Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 17 genes and 12 molecular subtypes across 178 patients, 8 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • NFE2L2 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • KEAP1 mutation correlated to 'MRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 17 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 8 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
NFE2L2 27 (15%) 151 0.00019
(0.0344) 		0.00017
(0.0309) 		0.0175
(1.00) 		0.0374
(1.00) 		0.255
(1.00) 		0.737
(1.00) 		1e-05
(0.00186) 		1e-05
(0.00186) 		0.0289
(1.00) 		2e-05
(0.00368) 		0.591
(1.00) 		0.114
(1.00)
TP53 141 (79%) 37 0.0452
(1.00) 		0.0261
(1.00) 		0.0001
(0.0183) 		0.00141
(0.251) 		1
(1.00) 		0.698
(1.00) 		0.00124
(0.222) 		0.0456
(1.00) 		0.136
(1.00) 		0.325
(1.00) 		0.823
(1.00) 		0.392
(1.00)
KEAP1 22 (12%) 156 0.00154
(0.271) 		0.00049
(0.0882) 		0.165
(1.00) 		0.0758
(1.00) 		0.203
(1.00) 		0.148
(1.00) 		0.0733
(1.00) 		0.0162
(1.00) 		0.698
(1.00) 		0.248
(1.00) 		0.00522
(0.913) 		0.851
(1.00)
CDKN2A 26 (15%) 152 0.00144
(0.255) 		0.00556
(0.967) 		0.0181
(1.00) 		0.668
(1.00) 		0.341
(1.00) 		0.169
(1.00) 		0.384
(1.00) 		0.451
(1.00) 		0.783
(1.00) 		0.52
(1.00) 		1
(1.00) 		0.974
(1.00)
PTEN 14 (8%) 164 0.38
(1.00) 		0.324
(1.00) 		0.466
(1.00) 		0.133
(1.00) 		0.72
(1.00) 		0.96
(1.00) 		0.626
(1.00) 		0.446
(1.00) 		0.572
(1.00) 		0.488
(1.00) 		0.357
(1.00) 		0.789
(1.00)
PIK3CA 27 (15%) 151 0.689
(1.00) 		0.754
(1.00) 		0.451
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.331
(1.00) 		0.392
(1.00) 		0.613
(1.00) 		0.597
(1.00) 		0.455
(1.00) 		0.956
(1.00)
MLL2 35 (20%) 143 0.17
(1.00) 		0.464
(1.00) 		0.246
(1.00) 		0.314
(1.00) 		0.696
(1.00) 		0.362
(1.00) 		0.349
(1.00) 		0.301
(1.00) 		0.948
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.139
(1.00)
RB1 12 (7%) 166 0.315
(1.00) 		0.644
(1.00) 		0.45
(1.00) 		0.108
(1.00) 		0.655
(1.00) 		0.48
(1.00) 		0.569
(1.00) 		0.421
(1.00) 		0.574
(1.00) 		0.533
(1.00)
IBTK 5 (3%) 173 0.491
(1.00) 		0.848
(1.00) 		0.74
(1.00) 		0.807
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.847
(1.00)
CYP11B1 15 (8%) 163 0.651
(1.00) 		0.681
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.243
(1.00) 		0.0951
(1.00) 		0.637
(1.00) 		0.363
(1.00) 		0.585
(1.00) 		0.805
(1.00) 		0.187
(1.00) 		0.526
(1.00)
NOTCH1 14 (8%) 164 0.815
(1.00) 		0.606
(1.00) 		0.535
(1.00) 		0.0343
(1.00) 		0.591
(1.00) 		0.629
(1.00) 		0.744
(1.00) 		0.364
(1.00) 		0.183
(1.00) 		0.18
(1.00) 		0.485
(1.00) 		0.0366
(1.00)
SLC28A1 9 (5%) 169 0.0135
(1.00) 		0.0497
(1.00) 		0.0359
(1.00) 		0.135
(1.00) 		0.321
(1.00) 		0.525
(1.00) 		0.0446
(1.00) 		0.00807
(1.00) 		0.125
(1.00) 		0.505
(1.00) 		0.536
(1.00) 		0.283
(1.00)
ASB5 9 (5%) 169 0.492
(1.00) 		0.552
(1.00) 		0.279
(1.00) 		0.474
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.495
(1.00) 		0.438
(1.00) 		0.358
(1.00)
CPS1 25 (14%) 153 0.765
(1.00) 		0.236
(1.00) 		0.521
(1.00) 		0.892
(1.00) 		0.73
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.0723
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.428
(1.00)
EP300 8 (4%) 170 0.146
(1.00) 		0.119
(1.00) 		0.383
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.0925
(1.00) 		0.416
(1.00) 		0.44
(1.00) 		0.311
(1.00)
ARID1A 12 (7%) 166 0.311
(1.00) 		0.55
(1.00) 		0.807
(1.00) 		0.353
(1.00) 		0.496
(1.00) 		0.599
(1.00) 		0.135
(1.00) 		0.635
(1.00) 		0.175
(1.00) 		0.692
(1.00)
FBXW7 10 (6%) 168 0.493
(1.00) 		0.829
(1.00) 		0.551
(1.00) 		0.619
(1.00) 		0.789
(1.00) 		0.835
(1.00) 		0.636
(1.00) 		0.935
(1.00) 		0.364
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
TP53 MUTATED 29 43 10 14
TP53 WILD-TYPE 8 5 7 5

