CNTNAP1 WILD-TYPE 141 128 149
'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.88

Table S121.  Gene #16: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
CNTNAP1 MUTATED 2 4 1
CNTNAP1 WILD-TYPE 126 139 152
'CNTNAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S122.  Gene #16: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
CNTNAP1 MUTATED 2 4 1
CNTNAP1 WILD-TYPE 151 163 103
'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S123.  Gene #16: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
CNTNAP1 MUTATED 3 1 3
CNTNAP1 WILD-TYPE 141 122 151
'CNTNAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.34

Table S124.  Gene #16: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
CNTNAP1 MUTATED 0 0 1 4 2
CNTNAP1 WILD-TYPE 136 81 51 92 54

Figure S33.  Get High-res Image Gene #16: 'CNTNAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BMP2K MUTATION STATUS' versus 'CN_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.94

Table S125.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
BMP2K MUTATED 5 0 1
BMP2K WILD-TYPE 241 100 73
'BMP2K MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S126.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
BMP2K MUTATED 1 2 3
BMP2K WILD-TYPE 141 130 148
'BMP2K MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S127.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
BMP2K MUTATED 1 3 2
BMP2K WILD-TYPE 127 140 151
'BMP2K MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S128.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
BMP2K MUTATED 2 3 1
BMP2K WILD-TYPE 151 164 103
'BMP2K MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.521 (Fisher's exact test), Q value = 1

Table S129.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
BMP2K MUTATED 1 3 2
BMP2K WILD-TYPE 143 120 152
'BMP2K MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S130.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
BMP2K MUTATED 2 1 0 1 2
BMP2K WILD-TYPE 134 80 52 95 54
'BMP2K MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.83

Table S131.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
BMP2K MUTATED 2 0 0 1
BMP2K WILD-TYPE 57 74 45 79
'BMP2K MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S132.  Gene #17: 'BMP2K MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
BMP2K MUTATED 1 0 0 0 1 1
BMP2K WILD-TYPE 63 29 21 60 24 58
'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.089 (Fisher's exact test), Q value = 0.61

Table S133.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
RPTN MUTATED 3 0 3
RPTN WILD-TYPE 243 100 71
'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.94

Table S134.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
RPTN MUTATED 2 3 1
RPTN WILD-TYPE 140 129 150
'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S135.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
RPTN MUTATED 2 2 2
RPTN WILD-TYPE 126 141 151
'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S136.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
RPTN MUTATED 2 3 1
RPTN WILD-TYPE 151 164 103
'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S137.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
RPTN MUTATED 2 1 3
RPTN WILD-TYPE 142 122 151
'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0815 (Fisher's exact test), Q value = 0.61

Table S138.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
RPTN MUTATED 1 0 0 2 3
RPTN WILD-TYPE 135 81 52 94 53
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.9

Table S139.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
RPTN MUTATED 0 2 0 3
RPTN WILD-TYPE 59 72 45 77
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S140.  Gene #18: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
RPTN MUTATED 1 0 0 1 0 3
RPTN WILD-TYPE 63 29 21 59 25 56
'TCEB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S141.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
TCEB3 MUTATED 2 1 1
TCEB3 WILD-TYPE 244 99 73
'TCEB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 1

Table S142.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
TCEB3 MUTATED 2 0 2
TCEB3 WILD-TYPE 140 132 149
'TCEB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.81

Table S143.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
TCEB3 MUTATED 1 0 3
TCEB3 WILD-TYPE 127 143 150
'TCEB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.42

Table S144.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
TCEB3 MUTATED 1 0 3
TCEB3 WILD-TYPE 152 167 101

Figure S34.  Get High-res Image Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.73

Table S145.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
TCEB3 MUTATED 3 1 0
TCEB3 WILD-TYPE 141 122 154
'TCEB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.77

Table S146.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
TCEB3 MUTATED 1 1 2 0 0
TCEB3 WILD-TYPE 135 80 50 96 56
'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.9

Table S147.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
TCEB3 MUTATED 1 2 0 0
TCEB3 WILD-TYPE 58 72 45 80
'TCEB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S148.  Gene #19: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
TCEB3 MUTATED 1 0 0 1 1 0
TCEB3 WILD-TYPE 63 29 21 59 24 59
'NTM MUTATION STATUS' versus 'CN_CNMF'

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

Table S149.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
NTM MUTATED 4 1 1
NTM WILD-TYPE 242 99 73
'NTM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S150.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
NTM MUTATED 2 1 3
NTM WILD-TYPE 140 131 148
'NTM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.77

Table S151.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
NTM MUTATED 3 0 3
NTM WILD-TYPE 125 143 150
'NTM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S152.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
NTM MUTATED 3 1 2
NTM WILD-TYPE 150 166 102
'NTM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S153.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
NTM MUTATED 3 1 2
NTM WILD-TYPE 141 122 152
'NTM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S154.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
NTM MUTATED 3 0 1 1 1
NTM WILD-TYPE 133 81 51 95 55
'NTM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 0.88

Table S155.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
NTM MUTATED 0 0 1 2
NTM WILD-TYPE 59 74 44 78
'NTM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S156.  Gene #20: 'NTM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
NTM MUTATED 1 0 0 0 0 2
NTM WILD-TYPE 63 29 21 60 25 57
'MED12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.65

Table S157.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
MED12 MUTATED 4 0 3
MED12 WILD-TYPE 242 100 71
'MED12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S158.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
MED12 MUTATED 2 3 2
MED12 WILD-TYPE 140 129 149
'MED12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S159.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
MED12 MUTATED 2 3 2
MED12 WILD-TYPE 126 140 151
'MED12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.77

Table S160.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
MED12 MUTATED 1 5 1
MED12 WILD-TYPE 152 162 103
'MED12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S161.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
MED12 MUTATED 2 1 4
MED12 WILD-TYPE 142 122 150
'MED12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.957 (Fisher's exact test), Q value = 1

Table S162.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
MED12 MUTATED 3 1 0 2 1
MED12 WILD-TYPE 133 80 52 94 55
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.77

Table S163.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
MED12 MUTATED 0 2 1 0
MED12 WILD-TYPE 59 72 44 80
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S164.  Gene #21: 'MED12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
MED12 MUTATED 1 1 0 1 0 0
MED12 WILD-TYPE 63 28 21 59 25 59
'MED15 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.94

Table S165.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
MED15 MUTATED 5 0 1
MED15 WILD-TYPE 241 100 73
'MED15 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0872 (Fisher's exact test), Q value = 0.61

Table S166.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
MED15 MUTATED 0 4 2
MED15 WILD-TYPE 142 128 149
'MED15 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S167.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
MED15 MUTATED 1 2 3
MED15 WILD-TYPE 127 141 150
'MED15 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 0.82

Table S168.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
MED15 MUTATED 2 4 0
MED15 WILD-TYPE 151 163 104
'MED15 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S169.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
MED15 MUTATED 2 1 3
MED15 WILD-TYPE 142 122 151
'MED15 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S170.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
MED15 MUTATED 2 1 0 1 2
MED15 WILD-TYPE 134 80 52 95 54
'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S171.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
MED15 MUTATED 1 2 1 1
MED15 WILD-TYPE 58 72 44 79
'MED15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S172.  Gene #22: 'MED15 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
MED15 MUTATED 0 1 0 1 1 2
MED15 WILD-TYPE 64 28 21 59 24 57
'ERN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.77

Table S173.  Gene #23: 'ERN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ERN1 MUTATED 1 2 0
ERN1 WILD-TYPE 245 98 74
'ERN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.36

Table S174.  Gene #23: 'ERN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ERN1 MUTATED 0 3 0
ERN1 WILD-TYPE 142 129 151

Figure S35.  Get High-res Image Gene #23: 'ERN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ERN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.9

Table S175.  Gene #23: 'ERN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ERN1 MUTATED 1 2 0
ERN1 WILD-TYPE 127 141 153
'ERN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S176.  Gene #23: 'ERN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ERN1 MUTATED 1 2 0
ERN1 WILD-TYPE 152 165 104
'ERN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S177.  Gene #23: 'ERN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ERN1 MUTATED 1 0 2
ERN1 WILD-TYPE 143 123 152
'ERN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S178.  Gene #23: 'ERN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ERN1 MUTATED 2 0 0 1 0
ERN1 WILD-TYPE 134 81 52 95 56
'LMOD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S179.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
LMOD2 MUTATED 3 1 1
LMOD2 WILD-TYPE 243 99 73
'LMOD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S180.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
LMOD2 MUTATED 2 1 2
LMOD2 WILD-TYPE 140 131 149
'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S181.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
LMOD2 MUTATED 1 2 2
LMOD2 WILD-TYPE 127 141 151
'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S182.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
LMOD2 MUTATED 1 2 2
LMOD2 WILD-TYPE 152 165 102
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S183.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
LMOD2 MUTATED 2 2 1
LMOD2 WILD-TYPE 142 121 153
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S184.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
LMOD2 MUTATED 1 2 0 1 1
LMOD2 WILD-TYPE 135 79 52 95 55
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S185.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
LMOD2 MUTATED 1 1 2 1
LMOD2 WILD-TYPE 58 73 43 79
'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S186.  Gene #24: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
LMOD2 MUTATED 1 2 0 1 0 1
LMOD2 WILD-TYPE 63 27 21 59 25 58
'FAM111A MUTATION STATUS' versus 'CN_CNMF'

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

Table S187.  Gene #25: 'FAM111A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
FAM111A MUTATED 2 1 0
FAM111A WILD-TYPE 244 99 74
'FAM111A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S188.  Gene #25: 'FAM111A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
FAM111A MUTATED 0 1 2
FAM111A WILD-TYPE 142 131 149
'FAM111A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.65

Table S189.  Gene #25: 'FAM111A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
FAM111A MUTATED 0 0 3
FAM111A WILD-TYPE 128 143 150
'FAM111A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.257 (Fisher's exact test), Q value = 0.81

Table S190.  Gene #25: 'FAM111A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
FAM111A MUTATED 0 1 2
FAM111A WILD-TYPE 153 166 102
'FAM111A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S191.  Gene #25: 'FAM111A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
FAM111A MUTATED 1 0 2
FAM111A WILD-TYPE 143 123 152
'FAM111A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 0.65

Table S192.  Gene #25: 'FAM111A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
FAM111A MUTATED 1 0 2 0 0
FAM111A WILD-TYPE 135 81 50 96 56
'ZNF709 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.77

Table S193.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ZNF709 MUTATED 3 0 2
ZNF709 WILD-TYPE 243 100 72
'ZNF709 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S194.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ZNF709 MUTATED 2 1 2
ZNF709 WILD-TYPE 140 131 149
'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.82

Table S195.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ZNF709 MUTATED 2 0 3
ZNF709 WILD-TYPE 126 143 150
'ZNF709 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S196.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ZNF709 MUTATED 2 1 2
ZNF709 WILD-TYPE 151 166 102
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S197.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ZNF709 MUTATED 1 2 2
ZNF709 WILD-TYPE 143 121 152
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.81

Table S198.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ZNF709 MUTATED 1 0 0 2 2
ZNF709 WILD-TYPE 135 81 52 94 54
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S199.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
ZNF709 MUTATED 1 1 0 3
ZNF709 WILD-TYPE 58 73 45 77
'ZNF709 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S200.  Gene #26: 'ZNF709 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
ZNF709 MUTATED 1 0 0 1 0 3
ZNF709 WILD-TYPE 63 29 21 59 25 56
'MLLT10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S201.  Gene #27: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
MLLT10 MUTATED 2 1 1
MLLT10 WILD-TYPE 244 99 73
'MLLT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.74

Table S202.  Gene #27: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
MLLT10 MUTATED 3 1 0
MLLT10 WILD-TYPE 139 131 151
'MLLT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S203.  Gene #27: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
MLLT10 MUTATED 1 1 2
MLLT10 WILD-TYPE 127 142 151
'MLLT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S204.  Gene #27: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
MLLT10 MUTATED 2 2 0
MLLT10 WILD-TYPE 151 165 104
'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.81

Table S205.  Gene #27: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
MLLT10 MUTATED 3 0 1
MLLT10 WILD-TYPE 141 123 153
'MLLT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S206.  Gene #27: 'MLLT10 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
MLLT10 MUTATED 3 0 0 1 0
MLLT10 WILD-TYPE 133 81 52 95 56
'TNRC18 MUTATION STATUS' versus 'CN_CNMF'

