Correlation between gene mutation status and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C14J0D7X
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14J0D7X
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] 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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle