Correlation between gene mutation status and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1B56J17
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/C1B56J17
Overview
Introduction

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

Summary

Testing the association between mutation status of 22 genes and 10 molecular subtypes across 332 patients, 20 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_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • ATM mutation correlated to 'CN_CNMF'.

  • MED12 mutation correlated to 'CN_CNMF'.

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

  • MLL2 mutation correlated to 'CN_CNMF'.

  • ZMYM3 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CDK12 mutation correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 22 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 20 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
SPOP 37 (11%) 295 1e-05
(0.00055) 		1e-05
(0.00055) 		0.641
(1.00) 		0.9
(1.00) 		1e-05
(0.00055) 		1e-05
(0.00055) 		0.782
(1.00) 		0.108
(0.567) 		0.17
(0.635) 		0.315
(0.786)
TP53 23 (7%) 309 0.00025
(0.00687) 		0.0159
(0.233) 		0.0915
(0.559) 		0.896
(1.00) 		0.0665
(0.515) 		0.018
(0.233) 		0.688
(1.00) 		0.00063
(0.0139) 		0.319
(0.789) 		0.132
(0.611)
FOXA1 13 (4%) 319 3e-05
(0.0011) 		2e-05
(0.00088) 		0.457
(0.94) 		0.11
(0.567) 		0.00023
(0.00687) 		0.00029
(0.00709) 		0.43
(0.901) 		0.0974
(0.564) 		0.567
(0.998) 		0.8
(1.00)
KDM6A 6 (2%) 326 0.0201
(0.233) 		0.257
(0.741) 		0.539
(0.974) 		0.928
(1.00) 		0.0266
(0.279) 		0.578
(1.00) 		0.533
(0.974) 		0.356
(0.834) 		0.339
(0.814) 		0.0129
(0.203)
CDK12 6 (2%) 326 0.0119
(0.201) 		0.224
(0.705) 		0.168
(0.635) 		0.00542
(0.108) 		0.878
(1.00) 		0.169
(0.635) 		0.0418
(0.379) 		0.221
(0.705) 		1
(1.00) 		0.824
(1.00)
ATM 13 (4%) 319 0.0118
(0.201) 		0.116
(0.568) 		0.557
(0.987) 		0.215
(0.705) 		0.732
(1.00) 		0.21
(0.705) 		0.144
(0.622) 		0.713
(1.00) 		0.506
(0.974) 		0.785
(1.00)
MED12 6 (2%) 326 0.0196
(0.233) 		0.522
(0.974) 		0.54
(0.974) 		0.766
(1.00) 		0.518
(0.974) 		0.144
(0.622) 		1
(1.00) 		0.947
(1.00) 		0.0701
(0.515) 		0.0503
(0.426)
MLL2 11 (3%) 321 0.0227
(0.25) 		0.798
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.201
(0.705) 		0.0946
(0.563) 		0.743
(1.00) 		0.119
(0.57) 		0.395
(0.86) 		0.39
(0.86)
ZMYM3 6 (2%) 326 0.628
(1.00) 		0.599
(1.00) 		0.372
(0.847) 		0.818
(1.00) 		0.879
(1.00) 		0.667
(1.00) 		0.875
(1.00) 		0.532
(0.974) 		0.0702
(0.515) 		0.0174
(0.233)
BRAF 8 (2%) 324 0.331
(0.81) 		0.256
(0.741) 		0.258
(0.741) 		0.908
(1.00) 		0.179
(0.656) 		0.477
(0.955) 		0.823
(1.00) 		0.825
(1.00) 		0.829
(1.00) 		0.288
(0.741)
PTEN 9 (3%) 323 0.811
(1.00) 		0.164
(0.635) 		0.241
(0.738) 		0.747
(1.00) 		0.224
(0.705) 		0.0288
(0.288) 		0.706
(1.00) 		0.412
(0.888) 		0.955
(1.00) 		0.72
(1.00)
CTNNB1 8 (2%) 324 0.794
(1.00) 		0.0431
(0.379) 		0.168
(0.635) 		0.0872
(0.552) 		0.361
(0.837) 		0.0787
(0.552) 		0.289
(0.741) 		0.133
(0.611) 		0.54
(0.974) 		0.293
(0.741)
AKT1 3 (1%) 329 1
(1.00) 		0.11
(0.567) 		0.112
(0.567) 		0.265
(0.741) 		1
(1.00) 		1
(1.00)
HRAS 4 (1%) 328 1
(1.00) 		0.836
(1.00) 		1
(1.00) 		0.252
(0.741) 		0.833
(1.00) 		1
(1.00) 		0.842
(1.00) 		0.222
(0.705) 		0.698
(1.00) 		0.843
(1.00)
XPO5 3 (1%) 329 1
(1.00) 		0.11
(0.567) 		0.113
(0.567) 		0.19
(0.685)
KLHL2 4 (1%) 328 0.818
(1.00) 		0.692
(1.00) 		0.0341
(0.326) 		0.465
(0.947) 		1
(1.00) 		1
(1.00) 		0.694
(1.00) 		0.374
(0.847) 		0.705
(1.00) 		0.963
(1.00)
AMFR 3 (1%) 329 0.139
(0.622) 		1
(1.00) 		0.608
(1.00) 		0.351
(0.831) 		1
(1.00) 		1
(1.00) 		0.537
(0.974) 		0.0819
(0.552)
IL6ST 3 (1%) 329 0.0847
(0.552) 		1
(1.00) 		0.795
(1.00) 		0.472
(0.953) 		0.291
(0.741) 		0.789
(1.00) 		0.423
(0.901) 		0.856
(1.00)
NKX3-1 4 (1%) 328 0.384
(0.86) 		1
(1.00) 		0.0545
(0.444) 		0.504
(0.974) 		0.556
(0.987) 		0.238
(0.738) 		0.169
(0.635) 		0.524
(0.974)
IRF4 4 (1%) 328 0.817
(1.00) 		1
(1.00) 		0.792
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.829
(1.00) 		0.22
(0.705) 		0.0878
(0.552) 		0.28
(0.741) 		0.34
(0.814)
ASH1L 7 (2%) 325 0.765
(1.00) 		0.64
(1.00) 		0.28
(0.741) 		0.892
(1.00) 		0.163
(0.635) 		0.497
(0.974) 		0.15
(0.635) 		0.452
(0.938) 		1
(1.00) 		0.267
(0.741)
MLL3 13 (4%) 319 0.285
(0.741) 		0.777
(1.00) 		1
(1.00) 		0.279
(0.741) 		0.834
(1.00) 		0.395
(0.86) 		0.427
(0.901) 		0.27
(0.741) 		0.216
(0.705) 		0.776
(1.00)
'SPOP MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
SPOP MUTATED 6 11 20
SPOP WILD-TYPE 179 77 39

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

'SPOP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
SPOP MUTATED 6 30 1
SPOP WILD-TYPE 101 73 121

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

'SPOP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
SPOP MUTATED 6 6 11
SPOP WILD-TYPE 82 51 93
'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
SPOP MUTATED 5 8 5 5
SPOP WILD-TYPE 53 74 61 38
'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
SPOP MUTATED 7 30 0
SPOP WILD-TYPE 96 73 126

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

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
SPOP MUTATED 3 34 0
SPOP WILD-TYPE 113 98 84

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

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
SPOP MUTATED 11 11 15
SPOP WILD-TYPE 94 98 100
'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
SPOP MUTATED 8 8 1 12 8
SPOP WILD-TYPE 92 60 38 60 42
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
SPOP MUTATED 2 8 2 9
SPOP WILD-TYPE 48 42 34 66
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
SPOP MUTATED 3 3 1 7 0 7
SPOP WILD-TYPE 36 20 20 38 25 51
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0069

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
TP53 MUTATED 6 15 2
TP53 WILD-TYPE 179 73 57

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
TP53 MUTATED 5 3 15
TP53 WILD-TYPE 102 100 107

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0915 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
TP53 MUTATED 3 2 11
TP53 WILD-TYPE 85 55 93
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
TP53 MUTATED 4 4 5 3
TP53 WILD-TYPE 54 78 61 40
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0665 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
TP53 MUTATED 4 5 14
TP53 WILD-TYPE 99 98 112
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
TP53 MUTATED 5 6 12
TP53 WILD-TYPE 111 126 72

