Correlation between gene mutation status and molecular subtypes
Bladder Urothelial Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1C24V01
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1C24V01
Overview
Introduction

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

Summary

Testing the association between mutation status of 23 genes and 10 molecular subtypes across 130 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 23 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, no significant finding 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 Chi-square test Fisher's exact test Chi-square 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
PIK3CA 26 (20%) 104 0.22
(1.00) 		0.797
(1.00) 		0.167
(1.00) 		0.784
(1.00) 		0.363
(1.00) 		0.269
(1.00) 		0.656
(1.00) 		0.0534
(1.00) 		0.456
(1.00) 		0.547
(1.00)
TP53 64 (49%) 66 0.0712
(1.00) 		0.233
(1.00) 		0.0409
(1.00) 		0.013
(1.00) 		0.103
(1.00) 		0.261
(1.00) 		0.415
(1.00) 		0.589
(1.00) 		0.237
(1.00) 		0.325
(1.00)
CDKN1A 18 (14%) 112 0.246
(1.00) 		0.499
(1.00) 		0.861
(1.00) 		0.491
(1.00) 		0.923
(1.00) 		0.775
(1.00) 		0.868
(1.00) 		0.911
(1.00) 		0.539
(1.00) 		0.538
(1.00)
RB1 17 (13%) 113 0.0209
(1.00) 		0.331
(1.00) 		0.518
(1.00) 		0.115
(1.00) 		0.501
(1.00) 		0.628
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.329
(1.00)
ARID1A 32 (25%) 98 0.79
(1.00) 		0.753
(1.00) 		0.614
(1.00) 		0.21
(1.00) 		0.575
(1.00) 		0.501
(1.00) 		0.0506
(1.00) 		0.145
(1.00) 		0.235
(1.00) 		0.185
(1.00)
MLL2 36 (28%) 94 0.293
(1.00) 		0.66
(1.00) 		0.369
(1.00) 		0.205
(1.00) 		0.245
(1.00) 		0.621
(1.00) 		0.538
(1.00) 		0.814
(1.00) 		0.473
(1.00) 		0.648
(1.00)
FBXW7 13 (10%) 117 0.91
(1.00) 		0.0265
(1.00) 		0.385
(1.00) 		0.349
(1.00) 		0.0895
(1.00) 		0.139
(1.00) 		0.212
(1.00) 		0.167
(1.00) 		0.0145
(1.00) 		0.12
(1.00)
KDM6A 31 (24%) 99 0.345
(1.00) 		0.942
(1.00) 		0.362
(1.00) 		0.193
(1.00) 		0.514
(1.00) 		0.886
(1.00) 		0.142
(1.00) 		0.195
(1.00) 		0.779
(1.00) 		0.201
(1.00)
ELF3 11 (8%) 119 0.761
(1.00) 		0.0233
(1.00) 		0.631
(1.00) 		0.585
(1.00) 		0.674
(1.00) 		0.154
(1.00) 		0.482
(1.00) 		0.662
(1.00) 		0.78
(1.00) 		0.422
(1.00)
FGFR3 16 (12%) 114 0.55
(1.00) 		0.119
(1.00) 		0.0621
(1.00) 		0.0238
(1.00) 		0.0801
(1.00) 		0.0114
(1.00) 		0.289
(1.00) 		0.609
(1.00) 		0.0117
(1.00) 		0.0318
(1.00)
FOXQ1 7 (5%) 123 0.49
(1.00) 		0.41
(1.00) 		0.486
(1.00) 		0.295
(1.00) 		0.721
(1.00) 		0.891
(1.00) 		0.253
(1.00) 		0.805
(1.00) 		0.466
(1.00) 		0.568
(1.00)
STAG2 14 (11%) 116 0.387
(1.00) 		0.173
(1.00) 		0.24
(1.00) 		0.547
(1.00) 		0.374
(1.00) 		0.127
(1.00) 		0.278
(1.00) 		0.636
(1.00) 		0.127
(1.00) 		0.0123
(1.00)
NFE2L2 11 (8%) 119 0.233
(1.00) 		0.212
(1.00) 		0.484
(1.00) 		0.672
(1.00) 		0.0822
(1.00) 		0.232
(1.00) 		0.853
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.69
(1.00)
CDKN2A 7 (5%) 123 0.37
(1.00) 		0.523
(1.00) 		0.356
(1.00) 		0.111
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.419
(1.00) 		0.805
(1.00) 		0.466
(1.00) 		1
(1.00)
KLF5 10 (8%) 120 0.711
(1.00) 		0.768
(1.00) 		0.377
(1.00) 		0.317
(1.00) 		0.916
(1.00) 		0.129
(1.00) 		0.765
(1.00) 		0.869
(1.00) 		0.352
(1.00) 		0.0246
(1.00)
ASXL2 9 (7%) 121 0.326
(1.00) 		0.49
(1.00) 		0.421
(1.00) 		0.194
(1.00) 		0.618
(1.00) 		0.374
(1.00) 		0.756
(1.00) 		0.845
(1.00) 		0.147
(1.00) 		0.506
(1.00)
TSC1 11 (8%) 119 0.511
(1.00) 		0.51
(1.00) 		0.346
(1.00) 		0.139
(1.00) 		0.343
(1.00) 		0.0198
(1.00) 		0.521
(1.00) 		0.662
(1.00) 		0.661
(1.00) 		0.135
(1.00)
ERCC2 16 (12%) 114 0.897
(1.00) 		0.604
(1.00) 		0.139
(1.00) 		0.0442
(1.00) 		0.134
(1.00) 		0.219
(1.00) 		0.176
(1.00) 		0.392
(1.00) 		0.871
(1.00) 		1
(1.00)
TXNIP 9 (7%) 121 0.66
(1.00) 		0.91
(1.00) 		0.796
(1.00) 		0.439
(1.00) 		0.562
(1.00) 		0.495
(1.00) 		1
(1.00) 		0.0713
(1.00) 		0.488
(1.00) 		1
(1.00)
EP300 21 (16%) 109 0.594
(1.00) 		0.455
(1.00) 		0.45
(1.00) 		0.587
(1.00) 		0.525
(1.00) 		0.797
(1.00) 		0.302
(1.00) 		0.63
(1.00) 		0.337
(1.00) 		0.337
(1.00)
RXRA 12 (9%) 118 0.837
(1.00) 		0.061
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.147
(1.00) 		0.467
(1.00) 		0.204
(1.00) 		0.856
(1.00) 		0.456
(1.00)
FOXA1 7 (5%) 123 0.403
(1.00) 		0.608
(1.00) 		0.668
(1.00) 		0.85
(1.00) 		0.368
(1.00) 		0.543
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.654
(1.00)
PHLDA3 4 (3%) 126 0.467
(1.00) 		0.53
(1.00) 		0.508
(1.00) 		0.51
(1.00) 		0.219
(1.00) 		0.356
(1.00) 		0.683
(1.00) 		1
(1.00) 		0.833
(1.00) 		0.386
(1.00)
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.22 (Chi-square test), Q value = 1

Table S1.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
PIK3CA MUTATED 1 10 3 2 2 4 1 3
PIK3CA WILD-TYPE 8 31 9 5 20 13 13 2
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
PIK3CA MUTATED 9 12 5
PIK3CA WILD-TYPE 42 41 21
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.167 (Chi-square test), Q value = 1

Table S3.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
PIK3CA MUTATED 5 6 11 0 2
PIK3CA WILD-TYPE 31 22 22 5 15
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
PIK3CA MUTATED 9 2 4 9
PIK3CA WILD-TYPE 33 16 13 33
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
PIK3CA MUTATED 8 10 8
PIK3CA WILD-TYPE 46 28 29
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
PIK3CA MUTATED 11 9 6
PIK3CA WILD-TYPE 43 22 38
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
PIK3CA MUTATED 5 13 8
PIK3CA WILD-TYPE 28 43 33
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0534 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
PIK3CA MUTATED 19 4 3
PIK3CA WILD-TYPE 70 5 29
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
PIK3CA MUTATED 3 10 13
PIK3CA WILD-TYPE 23 39 42
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.547 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
PIK3CA MUTATED 6 17 3
PIK3CA WILD-TYPE 25 57 22
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0712 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
TP53 MUTATED 4 12 8 5 12 12 7 3
TP53 WILD-TYPE 5 29 4 2 10 5 7 2
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
TP53 MUTATED 28 27 9
TP53 WILD-TYPE 23 26 17
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0409 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
TP53 MUTATED 14 11 23 1 9
TP53 WILD-TYPE 22 17 10 4 8

Figure S1.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.013 (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 42 18 17 42
TP53 MUTATED 15 9 14 20
TP53 WILD-TYPE 27 9 3 22

Figure S2.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
TP53 MUTATED 21 23 20
TP53 WILD-TYPE 33 15 17
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
TP53 MUTATED 31 15 18
TP53 WILD-TYPE 23 16 26
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.415 (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 33 56 41
TP53 MUTATED 13 30 21
TP53 WILD-TYPE 20 26 20
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
TP53 MUTATED 46 3 15
TP53 WILD-TYPE 43 6 17
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
TP53 MUTATED 9 25 30
TP53 WILD-TYPE 17 24 25
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.325 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
TP53 MUTATED 17 38 9
TP53 WILD-TYPE 14 36 16
'CDKN1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.246 (Chi-square test), Q value = 1