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

Table S207.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
TNRC18 MUTATED 3 2 1
TNRC18 WILD-TYPE 243 98 73
'TNRC18 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S208.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
TNRC18 MUTATED 2 1 3
TNRC18 WILD-TYPE 140 131 148
'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S209.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
TNRC18 MUTATED 2 1 3
TNRC18 WILD-TYPE 126 142 150
'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 0.89

Table S210.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
TNRC18 MUTATED 1 2 3
TNRC18 WILD-TYPE 152 165 101
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S211.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
TNRC18 MUTATED 1 2 3
TNRC18 WILD-TYPE 143 121 151
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S212.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
TNRC18 MUTATED 1 1 1 3 0
TNRC18 WILD-TYPE 135 80 51 93 56
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S213.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
TNRC18 MUTATED 0 2 1 2
TNRC18 WILD-TYPE 59 72 44 78
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S214.  Gene #28: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
TNRC18 MUTATED 1 0 1 1 0 2
TNRC18 WILD-TYPE 63 29 20 59 25 57
'GAGE2D MUTATION STATUS' versus 'CN_CNMF'

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

Table S215.  Gene #29: 'GAGE2D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
GAGE2D MUTATED 3 0 0
GAGE2D WILD-TYPE 243 100 74
'GAGE2D MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0675 (Fisher's exact test), Q value = 0.59

Table S216.  Gene #29: 'GAGE2D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
GAGE2D MUTATED 3 0 0
GAGE2D WILD-TYPE 139 132 151
'GAGE2D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.34

Table S217.  Gene #29: 'GAGE2D MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
GAGE2D MUTATED 3 0 0
GAGE2D WILD-TYPE 125 143 153

Figure S36.  Get High-res Image Gene #29: 'GAGE2D MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'GAGE2D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0614 (Fisher's exact test), Q value = 0.57

Table S218.  Gene #29: 'GAGE2D MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
GAGE2D MUTATED 3 0 0
GAGE2D WILD-TYPE 150 167 104
'GAGE2D MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S219.  Gene #29: 'GAGE2D MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
GAGE2D MUTATED 2 0 1
GAGE2D WILD-TYPE 142 123 153
'GAGE2D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.88

Table S220.  Gene #29: 'GAGE2D MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
GAGE2D MUTATED 3 0 0 0 0
GAGE2D WILD-TYPE 133 81 52 96 56
'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 0.97

Table S221.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
EMG1 MUTATED 2 2 0
EMG1 WILD-TYPE 244 98 74
'EMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.81

Table S222.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
EMG1 MUTATED 0 1 3
EMG1 WILD-TYPE 142 131 148
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S223.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
EMG1 MUTATED 0 2 2
EMG1 WILD-TYPE 128 141 151
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.77

Table S224.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
EMG1 MUTATED 0 2 2
EMG1 WILD-TYPE 153 165 102
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.41

Table S225.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
EMG1 MUTATED 0 0 4
EMG1 WILD-TYPE 144 123 150

Figure S37.  Get High-res Image Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.092

Table S226.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
EMG1 MUTATED 0 0 1 0 3
EMG1 WILD-TYPE 136 81 51 96 53

Figure S38.  Get High-res Image Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'LAMA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.88

Table S227.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
LAMA3 MUTATED 4 3 0
LAMA3 WILD-TYPE 242 97 74
'LAMA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.81

Table S228.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
LAMA3 MUTATED 2 4 1
LAMA3 WILD-TYPE 140 128 150
'LAMA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.88

Table S229.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
LAMA3 MUTATED 2 4 1
LAMA3 WILD-TYPE 126 139 152
'LAMA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S230.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
LAMA3 MUTATED 2 4 1
LAMA3 WILD-TYPE 151 163 103
'LAMA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S231.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
LAMA3 MUTATED 2 2 3
LAMA3 WILD-TYPE 142 121 151
'LAMA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S232.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
LAMA3 MUTATED 2 1 1 2 1
LAMA3 WILD-TYPE 134 80 51 94 55
'LAMA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S233.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
LAMA3 MUTATED 0 1 1 1
LAMA3 WILD-TYPE 59 73 44 79
'LAMA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S234.  Gene #31: 'LAMA3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
LAMA3 MUTATED 0 0 0 1 0 2
LAMA3 WILD-TYPE 64 29 21 59 25 57
'RPL11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S235.  Gene #32: 'RPL11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
RPL11 MUTATED 3 0 1
RPL11 WILD-TYPE 243 100 73
'RPL11 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S236.  Gene #32: 'RPL11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
RPL11 MUTATED 1 1 2
RPL11 WILD-TYPE 141 131 149
'RPL11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S237.  Gene #32: 'RPL11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
RPL11 MUTATED 0 2 2
RPL11 WILD-TYPE 128 141 151
'RPL11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S238.  Gene #32: 'RPL11 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
RPL11 MUTATED 1 1 2
RPL11 WILD-TYPE 152 166 102
'RPL11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S239.  Gene #32: 'RPL11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
RPL11 MUTATED 1 1 2
RPL11 WILD-TYPE 143 122 152
'RPL11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S240.  Gene #32: 'RPL11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
RPL11 MUTATED 2 0 0 1 1
RPL11 WILD-TYPE 134 81 52 95 55
'ZFHX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.66

Table S241.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ZFHX3 MUTATED 5 3 5
ZFHX3 WILD-TYPE 241 97 69
'ZFHX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.77

Table S242.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ZFHX3 MUTATED 3 7 3
ZFHX3 WILD-TYPE 139 125 148
'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.69

Table S243.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ZFHX3 MUTATED 1 7 5
ZFHX3 WILD-TYPE 127 136 148
'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.65

Table S244.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ZFHX3 MUTATED 2 9 2
ZFHX3 WILD-TYPE 151 158 102
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.82

Table S245.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ZFHX3 MUTATED 2 4 7
ZFHX3 WILD-TYPE 142 119 147
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.492 (Fisher's exact test), Q value = 0.97

Table S246.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ZFHX3 MUTATED 3 2 1 3 4
ZFHX3 WILD-TYPE 133 79 51 93 52
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.84

Table S247.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
ZFHX3 MUTATED 0 4 1 3
ZFHX3 WILD-TYPE 59 70 44 77
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.99 (Fisher's exact test), Q value = 1

Table S248.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
ZFHX3 MUTATED 2 1 1 2 0 2
ZFHX3 WILD-TYPE 62 28 20 58 25 57
'MUC17 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.7

Table S249.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
MUC17 MUTATED 11 6 8
MUC17 WILD-TYPE 235 94 66
'MUC17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.66