Figure S7.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
TP53 MUTATED 6 7 10
TP53 WILD-TYPE 99 102 105
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
TP53 MUTATED 3 1 9 6 4
TP53 WILD-TYPE 97 67 30 66 46

Figure S8.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
TP53 MUTATED 1 4 2 8
TP53 WILD-TYPE 49 46 34 67
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
TP53 MUTATED 2 0 4 4 0 5
TP53 WILD-TYPE 37 23 17 41 25 53
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0011

Table S21.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
FOXA1 MUTATED 0 7 6
FOXA1 WILD-TYPE 185 81 53

Figure S9.  Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00088

Table S22.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
FOXA1 MUTATED 1 12 0
FOXA1 WILD-TYPE 106 91 122

Figure S10.  Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.94

Table S23.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
FOXA1 MUTATED 2 2 6
FOXA1 WILD-TYPE 86 55 98
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.57

Table S24.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
FOXA1 MUTATED 0 3 3 4
FOXA1 WILD-TYPE 58 79 63 39
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0069

Table S25.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
FOXA1 MUTATED 3 10 0
FOXA1 WILD-TYPE 100 93 126

Figure S11.  Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0071

Table S26.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
FOXA1 MUTATED 1 12 0
FOXA1 WILD-TYPE 115 120 84

Figure S12.  Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.9

Table S27.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
FOXA1 MUTATED 3 3 7
FOXA1 WILD-TYPE 102 106 108
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0974 (Fisher's exact test), Q value = 0.56

Table S28.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
FOXA1 MUTATED 1 4 0 5 3
FOXA1 WILD-TYPE 99 64 39 67 47
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
FOXA1 MUTATED 1 1 1 5
FOXA1 WILD-TYPE 49 49 35 70
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S30.  Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
FOXA1 MUTATED 1 1 0 2 0 4
FOXA1 WILD-TYPE 38 22 21 43 25 54
'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
BRAF MUTATED 4 1 3
BRAF WILD-TYPE 181 87 56
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
BRAF MUTATED 3 4 1
BRAF WILD-TYPE 104 99 121
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
BRAF MUTATED 4 2 1
BRAF WILD-TYPE 84 55 103
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.908 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
BRAF MUTATED 2 3 1 1
BRAF WILD-TYPE 56 79 65 42
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
BRAF MUTATED 2 5 1
BRAF WILD-TYPE 101 98 125
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
BRAF MUTATED 2 5 1
BRAF WILD-TYPE 114 127 83
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
BRAF MUTATED 3 3 2
BRAF WILD-TYPE 102 106 113
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.825 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
BRAF MUTATED 4 1 0 2 1
BRAF WILD-TYPE 96 67 39 70 49
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
BRAF MUTATED 1 0 1 2
BRAF WILD-TYPE 49 50 35 73
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
BRAF MUTATED 0 1 1 0 1 1
BRAF WILD-TYPE 39 22 20 45 24 57
'PTEN MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
PTEN MUTATED 5 3 1
PTEN WILD-TYPE 180 85 58
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
PTEN MUTATED 1 2 6
PTEN WILD-TYPE 106 101 116
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
PTEN MUTATED 2 4 2
PTEN WILD-TYPE 86 53 102
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.747 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
PTEN MUTATED 2 4 1 1
PTEN WILD-TYPE 56 78 65 42
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
PTEN MUTATED 1 2 6
PTEN WILD-TYPE 102 101 120
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
PTEN MUTATED 1 2 6
PTEN WILD-TYPE 115 130 78

Figure S13.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
PTEN MUTATED 4 2 3
PTEN WILD-TYPE 101 107 112
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
PTEN MUTATED 4 1 0 1 3
PTEN WILD-TYPE 96 67 39 71 47
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.955 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
PTEN MUTATED 1 2 1 3
PTEN WILD-TYPE 49 48 35 72
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
PTEN MUTATED 1 0 0 3 0 3
PTEN WILD-TYPE 38 23 21 42 25 55
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
ATM MUTATED 3 8 2
ATM WILD-TYPE 182 80 57