Table S21.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
CDKN1A MUTATED 0 5 0 1 4 2 4 2
CDKN1A WILD-TYPE 9 36 12 6 18 15 10 3
'CDKN1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
CDKN1A MUTATED 9 7 2
CDKN1A WILD-TYPE 42 46 24
'CDKN1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.861 (Chi-square test), Q value = 1

Table S23.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
CDKN1A MUTATED 6 4 5 1 1
CDKN1A WILD-TYPE 30 24 28 4 16
'CDKN1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
CDKN1A MUTATED 7 2 4 4
CDKN1A WILD-TYPE 35 16 13 38
'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S25.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
CDKN1A MUTATED 7 6 5
CDKN1A WILD-TYPE 47 32 32
'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
CDKN1A MUTATED 8 3 7
CDKN1A WILD-TYPE 46 28 37
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S27.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
CDKN1A MUTATED 5 7 6
CDKN1A WILD-TYPE 28 49 35
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
CDKN1A MUTATED 12 1 5
CDKN1A WILD-TYPE 77 8 27
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
CDKN1A MUTATED 5 7 6
CDKN1A WILD-TYPE 21 42 49
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
CDKN1A MUTATED 3 10 5
CDKN1A WILD-TYPE 28 64 20
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0209 (Chi-square test), Q value = 1

Table S31.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
RB1 MUTATED 0 2 1 2 3 4 2 3
RB1 WILD-TYPE 9 39 11 5 19 13 12 2

Figure S3.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
RB1 MUTATED 5 10 2
RB1 WILD-TYPE 46 43 24
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.518 (Chi-square test), Q value = 1

Table S33.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
RB1 MUTATED 3 6 5 0 2
RB1 WILD-TYPE 33 22 28 5 15
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
RB1 MUTATED 2 2 4 8
RB1 WILD-TYPE 40 16 13 34
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
RB1 MUTATED 6 4 7
RB1 WILD-TYPE 48 34 30
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
RB1 MUTATED 9 3 5
RB1 WILD-TYPE 45 28 39
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
RB1 MUTATED 3 9 5
RB1 WILD-TYPE 30 47 36
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S38.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
RB1 MUTATED 12 1 4
RB1 WILD-TYPE 77 8 28
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
RB1 MUTATED 1 6 10
RB1 WILD-TYPE 25 43 45
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
RB1 MUTATED 4 12 1
RB1 WILD-TYPE 27 62 24
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.79 (Chi-square test), Q value = 1

Table S41.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
ARID1A MUTATED 2 9 3 1 7 6 4 0
ARID1A WILD-TYPE 7 32 9 6 15 11 10 5
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
ARID1A MUTATED 14 13 5
ARID1A WILD-TYPE 37 40 21
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.614 (Chi-square test), Q value = 1

Table S43.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ARID1A MUTATED 11 8 6 2 3
ARID1A WILD-TYPE 25 20 27 3 14
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
ARID1A MUTATED 10 2 3 15
ARID1A WILD-TYPE 32 16 14 27
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
ARID1A MUTATED 14 11 7
ARID1A WILD-TYPE 40 27 30
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
ARID1A MUTATED 13 10 9
ARID1A WILD-TYPE 41 21 35
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0506 (Fisher's exact test), Q value = 1

Table S47.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
ARID1A MUTATED 10 8 14
ARID1A WILD-TYPE 23 48 27
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
ARID1A MUTATED 18 2 12
ARID1A WILD-TYPE 71 7 20
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
ARID1A MUTATED 8 8 16
ARID1A WILD-TYPE 18 41 39
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
ARID1A MUTATED 4 20 8
ARID1A WILD-TYPE 27 54 17
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.293 (Chi-square test), Q value = 1

Table S51.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
MLL2 MUTATED 1 12 2 1 8 7 1 2
MLL2 WILD-TYPE 8 29 10 6 14 10 13 3
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
MLL2 MUTATED 13 17 6
MLL2 WILD-TYPE 38 36 20
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.369 (Chi-square test), Q value = 1

Table S53.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
MLL2 MUTATED 9 5 12 1 7
MLL2 WILD-TYPE 27 23 21 4 10
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
MLL2 MUTATED 12 8 6 8
MLL2 WILD-TYPE 30 10 11 34
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
MLL2 MUTATED 12 9 14
MLL2 WILD-TYPE 42 29 23
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
MLL2 MUTATED 17 8 10
MLL2 WILD-TYPE 37 23 34
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S57.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
MLL2 MUTATED 9 18 9
MLL2 WILD-TYPE 24 38 32
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.814 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
MLL2 MUTATED 25 3 8
MLL2 WILD-TYPE 64 6 24
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
MLL2 MUTATED 5 16 15
MLL2 WILD-TYPE 21 33 40
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
MLL2 MUTATED 7 23 6
MLL2 WILD-TYPE 24 51 19
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.91 (Chi-square test), Q value = 1