Table S250.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
MUC17 MUTATED 4 11 10
MUC17 WILD-TYPE 138 121 141
'MUC17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.084 (Fisher's exact test), Q value = 0.61

Table S251.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
MUC17 MUTATED 3 12 10
MUC17 WILD-TYPE 125 131 143
'MUC17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.87

Table S252.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
MUC17 MUTATED 6 13 6
MUC17 WILD-TYPE 147 154 98
'MUC17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0825 (Fisher's exact test), Q value = 0.61

Table S253.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
MUC17 MUTATED 6 4 14
MUC17 WILD-TYPE 138 119 140
'MUC17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S254.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
MUC17 MUTATED 8 4 2 8 2
MUC17 WILD-TYPE 128 77 50 88 54
'MUC17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S255.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
MUC17 MUTATED 3 4 2 3
MUC17 WILD-TYPE 56 70 43 77
'MUC17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.82

Table S256.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
MUC17 MUTATED 3 0 3 3 0 3
MUC17 WILD-TYPE 61 29 18 57 25 56
'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S257.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
CDKN1B MUTATED 3 1 1
CDKN1B WILD-TYPE 243 99 73
'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S258.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
CDKN1B MUTATED 1 2 2
CDKN1B WILD-TYPE 141 130 149
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.89

Table S259.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
CDKN1B MUTATED 0 2 3
CDKN1B WILD-TYPE 128 141 150
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.72

Table S260.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
CDKN1B MUTATED 0 4 1
CDKN1B WILD-TYPE 153 163 103
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.81

Table S261.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
CDKN1B MUTATED 0 2 3
CDKN1B WILD-TYPE 144 121 151
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 0.65

Table S262.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
CDKN1B MUTATED 0 2 0 3 0
CDKN1B WILD-TYPE 136 79 52 93 56
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S263.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
CDKN1B MUTATED 0 2 0 1
CDKN1B WILD-TYPE 59 72 45 79
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.88

Table S264.  Gene #35: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
CDKN1B MUTATED 0 1 0 2 0 0
CDKN1B WILD-TYPE 64 28 21 58 25 59
'POM121 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S265.  Gene #36: 'POM121 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
POM121 MUTATED 3 0 0
POM121 WILD-TYPE 243 100 74
'POM121 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.9

Table S266.  Gene #36: 'POM121 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
POM121 MUTATED 2 1 0
POM121 WILD-TYPE 140 131 151
'POM121 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.89

Table S267.  Gene #36: 'POM121 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
POM121 MUTATED 1 2 0
POM121 WILD-TYPE 127 141 153
'POM121 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S268.  Gene #36: 'POM121 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
POM121 MUTATED 2 1 0
POM121 WILD-TYPE 151 166 104
'POM121 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.77

Table S269.  Gene #36: 'POM121 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
POM121 MUTATED 1 2 0
POM121 WILD-TYPE 143 121 154
'POM121 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S270.  Gene #36: 'POM121 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
POM121 MUTATED 1 1 0 0 1
POM121 WILD-TYPE 135 80 52 96 55
'ESCO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S271.  Gene #37: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ESCO1 MUTATED 3 0 1
ESCO1 WILD-TYPE 243 100 73
'ESCO1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S272.  Gene #37: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ESCO1 MUTATED 2 1 1
ESCO1 WILD-TYPE 140 131 150
'ESCO1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.66

Table S273.  Gene #37: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ESCO1 MUTATED 3 0 1
ESCO1 WILD-TYPE 125 143 152
'ESCO1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.7

Table S274.  Gene #37: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ESCO1 MUTATED 3 0 1
ESCO1 WILD-TYPE 150 167 103
'ESCO1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.81

Table S275.  Gene #37: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ESCO1 MUTATED 3 0 1
ESCO1 WILD-TYPE 141 123 153
'ESCO1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.433 (Fisher's exact test), Q value = 0.93

Table S276.  Gene #37: 'ESCO1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ESCO1 MUTATED 2 0 1 0 1
ESCO1 WILD-TYPE 134 81 51 96 55
'MYOT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S277.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
MYOT MUTATED 2 0 1
MYOT WILD-TYPE 244 100 73
'MYOT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00891 (Fisher's exact test), Q value = 0.17

Table S278.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
MYOT MUTATED 0 4 0
MYOT WILD-TYPE 142 128 151

Figure S39.  Get High-res Image Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MYOT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.77

Table S279.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
MYOT MUTATED 0 3 1
MYOT WILD-TYPE 128 140 152
'MYOT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.94

Table S280.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
MYOT MUTATED 1 3 0
MYOT WILD-TYPE 152 164 104
'MYOT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.95

Table S281.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
MYOT MUTATED 0 2 2
MYOT WILD-TYPE 144 121 152
'MYOT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.69

Table S282.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
MYOT MUTATED 0 1 0 3 0
MYOT WILD-TYPE 136 80 52 93 56
'MYOT MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.77

Table S283.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
MYOT MUTATED 0 2 1 0
MYOT WILD-TYPE 59 72 44 80
'MYOT MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.77

Table S284.  Gene #38: 'MYOT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
MYOT MUTATED 0 0 1 2 0 0
MYOT WILD-TYPE 64 29 20 58 25 59
'L1CAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S285.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
L1CAM MUTATED 3 2 2
L1CAM WILD-TYPE 243 98 72
'L1CAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.34

Table S286.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
L1CAM MUTATED 2 5 0
L1CAM WILD-TYPE 140 127 151

Figure S40.  Get High-res Image Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'L1CAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.404 (Fisher's exact test), Q value = 0.89

Table S287.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
L1CAM MUTATED 1 4 2
L1CAM WILD-TYPE 127 139 151
'L1CAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.77

Table S288.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
L1CAM MUTATED 2 5 0
L1CAM WILD-TYPE 151 162 104
'L1CAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S289.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
L1CAM MUTATED 2 2 3
L1CAM WILD-TYPE 142 121 151
'L1CAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.29

Table S290.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
L1CAM MUTATED 0 4 0 3 0
L1CAM WILD-TYPE 136 77 52 93 56

Figure S41.  Get High-res Image Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'L1CAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.79

Table S291.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
L1CAM MUTATED 1 2 2 0
L1CAM WILD-TYPE 58 72 43 80
'L1CAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 0.81