Figure S14.  Get High-res Image Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
ATM MUTATED 1 6 6
ATM WILD-TYPE 106 97 116
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
ATM MUTATED 3 2 7
ATM WILD-TYPE 85 55 97
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
ATM MUTATED 2 3 2 5
ATM WILD-TYPE 56 79 64 38
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
ATM MUTATED 3 5 5
ATM WILD-TYPE 100 98 121
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
ATM MUTATED 2 8 3
ATM WILD-TYPE 114 124 81
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
ATM MUTATED 1 6 6
ATM WILD-TYPE 104 103 109
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
ATM MUTATED 2 4 2 3 2
ATM WILD-TYPE 98 64 37 69 48
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
ATM MUTATED 1 3 0 4
ATM WILD-TYPE 49 47 36 71
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
ATM MUTATED 0 1 1 2 1 3
ATM WILD-TYPE 39 22 20 43 24 55
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
CTNNB1 MUTATED 4 3 1
CTNNB1 WILD-TYPE 181 85 58
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.38

Table S62.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
CTNNB1 MUTATED 0 2 6
CTNNB1 WILD-TYPE 107 101 116

Figure S15.  Get High-res Image Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.64

Table S63.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
CTNNB1 MUTATED 0 1 4
CTNNB1 WILD-TYPE 88 56 100
'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0872 (Fisher's exact test), Q value = 0.55

Table S64.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
CTNNB1 MUTATED 0 1 1 3
CTNNB1 WILD-TYPE 58 81 65 40
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.84

Table S65.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
CTNNB1 MUTATED 1 2 5
CTNNB1 WILD-TYPE 102 101 121
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0787 (Fisher's exact test), Q value = 0.55

Table S66.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
CTNNB1 MUTATED 1 2 5
CTNNB1 WILD-TYPE 115 130 79
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.74

Table S67.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
CTNNB1 MUTATED 1 2 5
CTNNB1 WILD-TYPE 104 107 110
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.61

Table S68.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
CTNNB1 MUTATED 1 0 1 3 3
CTNNB1 WILD-TYPE 99 68 38 69 47
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.97

Table S69.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
CTNNB1 MUTATED 1 3 0 3
CTNNB1 WILD-TYPE 49 47 36 72
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 0.74

Table S70.  Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
CTNNB1 MUTATED 0 0 0 4 1 2
CTNNB1 WILD-TYPE 39 23 21 41 24 56
'MED12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.23

Table S71.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
MED12 MUTATED 2 0 4
MED12 WILD-TYPE 183 88 55

Figure S16.  Get High-res Image Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MED12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.97

Table S72.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
MED12 MUTATED 3 2 1
MED12 WILD-TYPE 104 101 121
'MED12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.97

Table S73.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
MED12 MUTATED 3 1 1
MED12 WILD-TYPE 85 56 103
'MED12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
MED12 MUTATED 2 2 1 0
MED12 WILD-TYPE 56 80 65 43
'MED12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 0.97

Table S75.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
MED12 MUTATED 2 3 1
MED12 WILD-TYPE 101 100 125
'MED12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.62

Table S76.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
MED12 MUTATED 1 5 0
MED12 WILD-TYPE 115 127 84
'MED12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S77.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
MED12 MUTATED 2 2 2
MED12 WILD-TYPE 103 107 113
'MED12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
MED12 MUTATED 2 2 0 1 1
MED12 WILD-TYPE 98 66 39 71 49
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0701 (Fisher's exact test), Q value = 0.51

Table S79.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
MED12 MUTATED 0 1 2 0
MED12 WILD-TYPE 50 49 34 75
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0503 (Fisher's exact test), Q value = 0.43

Table S80.  Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
MED12 MUTATED 1 2 0 0 0 0
MED12 WILD-TYPE 38 21 21 45 25 58
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.23

Table S81.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
KDM6A MUTATED 2 0 4
KDM6A WILD-TYPE 183 88 55

Figure S17.  Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.74

Table S82.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
KDM6A MUTATED 1 4 1
KDM6A WILD-TYPE 106 99 121
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.97

Table S83.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
KDM6A MUTATED 3 1 1
KDM6A WILD-TYPE 85 56 103
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S84.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
KDM6A MUTATED 1 1 2 1
KDM6A WILD-TYPE 57 81 64 42
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.28