Table S61.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
FBXW7 MUTATED 1 5 2 0 2 1 1 0
FBXW7 WILD-TYPE 8 36 10 7 20 16 13 5
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
FBXW7 MUTATED 2 10 1
FBXW7 WILD-TYPE 49 43 25

Figure S4.  Get High-res Image Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.385 (Chi-square test), Q value = 1

Table S63.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FBXW7 MUTATED 1 3 5 1 1
FBXW7 WILD-TYPE 35 25 28 4 16
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
FBXW7 MUTATED 2 1 3 5
FBXW7 WILD-TYPE 40 17 14 37
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0895 (Fisher's exact test), Q value = 1

Table S65.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
FBXW7 MUTATED 2 5 6
FBXW7 WILD-TYPE 52 33 31
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S66.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
FBXW7 MUTATED 9 2 2
FBXW7 WILD-TYPE 45 29 42
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
FBXW7 MUTATED 6 4 3
FBXW7 WILD-TYPE 27 52 38
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S68.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
FBXW7 MUTATED 7 0 6
FBXW7 WILD-TYPE 82 9 26
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
FBXW7 MUTATED 6 1 6
FBXW7 WILD-TYPE 20 48 49

Figure S5.  Get High-res Image Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S70.  Gene #7: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
FBXW7 MUTATED 1 7 5
FBXW7 WILD-TYPE 30 67 20
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.345 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
KDM6A MUTATED 3 7 5 3 4 4 5 0
KDM6A WILD-TYPE 6 34 7 4 18 13 9 5
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.942 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
KDM6A MUTATED 13 12 6
KDM6A WILD-TYPE 38 41 20
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.362 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
KDM6A MUTATED 9 4 10 2 2
KDM6A WILD-TYPE 27 24 23 3 15
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
KDM6A MUTATED 8 2 7 10
KDM6A WILD-TYPE 34 16 10 32
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
KDM6A MUTATED 13 7 11
KDM6A WILD-TYPE 41 31 26
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
KDM6A MUTATED 12 8 11
KDM6A WILD-TYPE 42 23 33
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
KDM6A MUTATED 4 17 10
KDM6A WILD-TYPE 29 39 31
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
KDM6A MUTATED 24 0 7
KDM6A WILD-TYPE 65 9 25
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
KDM6A MUTATED 5 13 13
KDM6A WILD-TYPE 21 36 42
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
KDM6A MUTATED 10 18 3
KDM6A WILD-TYPE 21 56 22
'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.761 (Chi-square test), Q value = 1

Table S81.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
ELF3 MUTATED 1 4 2 1 1 1 0 1
ELF3 WILD-TYPE 8 37 10 6 21 16 14 4
'ELF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 1

Table S82.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
ELF3 MUTATED 5 1 5
ELF3 WILD-TYPE 46 52 21

Figure S6.  Get High-res Image Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.631 (Chi-square test), Q value = 1

Table S83.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ELF3 MUTATED 4 3 3 0 0
ELF3 WILD-TYPE 32 25 30 5 17
'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
ELF3 MUTATED 4 0 2 4
ELF3 WILD-TYPE 38 18 15 38
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
ELF3 MUTATED 6 3 2
ELF3 WILD-TYPE 48 35 35
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
ELF3 MUTATED 2 5 4
ELF3 WILD-TYPE 52 26 40
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
ELF3 MUTATED 3 3 5
ELF3 WILD-TYPE 30 53 36
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
ELF3 MUTATED 7 1 3
ELF3 WILD-TYPE 82 8 29
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
ELF3 MUTATED 2 3 6
ELF3 WILD-TYPE 24 46 49
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S90.  Gene #9: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
ELF3 MUTATED 1 7 3
ELF3 WILD-TYPE 30 67 22
'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.55 (Chi-square test), Q value = 1

Table S91.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
FGFR3 MUTATED 1 7 3 1 3 1 0 0
FGFR3 WILD-TYPE 8 34 9 6 19 16 14 5
'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
FGFR3 MUTATED 8 3 5
FGFR3 WILD-TYPE 43 50 21
'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0621 (Chi-square test), Q value = 1

Table S93.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FGFR3 MUTATED 9 2 4 0 0
FGFR3 WILD-TYPE 27 26 29 5 17
'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
FGFR3 MUTATED 10 2 2 1
FGFR3 WILD-TYPE 32 16 15 41