Table S292.  Gene #39: 'L1CAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
L1CAM MUTATED 0 2 0 2 0 1
L1CAM WILD-TYPE 64 27 21 58 25 58
'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.69

Table S293.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
FAM47C MUTATED 6 0 3
FAM47C WILD-TYPE 240 100 71
'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.96

Table S294.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
FAM47C MUTATED 4 1 4
FAM47C WILD-TYPE 138 131 147
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S295.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
FAM47C MUTATED 2 4 3
FAM47C WILD-TYPE 126 139 150
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S296.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
FAM47C MUTATED 3 5 1
FAM47C WILD-TYPE 150 162 103
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S297.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
FAM47C MUTATED 3 4 2
FAM47C WILD-TYPE 141 119 152
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.89

Table S298.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
FAM47C MUTATED 3 2 0 1 3
FAM47C WILD-TYPE 133 79 52 95 53
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S299.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
FAM47C MUTATED 1 2 2 2
FAM47C WILD-TYPE 58 72 43 78
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.88

Table S300.  Gene #40: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
FAM47C MUTATED 2 2 0 0 1 2
FAM47C WILD-TYPE 62 27 21 60 24 57
'CR1L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S301.  Gene #41: 'CR1L MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
CR1L MUTATED 3 2 0
CR1L WILD-TYPE 243 98 74
'CR1L MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 0.94

Table S302.  Gene #41: 'CR1L MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
CR1L MUTATED 1 3 1
CR1L WILD-TYPE 141 129 150
'CR1L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S303.  Gene #41: 'CR1L MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
CR1L MUTATED 1 1 3
CR1L WILD-TYPE 127 142 150
'CR1L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.72

Table S304.  Gene #41: 'CR1L MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
CR1L MUTATED 0 4 1
CR1L WILD-TYPE 153 163 103
'CR1L MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S305.  Gene #41: 'CR1L MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
CR1L MUTATED 1 1 3
CR1L WILD-TYPE 143 122 151
'CR1L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S306.  Gene #41: 'CR1L MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
CR1L MUTATED 2 1 0 2 0
CR1L WILD-TYPE 134 80 52 94 56
'FAM120B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.77

Table S307.  Gene #42: 'FAM120B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
FAM120B MUTATED 1 2 0
FAM120B WILD-TYPE 245 98 74
'FAM120B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S308.  Gene #42: 'FAM120B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
FAM120B MUTATED 1 1 1
FAM120B WILD-TYPE 141 131 150
'FAM120B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S309.  Gene #42: 'FAM120B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
FAM120B MUTATED 0 2 1
FAM120B WILD-TYPE 128 141 152
'FAM120B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S310.  Gene #42: 'FAM120B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
FAM120B MUTATED 1 2 0
FAM120B WILD-TYPE 152 165 104
'FAM120B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.82

Table S311.  Gene #42: 'FAM120B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
FAM120B MUTATED 0 2 1
FAM120B WILD-TYPE 144 121 153
'FAM120B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.26

Table S312.  Gene #42: 'FAM120B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
FAM120B MUTATED 0 0 1 0 2
FAM120B WILD-TYPE 136 81 51 96 54

Figure S42.  Get High-res Image Gene #42: 'FAM120B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EDC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0701 (Fisher's exact test), Q value = 0.59

Table S313.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
EDC4 MUTATED 0 2 1
EDC4 WILD-TYPE 246 98 73
'EDC4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.77

Table S314.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
EDC4 MUTATED 1 2 0
EDC4 WILD-TYPE 141 130 151
'EDC4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S315.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
EDC4 MUTATED 1 1 1
EDC4 WILD-TYPE 127 142 152
'EDC4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.95

Table S316.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
EDC4 MUTATED 0 2 1
EDC4 WILD-TYPE 153 165 103
'EDC4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S317.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
EDC4 MUTATED 0 1 2
EDC4 WILD-TYPE 144 122 152
'EDC4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00388 (Fisher's exact test), Q value = 0.11

Table S318.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
EDC4 MUTATED 0 0 0 0 3
EDC4 WILD-TYPE 136 81 52 96 53

Figure S43.  Get High-res Image Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EDC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.74

Table S319.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
EDC4 MUTATED 0 0 0 3
EDC4 WILD-TYPE 59 74 45 77
'EDC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S320.  Gene #43: 'EDC4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
EDC4 MUTATED 0 0 0 1 0 2
EDC4 WILD-TYPE 64 29 21 59 25 57
'KIRREL MUTATION STATUS' versus 'CN_CNMF'

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

Table S321.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
KIRREL MUTATED 3 1 1
KIRREL WILD-TYPE 243 99 73
'KIRREL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S322.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
KIRREL MUTATED 2 2 1
KIRREL WILD-TYPE 140 130 150
'KIRREL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.94

Table S323.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
KIRREL MUTATED 3 1 1
KIRREL WILD-TYPE 125 142 152
'KIRREL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.88

Table S324.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
KIRREL MUTATED 3 2 0
KIRREL WILD-TYPE 150 165 104
'KIRREL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S325.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
KIRREL MUTATED 2 1 2
KIRREL WILD-TYPE 142 122 152
'KIRREL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S326.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
KIRREL MUTATED 3 0 0 1 1
KIRREL WILD-TYPE 133 81 52 95 55
'KIRREL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S327.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
KIRREL MUTATED 0 1 0 2
KIRREL WILD-TYPE 59 73 45 78
'KIRREL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S328.  Gene #44: 'KIRREL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
KIRREL MUTATED 1 0 0 1 0 1
KIRREL WILD-TYPE 63 29 21 59 25 58
'TCERG1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S329.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
TCERG1 MUTATED 3 1 0
TCERG1 WILD-TYPE 243 99 74
'TCERG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.86

Table S330.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
TCERG1 MUTATED 1 0 3
TCERG1 WILD-TYPE 141 132 148
'TCERG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.81

Table S331.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
TCERG1 MUTATED 1 0 3
TCERG1 WILD-TYPE 127 143 150
'TCERG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S332.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
TCERG1 MUTATED 1 1 2
TCERG1 WILD-TYPE 152 166 102
'TCERG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S333.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
TCERG1 MUTATED 2 1 1
TCERG1 WILD-TYPE 142 122 153
'TCERG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.83

Table S334.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
TCERG1 MUTATED 1 0 0 1 2
TCERG1 WILD-TYPE 135 81 52 95 54
'TCERG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S335.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
TCERG1 MUTATED 1 1 0 2
TCERG1 WILD-TYPE 58 73 45 78
'TCERG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.26