Table S85.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
KDM6A MUTATED 0 5 1
KDM6A WILD-TYPE 103 98 125

Figure S18.  Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
KDM6A MUTATED 1 4 1
KDM6A WILD-TYPE 115 128 83
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 0.97

Table S87.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
KDM6A MUTATED 2 3 1
KDM6A WILD-TYPE 103 106 114
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.83

Table S88.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
KDM6A MUTATED 2 3 0 0 1
KDM6A WILD-TYPE 98 65 39 72 49
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.81

Table S89.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
KDM6A MUTATED 0 0 1 3
KDM6A WILD-TYPE 50 50 35 72
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.2

Table S90.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
KDM6A MUTATED 0 3 0 0 0 1
KDM6A WILD-TYPE 39 20 21 45 25 57

Figure S19.  Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.25

Table S91.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
MLL2 MUTATED 2 5 4
MLL2 WILD-TYPE 183 83 55

Figure S20.  Get High-res Image Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
MLL2 MUTATED 4 4 3
MLL2 WILD-TYPE 103 99 119
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S93.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
MLL2 MUTATED 3 2 3
MLL2 WILD-TYPE 85 55 101
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S94.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
MLL2 MUTATED 1 3 3 1
MLL2 WILD-TYPE 57 79 63 42
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.71

Table S95.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
MLL2 MUTATED 3 6 2
MLL2 WILD-TYPE 100 97 124
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0946 (Fisher's exact test), Q value = 0.56

Table S96.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
MLL2 MUTATED 6 5 0
MLL2 WILD-TYPE 110 127 84
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S97.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
MLL2 MUTATED 3 5 3
MLL2 WILD-TYPE 102 104 112
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.57

Table S98.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
MLL2 MUTATED 3 4 3 0 1
MLL2 WILD-TYPE 97 64 36 72 49
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.86

Table S99.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
MLL2 MUTATED 0 2 2 2
MLL2 WILD-TYPE 50 48 34 73
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.86

Table S100.  Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
MLL2 MUTATED 0 2 0 2 0 2
MLL2 WILD-TYPE 39 21 21 43 25 56
'AKT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S101.  Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
AKT1 MUTATED 2 1 0
AKT1 WILD-TYPE 183 87 59
'AKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.57

Table S102.  Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
AKT1 MUTATED 0 0 3
AKT1 WILD-TYPE 107 103 119
'AKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.57

Table S103.  Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
AKT1 MUTATED 0 0 3
AKT1 WILD-TYPE 103 103 123
'AKT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.74

Table S104.  Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
AKT1 MUTATED 0 1 2
AKT1 WILD-TYPE 116 131 82
'AKT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S105.  Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
AKT1 MUTATED 1 1 1
AKT1 WILD-TYPE 104 108 114
'AKT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S106.  Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
AKT1 MUTATED 1 1 0 1 0
AKT1 WILD-TYPE 99 67 39 71 50
'HRAS MUTATION STATUS' versus 'CN_CNMF'

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

Table S107.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
HRAS MUTATED 3 1 0
HRAS WILD-TYPE 182 87 59
'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S108.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
HRAS MUTATED 2 1 1
HRAS WILD-TYPE 105 102 121
'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S109.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
HRAS MUTATED 1 1 1
HRAS WILD-TYPE 87 56 103
'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 0.74

Table S110.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
HRAS MUTATED 2 0 1 0
HRAS WILD-TYPE 56 82 65 43
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
HRAS MUTATED 1 2 1
HRAS WILD-TYPE 102 101 125
'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S112.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
HRAS MUTATED 1 2 1
HRAS WILD-TYPE 115 130 83
'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
HRAS MUTATED 1 2 1
HRAS WILD-TYPE 104 107 114
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.71

Table S114.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
HRAS MUTATED 1 0 0 3 0
HRAS WILD-TYPE 99 68 39 69 50
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S115.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
HRAS MUTATED 1 0 1 1
HRAS WILD-TYPE 49 50 35 74
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
HRAS MUTATED 1 0 0 0 0 2
HRAS WILD-TYPE 38 23 21 45 25 56
'XPO5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S117.  Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
XPO5 MUTATED 2 1 0
XPO5 WILD-TYPE 183 87 59
'XPO5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.57