Figure S7.  Get High-res Image Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0801 (Fisher's exact test), Q value = 1

Table S95.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
FGFR3 MUTATED 11 2 3
FGFR3 WILD-TYPE 43 36 34
'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
FGFR3 MUTATED 3 2 11
FGFR3 WILD-TYPE 51 29 33

Figure S8.  Get High-res Image Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S97.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
FGFR3 MUTATED 3 10 3
FGFR3 WILD-TYPE 30 46 38
'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
FGFR3 MUTATED 13 0 3
FGFR3 WILD-TYPE 76 9 29
'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
FGFR3 MUTATED 3 11 2
FGFR3 WILD-TYPE 23 38 53

Figure S9.  Get High-res Image Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 1

Table S100.  Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
FGFR3 MUTATED 8 5 3
FGFR3 WILD-TYPE 23 69 22

Figure S10.  Get High-res Image Gene #10: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FOXQ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Chi-square test), Q value = 1

Table S101.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
FOXQ1 MUTATED 0 2 0 1 1 2 0 1
FOXQ1 WILD-TYPE 9 39 12 6 21 15 14 4
'FOXQ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
FOXQ1 MUTATED 1 4 2
FOXQ1 WILD-TYPE 50 49 24
'FOXQ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.486 (Chi-square test), Q value = 1

Table S103.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FOXQ1 MUTATED 2 0 2 0 2
FOXQ1 WILD-TYPE 34 28 31 5 15
'FOXQ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S104.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
FOXQ1 MUTATED 3 2 0 1
FOXQ1 WILD-TYPE 39 16 17 41
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S105.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
FOXQ1 MUTATED 4 1 2
FOXQ1 WILD-TYPE 50 37 35
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S106.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
FOXQ1 MUTATED 3 1 3
FOXQ1 WILD-TYPE 51 30 41
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S107.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
FOXQ1 MUTATED 0 5 2
FOXQ1 WILD-TYPE 33 51 39
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S108.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
FOXQ1 MUTATED 6 0 1
FOXQ1 WILD-TYPE 83 9 31
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 1

Table S109.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
FOXQ1 MUTATED 0 4 3
FOXQ1 WILD-TYPE 26 45 52
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S110.  Gene #11: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
FOXQ1 MUTATED 2 5 0
FOXQ1 WILD-TYPE 29 69 25
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Chi-square test), Q value = 1

Table S111.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
STAG2 MUTATED 1 6 3 0 1 0 2 1
STAG2 WILD-TYPE 8 35 9 7 21 17 12 4
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
STAG2 MUTATED 6 3 5
STAG2 WILD-TYPE 45 50 21
'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.24 (Chi-square test), Q value = 1

Table S113.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
STAG2 MUTATED 7 3 3 0 0
STAG2 WILD-TYPE 29 25 30 5 17
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.547 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
STAG2 MUTATED 7 2 1 3
STAG2 WILD-TYPE 35 16 16 39
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
STAG2 MUTATED 8 4 2
STAG2 WILD-TYPE 46 34 35
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
STAG2 MUTATED 3 3 8
STAG2 WILD-TYPE 51 28 36
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
STAG2 MUTATED 2 9 3
STAG2 WILD-TYPE 31 47 38
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S118.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
STAG2 MUTATED 11 1 2
STAG2 WILD-TYPE 78 8 30
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
STAG2 MUTATED 2 9 3
STAG2 WILD-TYPE 24 40 52
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 1

Table S120.  Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
STAG2 MUTATED 8 4 2
STAG2 WILD-TYPE 23 70 23

Figure S11.  Get High-res Image Gene #12: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.233 (Chi-square test), Q value = 1

Table S121.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
NFE2L2 MUTATED 0 7 1 0 3 0 0 0
NFE2L2 WILD-TYPE 9 34 11 7 19 17 14 5
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S122.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
NFE2L2 MUTATED 5 6 0
NFE2L2 WILD-TYPE 46 47 26
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.484 (Chi-square test), Q value = 1

Table S123.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
NFE2L2 MUTATED 1 4 3 1 2
NFE2L2 WILD-TYPE 35 24 30 4 15
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
NFE2L2 MUTATED 3 1 3 4
NFE2L2 WILD-TYPE 39 17 14 38
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0822 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
NFE2L2 MUTATED 1 4 5
NFE2L2 WILD-TYPE 53 34 32
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S126.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
NFE2L2 MUTATED 6 3 1
NFE2L2 WILD-TYPE 48 28 43
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
NFE2L2 MUTATED 3 4 4
NFE2L2 WILD-TYPE 30 52 37
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S128.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
NFE2L2 MUTATED 7 2 2
NFE2L2 WILD-TYPE 82 7 30
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S129.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
NFE2L2 MUTATED 2 4 5
NFE2L2 WILD-TYPE 24 45 50
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S130.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
NFE2L2 MUTATED 2 8 1
NFE2L2 WILD-TYPE 29 66 24
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.37 (Chi-square test), Q value = 1