Table S336.  Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
TCERG1 MUTATED 0 0 2 0 1 1
TCERG1 WILD-TYPE 64 29 19 60 24 58

Figure S44.  Get High-res Image Gene #45: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SLC16A6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S337.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
SLC16A6 MUTATED 2 1 1
SLC16A6 WILD-TYPE 244 99 73
'SLC16A6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.81

Table S338.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
SLC16A6 MUTATED 0 1 3
SLC16A6 WILD-TYPE 142 131 148
'SLC16A6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.89

Table S339.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
SLC16A6 MUTATED 0 1 3
SLC16A6 WILD-TYPE 128 142 150
'SLC16A6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.065 (Fisher's exact test), Q value = 0.59

Table S340.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
SLC16A6 MUTATED 0 1 3
SLC16A6 WILD-TYPE 153 166 101
'SLC16A6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.41

Table S341.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
SLC16A6 MUTATED 0 0 4
SLC16A6 WILD-TYPE 144 123 150

Figure S45.  Get High-res Image Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'SLC16A6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.355 (Fisher's exact test), Q value = 0.88

Table S342.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
SLC16A6 MUTATED 0 1 1 1 1
SLC16A6 WILD-TYPE 136 80 51 95 55
'SLC16A6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S343.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
SLC16A6 MUTATED 0 2 0 1
SLC16A6 WILD-TYPE 59 72 45 79
'SLC16A6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S344.  Gene #46: 'SLC16A6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
SLC16A6 MUTATED 0 0 0 2 0 1
SLC16A6 WILD-TYPE 64 29 21 58 25 58
'NKX3-1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.88

Table S345.  Gene #47: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
NKX3-1 MUTATED 4 0 0
NKX3-1 WILD-TYPE 242 100 74
'NKX3-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S346.  Gene #47: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
NKX3-1 MUTATED 1 1 3
NKX3-1 WILD-TYPE 141 131 148
'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S347.  Gene #47: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
NKX3-1 MUTATED 1 2 2
NKX3-1 WILD-TYPE 127 141 151
'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S348.  Gene #47: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
NKX3-1 MUTATED 1 2 2
NKX3-1 WILD-TYPE 152 165 102
'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.7

Table S349.  Gene #47: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
NKX3-1 MUTATED 2 3 0
NKX3-1 WILD-TYPE 142 120 154
'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S350.  Gene #47: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
NKX3-1 MUTATED 2 2 0 0 1
NKX3-1 WILD-TYPE 134 79 52 96 55
'RNF17 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S351.  Gene #48: 'RNF17 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
RNF17 MUTATED 3 0 0
RNF17 WILD-TYPE 243 100 74
'RNF17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S352.  Gene #48: 'RNF17 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
RNF17 MUTATED 1 0 2
RNF17 WILD-TYPE 141 132 149
'RNF17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.65

Table S353.  Gene #48: 'RNF17 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
RNF17 MUTATED 0 0 3
RNF17 WILD-TYPE 128 143 150
'RNF17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.77

Table S354.  Gene #48: 'RNF17 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
RNF17 MUTATED 1 0 2
RNF17 WILD-TYPE 152 167 102
'RNF17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S355.  Gene #48: 'RNF17 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
RNF17 MUTATED 2 0 1
RNF17 WILD-TYPE 142 123 153
'RNF17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S356.  Gene #48: 'RNF17 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
RNF17 MUTATED 2 0 0 0 1
RNF17 WILD-TYPE 134 81 52 96 55
'KYNU MUTATION STATUS' versus 'CN_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S357.  Gene #49: 'KYNU MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
KYNU MUTATED 2 0 1
KYNU WILD-TYPE 244 100 73
'KYNU MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 0.9

Table S358.  Gene #49: 'KYNU MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
KYNU MUTATED 2 1 0
KYNU WILD-TYPE 140 131 151
'KYNU MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 0.77

Table S359.  Gene #49: 'KYNU MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
KYNU MUTATED 2 1 0
KYNU WILD-TYPE 126 142 153
'KYNU MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S360.  Gene #49: 'KYNU MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
KYNU MUTATED 1 2 0
KYNU WILD-TYPE 152 165 104
'KYNU MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S361.  Gene #49: 'KYNU MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
KYNU MUTATED 1 1 1
KYNU WILD-TYPE 143 122 153
'KYNU MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.94

Table S362.  Gene #49: 'KYNU MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
KYNU MUTATED 1 2 0 0 0
KYNU WILD-TYPE 135 79 52 96 56
'LARP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S363.  Gene #50: 'LARP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
LARP1 MUTATED 3 0 1
LARP1 WILD-TYPE 243 100 73
'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S364.  Gene #50: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
LARP1 MUTATED 2 1 1
LARP1 WILD-TYPE 140 131 150
'LARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.81

Table S365.  Gene #50: 'LARP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
LARP1 MUTATED 1 0 3
LARP1 WILD-TYPE 127 143 150
'LARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S366.  Gene #50: 'LARP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
LARP1 MUTATED 2 1 1
LARP1 WILD-TYPE 151 166 103
'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S367.  Gene #50: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
LARP1 MUTATED 1 1 2
LARP1 WILD-TYPE 143 122 152
'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 1

Table S368.  Gene #50: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
LARP1 MUTATED 2 1 0 0 1
LARP1 WILD-TYPE 134 80 52 96 55
'CDK12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.055

Table S369.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
CDK12 MUTATED 0 5 2
CDK12 WILD-TYPE 246 95 72

Figure S46.  Get High-res Image Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 0.77

Table S370.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
CDK12 MUTATED 1 5 2
CDK12 WILD-TYPE 141 127 149
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S371.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
CDK12 MUTATED 2 4 2
CDK12 WILD-TYPE 126 139 151
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.67

Table S372.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
CDK12 MUTATED 1 6 1
CDK12 WILD-TYPE 152 161 103
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.89

Table S373.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
CDK12 MUTATED 2 1 5
CDK12 WILD-TYPE 142 122 149
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.94

Table S374.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
CDK12 MUTATED 1 1 1 4 1
CDK12 WILD-TYPE 135 80 51 92 55
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.84

Table S375.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
CDK12 MUTATED 0 3 0 3
CDK12 WILD-TYPE 59 71 45 77
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S376.  Gene #51: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
CDK12 MUTATED 1 0 0 2 0 3
CDK12 WILD-TYPE 63 29 21 58 25 56
'ACPT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.88