Table S118.  Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
XPO5 MUTATED 0 0 3
XPO5 WILD-TYPE 107 103 119
'XPO5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.57

Table S119.  Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
XPO5 MUTATED 0 0 3
XPO5 WILD-TYPE 103 103 123
'XPO5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.68

Table S120.  Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
XPO5 MUTATED 1 0 2
XPO5 WILD-TYPE 115 132 82
'KLHL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S121.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
KLHL2 MUTATED 2 1 1
KLHL2 WILD-TYPE 183 87 58
'KLHL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S122.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
KLHL2 MUTATED 1 2 1
KLHL2 WILD-TYPE 106 101 121
'KLHL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.33

Table S123.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
KLHL2 MUTATED 1 3 0
KLHL2 WILD-TYPE 87 54 104

Figure S21.  Get High-res Image Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KLHL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 0.95

Table S124.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
KLHL2 MUTATED 2 1 0 1
KLHL2 WILD-TYPE 56 81 66 42
'KLHL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S125.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
KLHL2 MUTATED 1 1 2
KLHL2 WILD-TYPE 102 102 124
'KLHL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S126.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
KLHL2 MUTATED 1 2 1
KLHL2 WILD-TYPE 115 130 83
'KLHL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S127.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
KLHL2 MUTATED 2 1 1
KLHL2 WILD-TYPE 103 108 114
'KLHL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.85

Table S128.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
KLHL2 MUTATED 1 0 0 1 2
KLHL2 WILD-TYPE 99 68 39 71 48
'KLHL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S129.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
KLHL2 MUTATED 2 1 0 1
KLHL2 WILD-TYPE 48 49 36 74
'KLHL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S130.  Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
KLHL2 MUTATED 1 0 0 1 1 1
KLHL2 WILD-TYPE 38 23 21 44 24 57
'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S131.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
ZMYM3 MUTATED 3 1 2
ZMYM3 WILD-TYPE 182 87 57
'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S132.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
ZMYM3 MUTATED 1 3 2
ZMYM3 WILD-TYPE 106 100 120
'ZMYM3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.85

Table S133.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
ZMYM3 MUTATED 3 0 2
ZMYM3 WILD-TYPE 85 57 102
'ZMYM3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S134.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
ZMYM3 MUTATED 2 1 1 1
ZMYM3 WILD-TYPE 56 81 65 42
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S135.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
ZMYM3 MUTATED 2 1 3
ZMYM3 WILD-TYPE 101 102 123
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 1

Table S136.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
ZMYM3 MUTATED 1 3 2
ZMYM3 WILD-TYPE 115 129 82
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S137.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
ZMYM3 MUTATED 1 2 3
ZMYM3 WILD-TYPE 104 107 112
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 0.97

Table S138.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
ZMYM3 MUTATED 2 1 2 1 0
ZMYM3 WILD-TYPE 98 67 37 71 50
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0702 (Fisher's exact test), Q value = 0.51

Table S139.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
ZMYM3 MUTATED 3 2 0 0
ZMYM3 WILD-TYPE 47 48 36 75
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.23

Table S140.  Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
ZMYM3 MUTATED 0 0 0 2 3 0
ZMYM3 WILD-TYPE 39 23 21 43 22 58

Figure S22.  Get High-res Image Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AMFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.62

Table S141.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
AMFR MUTATED 1 0 2
AMFR WILD-TYPE 184 88 57
'AMFR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S142.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
AMFR MUTATED 1 1 1
AMFR WILD-TYPE 106 102 121
'AMFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S143.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
AMFR MUTATED 2 0 1
AMFR WILD-TYPE 86 57 103
'AMFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.351 (Fisher's exact test), Q value = 0.83

Table S144.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
AMFR MUTATED 2 1 0 0
AMFR WILD-TYPE 56 81 66 43
'AMFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S145.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
AMFR MUTATED 1 1 1
AMFR WILD-TYPE 102 102 125
'AMFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S146.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
AMFR MUTATED 1 1 1
AMFR WILD-TYPE 115 131 83
'AMFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 0.97