Table S131.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
CDKN2A MUTATED 0 1 2 1 1 2 0 0
CDKN2A WILD-TYPE 9 40 10 6 21 15 14 5
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S132.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
CDKN2A MUTATED 3 4 0
CDKN2A WILD-TYPE 48 49 26
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.356 (Chi-square test), Q value = 1

Table S133.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
CDKN2A MUTATED 2 0 4 0 1
CDKN2A WILD-TYPE 34 28 29 5 16
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S134.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
CDKN2A MUTATED 4 2 1 0
CDKN2A WILD-TYPE 38 16 16 42
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S135.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
CDKN2A MUTATED 3 2 2
CDKN2A WILD-TYPE 51 36 35
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S136.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
CDKN2A MUTATED 3 1 3
CDKN2A WILD-TYPE 51 30 41
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S137.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
CDKN2A MUTATED 1 5 1
CDKN2A WILD-TYPE 32 51 40
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S138.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
CDKN2A MUTATED 6 0 1
CDKN2A WILD-TYPE 83 9 31
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 1

Table S139.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
CDKN2A MUTATED 0 4 3
CDKN2A WILD-TYPE 26 45 52
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S140.  Gene #14: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
CDKN2A MUTATED 2 4 1
CDKN2A WILD-TYPE 29 70 24
'KLF5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.711 (Chi-square test), Q value = 1

Table S141.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
KLF5 MUTATED 0 4 2 1 2 0 1 0
KLF5 WILD-TYPE 9 37 10 6 20 17 13 5
'KLF5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
KLF5 MUTATED 5 4 1
KLF5 WILD-TYPE 46 49 25
'KLF5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.377 (Chi-square test), Q value = 1

Table S143.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
KLF5 MUTATED 4 1 4 1 0
KLF5 WILD-TYPE 32 27 29 4 17
'KLF5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
KLF5 MUTATED 6 0 1 3
KLF5 WILD-TYPE 36 18 16 39
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S145.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
KLF5 MUTATED 5 3 2
KLF5 WILD-TYPE 49 35 35
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
KLF5 MUTATED 5 0 5
KLF5 WILD-TYPE 49 31 39
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S147.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
KLF5 MUTATED 3 5 2
KLF5 WILD-TYPE 30 51 39
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S148.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
KLF5 MUTATED 7 0 3
KLF5 WILD-TYPE 82 9 29
'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S149.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
KLF5 MUTATED 3 5 2
KLF5 WILD-TYPE 23 44 53
'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S150.  Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
KLF5 MUTATED 5 2 3
KLF5 WILD-TYPE 26 72 22

Figure S12.  Get High-res Image Gene #15: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.326 (Chi-square test), Q value = 1

Table S151.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
ASXL2 MUTATED 0 2 1 2 2 2 0 0
ASXL2 WILD-TYPE 9 39 11 5 20 15 14 5
'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S152.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
ASXL2 MUTATED 5 2 2
ASXL2 WILD-TYPE 46 51 24
'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.421 (Chi-square test), Q value = 1

Table S153.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ASXL2 MUTATED 4 1 3 1 0
ASXL2 WILD-TYPE 32 27 30 4 17
'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
ASXL2 MUTATED 4 0 3 2
ASXL2 WILD-TYPE 38 18 14 40
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S155.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
ASXL2 MUTATED 3 2 4
ASXL2 WILD-TYPE 51 36 33
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S156.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
ASXL2 MUTATED 3 4 2
ASXL2 WILD-TYPE 51 27 42
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S157.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
ASXL2 MUTATED 3 3 3
ASXL2 WILD-TYPE 30 53 38
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S158.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
ASXL2 MUTATED 6 0 3
ASXL2 WILD-TYPE 83 9 29
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S159.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
ASXL2 MUTATED 4 3 2
ASXL2 WILD-TYPE 22 46 53
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S160.  Gene #16: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
ASXL2 MUTATED 2 4 3
ASXL2 WILD-TYPE 29 70 22
'TSC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.511 (Chi-square test), Q value = 1

Table S161.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
TSC1 MUTATED 0 5 0 1 3 0 2 0
TSC1 WILD-TYPE 9 36 12 6 19 17 12 5
'TSC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S162.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
TSC1 MUTATED 6 3 2
TSC1 WILD-TYPE 45 50 24
'TSC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.346 (Chi-square test), Q value = 1