Table S377.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ACPT MUTATED 1 1 1
ACPT WILD-TYPE 245 99 73
'ACPT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S378.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ACPT MUTATED 2 0 1
ACPT WILD-TYPE 140 132 150
'ACPT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.83

Table S379.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ACPT MUTATED 2 0 1
ACPT WILD-TYPE 126 143 152
'ACPT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.351 (Fisher's exact test), Q value = 0.88

Table S380.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ACPT MUTATED 2 0 1
ACPT WILD-TYPE 151 167 103
'ACPT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.89

Table S381.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ACPT MUTATED 2 1 0
ACPT WILD-TYPE 142 122 154
'ACPT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.522 (Fisher's exact test), Q value = 1

Table S382.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ACPT MUTATED 2 0 0 0 1
ACPT WILD-TYPE 134 81 52 96 55
'ACPT MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.96

Table S383.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
ACPT MUTATED 1 0 0 2
ACPT WILD-TYPE 58 74 45 78
'ACPT MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S384.  Gene #52: 'ACPT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
ACPT MUTATED 2 0 0 0 0 1
ACPT WILD-TYPE 62 29 21 60 25 58
'AP4B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.88

Table S385.  Gene #53: 'AP4B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
AP4B1 MUTATED 2 1 2
AP4B1 WILD-TYPE 244 99 72
'AP4B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.78

Table S386.  Gene #53: 'AP4B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
AP4B1 MUTATED 0 3 2
AP4B1 WILD-TYPE 142 129 149
'AP4B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.86

Table S387.  Gene #53: 'AP4B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
AP4B1 MUTATED 0 3 2
AP4B1 WILD-TYPE 128 140 151
'AP4B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S388.  Gene #53: 'AP4B1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
AP4B1 MUTATED 1 3 1
AP4B1 WILD-TYPE 152 164 103
'AP4B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S389.  Gene #53: 'AP4B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
AP4B1 MUTATED 2 1 2
AP4B1 WILD-TYPE 142 122 152
'AP4B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S390.  Gene #53: 'AP4B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
AP4B1 MUTATED 1 2 1 1 0
AP4B1 WILD-TYPE 135 79 51 95 56
'RAG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S391.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
RAG1 MUTATED 5 3 1
RAG1 WILD-TYPE 241 97 73
'RAG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.96

Table S392.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
RAG1 MUTATED 4 1 4
RAG1 WILD-TYPE 138 131 147
'RAG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S393.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
RAG1 MUTATED 2 2 5
RAG1 WILD-TYPE 126 141 148
'RAG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S394.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
RAG1 MUTATED 4 3 2
RAG1 WILD-TYPE 149 164 102
'RAG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.81

Table S395.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
RAG1 MUTATED 2 5 2
RAG1 WILD-TYPE 142 118 152
'RAG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.613 (Fisher's exact test), Q value = 1

Table S396.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
RAG1 MUTATED 2 2 2 1 2
RAG1 WILD-TYPE 134 79 50 95 54
'RAG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.77

Table S397.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
RAG1 MUTATED 1 1 0 5
RAG1 WILD-TYPE 58 73 45 75
'RAG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.83

Table S398.  Gene #54: 'RAG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
RAG1 MUTATED 2 1 0 0 0 4
RAG1 WILD-TYPE 62 28 21 60 25 55
'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0654 (Fisher's exact test), Q value = 0.59

Table S399.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
APC MUTATED 4 5 0
APC WILD-TYPE 242 95 74
'APC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.77

Table S400.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
APC MUTATED 1 5 3
APC WILD-TYPE 141 127 148
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.97

Table S401.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
APC MUTATED 1 4 4
APC WILD-TYPE 127 139 149
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.78

Table S402.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
APC MUTATED 1 6 2
APC WILD-TYPE 152 161 102
'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.33

Table S403.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
APC MUTATED 2 0 7
APC WILD-TYPE 142 123 147

Figure S47.  Get High-res Image Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.87

Table S404.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
APC MUTATED 1 1 1 4 2
APC WILD-TYPE 135 80 51 92 54
'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.74

Table S405.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
APC MUTATED 1 3 0 0
APC WILD-TYPE 58 71 45 80
'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S406.  Gene #55: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
APC MUTATED 1 1 0 2 0 0
APC WILD-TYPE 63 28 21 58 25 59
'MSLNL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S407.  Gene #56: 'MSLNL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
MSLNL MUTATED 2 1 1
MSLNL WILD-TYPE 244 99 73
'MSLNL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.66

Table S408.  Gene #56: 'MSLNL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
MSLNL MUTATED 0 3 1
MSLNL WILD-TYPE 142 129 150
'MSLNL MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S409.  Gene #56: 'MSLNL MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
MSLNL MUTATED 1 2 1
MSLNL WILD-TYPE 127 141 152
'MSLNL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S410.  Gene #56: 'MSLNL MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
MSLNL MUTATED 1 2 1
MSLNL WILD-TYPE 152 165 103
'MSLNL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S411.  Gene #56: 'MSLNL MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
MSLNL MUTATED 1 2 1
MSLNL WILD-TYPE 143 121 153
'MSLNL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.77

Table S412.  Gene #56: 'MSLNL MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
MSLNL MUTATED 1 1 0 0 2
MSLNL WILD-TYPE 135 80 52 96 54
'GAB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S413.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
GAB2 MUTATED 3 1 1
GAB2 WILD-TYPE 243 99 73
'GAB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S414.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
GAB2 MUTATED 1 2 2
GAB2 WILD-TYPE 141 130 149
'GAB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S415.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
GAB2 MUTATED 1 2 2
GAB2 WILD-TYPE 127 141 151
'GAB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S416.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
GAB2 MUTATED 2 2 1
GAB2 WILD-TYPE 151 165 103
'GAB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S417.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
GAB2 MUTATED 1 2 2
GAB2 WILD-TYPE 143 121 152
'GAB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 0.82

Table S418.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
GAB2 MUTATED 1 0 1 3 0
GAB2 WILD-TYPE 135 81 51 93 56
'GAB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.65 (Fisher's exact test), Q value = 1