Table S147.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
AMFR MUTATED 0 2 1
AMFR WILD-TYPE 105 107 114
'AMFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0819 (Fisher's exact test), Q value = 0.55

Table S148.  Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
AMFR MUTATED 0 1 0 0 2
AMFR WILD-TYPE 100 67 39 72 48
'IL6ST MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0847 (Fisher's exact test), Q value = 0.55

Table S149.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
IL6ST MUTATED 0 2 1
IL6ST WILD-TYPE 185 86 58
'IL6ST MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S150.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
IL6ST MUTATED 1 1 1
IL6ST WILD-TYPE 106 102 121
'IL6ST MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S151.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
IL6ST MUTATED 1 0 2
IL6ST WILD-TYPE 87 57 102
'IL6ST MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.472 (Fisher's exact test), Q value = 0.95

Table S152.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
IL6ST MUTATED 1 0 1 1
IL6ST WILD-TYPE 57 82 65 42
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.74

Table S153.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
IL6ST MUTATED 2 1 0
IL6ST WILD-TYPE 101 102 126
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S154.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
IL6ST MUTATED 1 2 0
IL6ST WILD-TYPE 115 130 84
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.9

Table S155.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
IL6ST MUTATED 2 0 1
IL6ST WILD-TYPE 103 109 114
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S156.  Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
IL6ST MUTATED 2 0 0 1 0
IL6ST WILD-TYPE 98 68 39 71 50
'CDK12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.2

Table S157.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
CDK12 MUTATED 1 5 0
CDK12 WILD-TYPE 184 83 59

Figure S23.  Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.71

Table S158.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
CDK12 MUTATED 0 3 3
CDK12 WILD-TYPE 107 100 119
'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.64

Table S159.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
CDK12 MUTATED 0 1 4
CDK12 WILD-TYPE 88 56 100
'CDK12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00542 (Fisher's exact test), Q value = 0.11

Table S160.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
CDK12 MUTATED 0 1 0 4
CDK12 WILD-TYPE 58 81 66 39

Figure S24.  Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S161.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
CDK12 MUTATED 1 2 3
CDK12 WILD-TYPE 102 101 123
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.64

Table S162.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
CDK12 MUTATED 0 4 2
CDK12 WILD-TYPE 116 128 82
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.38

Table S163.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
CDK12 MUTATED 1 0 5
CDK12 WILD-TYPE 104 109 110

Figure S25.  Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.71

Table S164.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
CDK12 MUTATED 0 1 1 3 1
CDK12 WILD-TYPE 100 67 38 69 49
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S165.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
CDK12 MUTATED 1 1 0 2
CDK12 WILD-TYPE 49 49 36 73
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S166.  Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
CDK12 MUTATED 0 0 0 1 1 2
CDK12 WILD-TYPE 39 23 21 44 24 56
'NKX3-1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.86

Table S167.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
NKX3-1 MUTATED 4 0 0
NKX3-1 WILD-TYPE 181 88 59
'NKX3-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S168.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
NKX3-1 MUTATED 1 1 2
NKX3-1 WILD-TYPE 106 102 120
'NKX3-1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0545 (Fisher's exact test), Q value = 0.44

Table S169.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
NKX3-1 MUTATED 0 3 1
NKX3-1 WILD-TYPE 88 54 103
'NKX3-1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.97

Table S170.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
NKX3-1 MUTATED 0 3 1 0
NKX3-1 WILD-TYPE 58 79 65 43
'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.99

Table S171.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
NKX3-1 MUTATED 0 2 2
NKX3-1 WILD-TYPE 103 101 124
'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S172.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
NKX3-1 MUTATED 0 2 2
NKX3-1 WILD-TYPE 116 130 82
'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.64

Table S173.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
NKX3-1 MUTATED 1 3 0
NKX3-1 WILD-TYPE 104 106 115
'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 0.97