Table S163.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
TSC1 MUTATED 6 1 2 0 2
TSC1 WILD-TYPE 30 27 31 5 15
'TSC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S164.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
TSC1 MUTATED 7 2 0 2
TSC1 WILD-TYPE 35 16 17 40
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
TSC1 MUTATED 6 4 1
TSC1 WILD-TYPE 48 34 36
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 1

Table S166.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
TSC1 MUTATED 1 6 4
TSC1 WILD-TYPE 53 25 40

Figure S13.  Get High-res Image Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TSC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S167.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
TSC1 MUTATED 4 3 4
TSC1 WILD-TYPE 29 53 37
'TSC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S168.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
TSC1 MUTATED 7 1 3
TSC1 WILD-TYPE 82 8 29
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S169.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
TSC1 MUTATED 3 3 5
TSC1 WILD-TYPE 23 46 50
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S170.  Gene #17: 'TSC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
TSC1 MUTATED 0 8 3
TSC1 WILD-TYPE 31 66 22
'ERCC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.897 (Chi-square test), Q value = 1

Table S171.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
ERCC2 MUTATED 1 4 2 1 2 3 3 0
ERCC2 WILD-TYPE 8 37 10 6 20 14 11 5
'ERCC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 1

Table S172.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
ERCC2 MUTATED 8 6 2
ERCC2 WILD-TYPE 43 47 24
'ERCC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.139 (Chi-square test), Q value = 1

Table S173.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ERCC2 MUTATED 3 0 6 1 1
ERCC2 WILD-TYPE 33 28 27 4 16
'ERCC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 1

Table S174.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
ERCC2 MUTATED 3 1 5 2
ERCC2 WILD-TYPE 39 17 12 40

Figure S14.  Get High-res Image Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S175.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
ERCC2 MUTATED 4 4 8
ERCC2 WILD-TYPE 50 34 29
'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
ERCC2 MUTATED 10 3 3
ERCC2 WILD-TYPE 44 28 41
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S177.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
ERCC2 MUTATED 6 8 2
ERCC2 WILD-TYPE 27 48 39
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S178.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
ERCC2 MUTATED 9 1 6
ERCC2 WILD-TYPE 80 8 26
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S179.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
ERCC2 MUTATED 4 6 6
ERCC2 WILD-TYPE 22 43 49
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S180.  Gene #18: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
ERCC2 MUTATED 4 9 3
ERCC2 WILD-TYPE 27 65 22
'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.66 (Chi-square test), Q value = 1

Table S181.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
TXNIP MUTATED 1 4 1 1 0 0 1 0
TXNIP WILD-TYPE 8 37 11 6 22 17 13 5
'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S182.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
TXNIP MUTATED 4 3 2
TXNIP WILD-TYPE 47 50 24
'TXNIP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.796 (Chi-square test), Q value = 1

Table S183.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
TXNIP MUTATED 2 2 4 0 1
TXNIP WILD-TYPE 34 26 29 5 16
'TXNIP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
TXNIP MUTATED 3 1 3 2
TXNIP WILD-TYPE 39 17 14 40
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S185.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
TXNIP MUTATED 5 3 1
TXNIP WILD-TYPE 49 35 36
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S186.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
TXNIP MUTATED 2 3 4
TXNIP WILD-TYPE 52 28 40
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
TXNIP MUTATED 2 4 3
TXNIP WILD-TYPE 31 52 38
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0713 (Fisher's exact test), Q value = 1

Table S188.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
TXNIP MUTATED 4 2 3
TXNIP WILD-TYPE 85 7 29
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S189.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
TXNIP MUTATED 3 2 4
TXNIP WILD-TYPE 23 47 51
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S190.  Gene #19: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
TXNIP MUTATED 2 5 2
TXNIP WILD-TYPE 29 69 23
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.594 (Chi-square test), Q value = 1

Table S191.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
EP300 MUTATED 1 8 2 2 1 3 2 2
EP300 WILD-TYPE 8 33 10 5 21 14 12 3
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 1

Table S192.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
EP300 MUTATED 9 10 2
EP300 WILD-TYPE 42 43 24
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.45 (Chi-square test), Q value = 1

Table S193.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
EP300 MUTATED 4 3 4 2 3
EP300 WILD-TYPE 32 25 29 3 14
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S194.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
EP300 MUTATED 6 4 2 4
EP300 WILD-TYPE 36 14 15 38
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S195.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
EP300 MUTATED 7 6 8
EP300 WILD-TYPE 47 32 29
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S196.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
EP300 MUTATED 10 4 7
EP300 WILD-TYPE 44 27 37
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 1