Table S419.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
GAB2 MUTATED 0 2 1 1
GAB2 WILD-TYPE 59 72 44 79
'GAB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S420.  Gene #57: 'GAB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
GAB2 MUTATED 0 0 0 2 0 2
GAB2 WILD-TYPE 64 29 21 58 25 57
'DNMT3B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S421.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
DNMT3B MUTATED 2 1 1
DNMT3B WILD-TYPE 244 99 73
'DNMT3B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00889 (Fisher's exact test), Q value = 0.17

Table S422.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
DNMT3B MUTATED 0 4 0
DNMT3B WILD-TYPE 142 128 151

Figure S48.  Get High-res Image Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.77

Table S423.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
DNMT3B MUTATED 0 3 1
DNMT3B WILD-TYPE 128 140 152
'DNMT3B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0877 (Fisher's exact test), Q value = 0.61

Table S424.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
DNMT3B MUTATED 0 4 0
DNMT3B WILD-TYPE 153 163 104
'DNMT3B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S425.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
DNMT3B MUTATED 1 1 2
DNMT3B WILD-TYPE 143 122 152
'DNMT3B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S426.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
DNMT3B MUTATED 1 1 0 2 0
DNMT3B WILD-TYPE 135 80 52 94 56
'DNMT3B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.77

Table S427.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
DNMT3B MUTATED 0 2 1 0
DNMT3B WILD-TYPE 59 72 44 80
'DNMT3B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.95

Table S428.  Gene #58: 'DNMT3B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
DNMT3B MUTATED 1 0 1 1 0 0
DNMT3B WILD-TYPE 63 29 20 59 25 59
'NCKAP1L MUTATION STATUS' versus 'CN_CNMF'

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

Table S429.  Gene #59: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
NCKAP1L MUTATED 3 2 0
NCKAP1L WILD-TYPE 243 98 74
'NCKAP1L MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.65

Table S430.  Gene #59: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
NCKAP1L MUTATED 0 1 4
NCKAP1L WILD-TYPE 142 131 147
'NCKAP1L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.89

Table S431.  Gene #59: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
NCKAP1L MUTATED 0 2 3
NCKAP1L WILD-TYPE 128 141 150
'NCKAP1L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.77

Table S432.  Gene #59: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
NCKAP1L MUTATED 0 3 2
NCKAP1L WILD-TYPE 153 164 102
'NCKAP1L MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S433.  Gene #59: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
NCKAP1L MUTATED 2 1 2
NCKAP1L WILD-TYPE 142 122 152
'NCKAP1L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S434.  Gene #59: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
NCKAP1L MUTATED 2 0 1 2 0
NCKAP1L WILD-TYPE 134 81 51 94 56
'PRTFDC1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S435.  Gene #60: 'PRTFDC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
PRTFDC1 MUTATED 3 0 0
PRTFDC1 WILD-TYPE 243 100 74
'PRTFDC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S436.  Gene #60: 'PRTFDC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
PRTFDC1 MUTATED 1 1 1
PRTFDC1 WILD-TYPE 141 131 150
'PRTFDC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S437.  Gene #60: 'PRTFDC1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
PRTFDC1 MUTATED 1 1 1
PRTFDC1 WILD-TYPE 127 142 152
'PRTFDC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0606 (Fisher's exact test), Q value = 0.57

Table S438.  Gene #60: 'PRTFDC1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
PRTFDC1 MUTATED 3 0 0
PRTFDC1 WILD-TYPE 150 167 104
'PRTFDC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.33

Table S439.  Gene #60: 'PRTFDC1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
PRTFDC1 MUTATED 0 3 0
PRTFDC1 WILD-TYPE 144 120 154

Figure S49.  Get High-res Image Gene #60: 'PRTFDC1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'PRTFDC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.83

Table S440.  Gene #60: 'PRTFDC1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
PRTFDC1 MUTATED 1 0 1 0 1
PRTFDC1 WILD-TYPE 135 81 51 96 55
'PCSK5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.88

Table S441.  Gene #61: 'PCSK5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
PCSK5 MUTATED 2 2 2
PCSK5 WILD-TYPE 244 98 72
'PCSK5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0671 (Fisher's exact test), Q value = 0.59

Table S442.  Gene #61: 'PCSK5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
PCSK5 MUTATED 2 4 0
PCSK5 WILD-TYPE 140 128 151
'PCSK5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.86

Table S443.  Gene #61: 'PCSK5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
PCSK5 MUTATED 1 4 1
PCSK5 WILD-TYPE 127 139 152
'PCSK5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.72

Table S444.  Gene #61: 'PCSK5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
PCSK5 MUTATED 1 5 0
PCSK5 WILD-TYPE 152 162 104
'PCSK5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S445.  Gene #61: 'PCSK5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
PCSK5 MUTATED 1 2 3
PCSK5 WILD-TYPE 143 121 151
'PCSK5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.972 (Fisher's exact test), Q value = 1

Table S446.  Gene #61: 'PCSK5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
PCSK5 MUTATED 2 1 0 2 1
PCSK5 WILD-TYPE 134 80 52 94 55
'ITGA2B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.88

Table S447.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 246 100 74
ITGA2B MUTATED 4 0 0
ITGA2B WILD-TYPE 242 100 74
'ITGA2B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S448.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 132 151
ITGA2B MUTATED 1 1 2
ITGA2B WILD-TYPE 141 131 149
'ITGA2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.89

Table S449.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 143 153
ITGA2B MUTATED 0 1 3
ITGA2B WILD-TYPE 128 142 150
'ITGA2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.82

Table S450.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 167 104
ITGA2B MUTATED 0 3 1
ITGA2B WILD-TYPE 153 164 103
'ITGA2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.77

Table S451.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 123 154
ITGA2B MUTATED 0 1 3
ITGA2B WILD-TYPE 144 122 151
'ITGA2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.84

Table S452.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 136 81 52 96 56
ITGA2B MUTATED 0 1 0 2 1
ITGA2B WILD-TYPE 136 80 52 94 55
'ITGA2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S453.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 59 74 45 80
ITGA2B MUTATED 0 1 1 1
ITGA2B WILD-TYPE 59 73 44 79
'ITGA2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S454.  Gene #62: 'ITGA2B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 29 21 60 25 59
ITGA2B MUTATED 0 0 0 2 0 1
ITGA2B WILD-TYPE 64 29 21 58 25 58
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/15170475/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/15115159/PRAD-TP.transferedmergedcluster.txt

  • Number of patients = 425

  • Number of significantly mutated genes = 62

  • Number of Molecular subtypes = 8

  • 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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