Table S174.  Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
NKX3-1 MUTATED 1 2 0 0 1
NKX3-1 WILD-TYPE 99 66 39 72 49
'IRF4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S175.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
IRF4 MUTATED 2 1 1
IRF4 WILD-TYPE 183 87 58
'IRF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S176.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
IRF4 MUTATED 1 1 2
IRF4 WILD-TYPE 106 102 120
'IRF4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S177.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
IRF4 MUTATED 1 0 2
IRF4 WILD-TYPE 87 57 102
'IRF4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S178.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
IRF4 MUTATED 1 1 0 1
IRF4 WILD-TYPE 57 81 66 42
'IRF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S179.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
IRF4 MUTATED 1 1 2
IRF4 WILD-TYPE 102 102 124
'IRF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
IRF4 MUTATED 2 1 1
IRF4 WILD-TYPE 114 131 83
'IRF4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.71

Table S181.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
IRF4 MUTATED 0 3 1
IRF4 WILD-TYPE 105 106 114
'IRF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0878 (Fisher's exact test), Q value = 0.55

Table S182.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
IRF4 MUTATED 0 0 1 1 2
IRF4 WILD-TYPE 100 68 38 71 48
'IRF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.74

Table S183.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
IRF4 MUTATED 0 0 0 3
IRF4 WILD-TYPE 50 50 36 72
'IRF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.34 (Fisher's exact test), Q value = 0.81

Table S184.  Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
IRF4 MUTATED 0 0 0 0 0 3
IRF4 WILD-TYPE 39 23 21 45 25 55
'ASH1L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S185.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
ASH1L MUTATED 4 1 2
ASH1L WILD-TYPE 181 87 57
'ASH1L MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S186.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
ASH1L MUTATED 1 3 3
ASH1L WILD-TYPE 106 100 119
'ASH1L MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.74

Table S187.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
ASH1L MUTATED 1 3 2
ASH1L WILD-TYPE 87 54 102
'ASH1L MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S188.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
ASH1L MUTATED 1 3 1 1
ASH1L WILD-TYPE 57 79 65 42
'ASH1L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.64

Table S189.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
ASH1L MUTATED 0 4 3
ASH1L WILD-TYPE 103 99 123
'ASH1L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 0.97

Table S190.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
ASH1L MUTATED 1 4 2
ASH1L WILD-TYPE 115 128 82
'ASH1L MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.64

Table S191.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
ASH1L MUTATED 3 0 4
ASH1L WILD-TYPE 102 109 111
'ASH1L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.94

Table S192.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
ASH1L MUTATED 3 0 0 2 2
ASH1L WILD-TYPE 97 68 39 70 48
'ASH1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S193.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
ASH1L MUTATED 1 1 0 1
ASH1L WILD-TYPE 49 49 36 74
'ASH1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.267 (Fisher's exact test), Q value = 0.74

Table S194.  Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
ASH1L MUTATED 0 0 0 2 1 0
ASH1L WILD-TYPE 39 23 21 43 24 58
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.74

Table S195.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 88 59
MLL3 MUTATED 6 6 1
MLL3 WILD-TYPE 179 82 58
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S196.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 103 122
MLL3 MUTATED 4 3 6
MLL3 WILD-TYPE 103 100 116
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S197.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 57 104
MLL3 MUTATED 3 2 4
MLL3 WILD-TYPE 85 55 100
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.74

Table S198.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 82 66 43
MLL3 MUTATED 0 3 4 2
MLL3 WILD-TYPE 58 79 62 41
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S199.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 103 126
MLL3 MUTATED 3 4 6
MLL3 WILD-TYPE 100 99 120
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.86

Table S200.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 132 84
MLL3 MUTATED 5 3 5
MLL3 WILD-TYPE 111 129 79
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.9

Table S201.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 109 115
MLL3 MUTATED 3 3 7
MLL3 WILD-TYPE 102 106 108
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 0.74

Table S202.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 68 39 72 50
MLL3 MUTATED 2 3 4 3 1
MLL3 WILD-TYPE 98 65 35 69 49
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.71

Table S203.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 50 50 36 75
MLL3 MUTATED 2 5 0 3
MLL3 WILD-TYPE 48 45 36 72
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S204.  Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 23 21 45 25 58
MLL3 MUTATED 2 0 1 4 1 2
MLL3 WILD-TYPE 37 23 20 41 24 56
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/20064817/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/20168456/PRAD-TP.transferedmergedcluster.txt

  • Number of patients = 332

  • Number of significantly mutated genes = 22

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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)
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