Table S197.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
EP300 MUTATED 5 12 4
EP300 WILD-TYPE 28 44 37
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S198.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
EP300 MUTATED 13 2 6
EP300 WILD-TYPE 76 7 26
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S199.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
EP300 MUTATED 3 11 7
EP300 WILD-TYPE 23 38 48
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S200.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
EP300 MUTATED 7 12 2
EP300 WILD-TYPE 24 62 23
'RXRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.837 (Chi-square test), Q value = 1

Table S201.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
RXRA MUTATED 1 2 1 1 2 3 2 0
RXRA WILD-TYPE 8 39 11 6 20 14 12 5
'RXRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.061 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
RXRA MUTATED 8 4 0
RXRA WILD-TYPE 43 49 26
'RXRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.181 (Chi-square test), Q value = 1

Table S203.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
RXRA MUTATED 7 1 2 1 1
RXRA WILD-TYPE 29 27 31 4 16
'RXRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S204.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
RXRA MUTATED 4 2 2 4
RXRA WILD-TYPE 38 16 15 38
'RXRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S205.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
RXRA MUTATED 6 4 2
RXRA WILD-TYPE 48 34 35
'RXRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S206.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
RXRA MUTATED 2 5 5
RXRA WILD-TYPE 52 26 39
'RXRA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S207.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
RXRA MUTATED 5 4 3
RXRA WILD-TYPE 28 52 38
'RXRA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S208.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
RXRA MUTATED 6 1 5
RXRA WILD-TYPE 83 8 27
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S209.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
RXRA MUTATED 3 4 5
RXRA WILD-TYPE 23 45 50
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S210.  Gene #21: 'RXRA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
RXRA MUTATED 2 6 4
RXRA WILD-TYPE 29 68 21
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.403 (Chi-square test), Q value = 1

Table S211.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
FOXA1 MUTATED 1 1 1 0 0 1 2 1
FOXA1 WILD-TYPE 8 40 11 7 22 16 12 4
'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S212.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
FOXA1 MUTATED 4 2 1
FOXA1 WILD-TYPE 47 51 25
'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.668 (Chi-square test), Q value = 1

Table S213.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FOXA1 MUTATED 2 2 1 1 1
FOXA1 WILD-TYPE 34 26 32 4 16
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S214.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
FOXA1 MUTATED 3 0 1 3
FOXA1 WILD-TYPE 39 18 16 39
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S215.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
FOXA1 MUTATED 2 4 1
FOXA1 WILD-TYPE 52 34 36
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 1

Table S216.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
FOXA1 MUTATED 2 3 2
FOXA1 WILD-TYPE 52 28 42
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S217.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
FOXA1 MUTATED 2 2 3
FOXA1 WILD-TYPE 31 54 38
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S218.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
FOXA1 MUTATED 5 0 2
FOXA1 WILD-TYPE 84 9 30
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S219.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
FOXA1 MUTATED 2 3 2
FOXA1 WILD-TYPE 24 46 53
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S220.  Gene #22: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
FOXA1 MUTATED 2 3 2
FOXA1 WILD-TYPE 29 71 23
'PHLDA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.467 (Chi-square test), Q value = 1

Table S221.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 9 41 12 7 22 17 14 5
PHLDA3 MUTATED 0 1 0 0 1 1 0 1
PHLDA3 WILD-TYPE 9 40 12 7 21 16 14 4
'PHLDA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 53 26
PHLDA3 MUTATED 1 3 0
PHLDA3 WILD-TYPE 50 50 26
'PHLDA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.508 (Chi-square test), Q value = 1

Table S223.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
PHLDA3 MUTATED 0 1 2 0 0
PHLDA3 WILD-TYPE 36 27 31 5 17
'PHLDA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 18 17 42
PHLDA3 MUTATED 0 1 0 2
PHLDA3 WILD-TYPE 42 17 17 40
'PHLDA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S225.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 38 37
PHLDA3 MUTATED 0 2 2
PHLDA3 WILD-TYPE 54 36 35
'PHLDA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 1

Table S226.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 31 44
PHLDA3 MUTATED 3 1 0
PHLDA3 WILD-TYPE 51 30 44
'PHLDA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S227.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 56 41
PHLDA3 MUTATED 0 2 2
PHLDA3 WILD-TYPE 33 54 39
'PHLDA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S228.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 9 32
PHLDA3 MUTATED 3 0 1
PHLDA3 WILD-TYPE 86 9 31
'PHLDA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S229.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 49 55
PHLDA3 MUTATED 0 2 2
PHLDA3 WILD-TYPE 26 47 53
'PHLDA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S230.  Gene #23: 'PHLDA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 25
PHLDA3 MUTATED 0 4 0
PHLDA3 WILD-TYPE 31 70 25
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 130

  • Number of significantly mutated genes = 23

  • Number of Molecular subtypes = 10

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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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