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
TP53 MUTATED 30 47 19
TP53 WILD-TYPE 11 5 9

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.018

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
TP53 MUTATED 38 63 40
TP53 WILD-TYPE 24 6 7

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.25

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
TP53 MUTATED 16 28 15
TP53 WILD-TYPE 11 1 3

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
TP53 MUTATED 26 37 24
TP53 WILD-TYPE 8 10 7
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
TP53 MUTATED 21 16 28 22
TP53 WILD-TYPE 8 6 6 5
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.22

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
TP53 MUTATED 30 55 42 14
TP53 WILD-TYPE 9 6 9 13

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
TP53 MUTATED 58 55 28
TP53 WILD-TYPE 23 7 7

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
TP53 MUTATED 83 14 15 21
TP53 WILD-TYPE 17 2 8 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
TP53 MUTATED 27 57 49
TP53 WILD-TYPE 4 17 8
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S11.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
TP53 MUTATED 13 14 15
TP53 WILD-TYPE 2 4 4
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S12.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
TP53 MUTATED 4 3 1 9 9 5 5 2 4
TP53 WILD-TYPE 1 0 2 4 1 2 0 0 0
'NFE2L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.034

Table S13.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
NFE2L2 MUTATED 0 14 1 1
NFE2L2 WILD-TYPE 37 34 16 18

Figure S7.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.031

Table S14.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
NFE2L2 MUTATED 0 14 2
NFE2L2 WILD-TYPE 41 38 26

Figure S8.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
NFE2L2 MUTATED 7 17 3
NFE2L2 WILD-TYPE 55 52 44

Figure S9.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
NFE2L2 MUTATED 4 8 0
NFE2L2 WILD-TYPE 23 21 18

Figure S10.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
NFE2L2 MUTATED 8 5 6
NFE2L2 WILD-TYPE 26 42 25
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
NFE2L2 MUTATED 5 5 4 5
NFE2L2 WILD-TYPE 24 17 30 22
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0019

Table S19.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
NFE2L2 MUTATED 2 21 1 3
NFE2L2 WILD-TYPE 37 40 50 24

Figure S11.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0019

Table S20.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
NFE2L2 MUTATED 4 22 1
NFE2L2 WILD-TYPE 77 40 34

Figure S12.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 1

Table S21.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
NFE2L2 MUTATED 15 0 3 8
NFE2L2 WILD-TYPE 85 16 20 15

Figure S13.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0037

Table S22.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
NFE2L2 MUTATED 15 9 2
NFE2L2 WILD-TYPE 16 65 55

Figure S14.  Get High-res Image Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S23.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
NFE2L2 MUTATED 4 2 3
NFE2L2 WILD-TYPE 11 16 16
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 1

Table S24.  Gene #2: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
NFE2L2 MUTATED 2 0 0 2 0 2 3 0 0
NFE2L2 WILD-TYPE 3 3 3 11 10 5 2 2 4
'CDKN2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.25

Table S25.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
CDKN2A MUTATED 0 13 3 2
CDKN2A WILD-TYPE 37 35 14 17

Figure S15.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDKN2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00556 (Fisher's exact test), Q value = 0.97

Table S26.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
CDKN2A MUTATED 1 13 4
CDKN2A WILD-TYPE 40 39 24

Figure S16.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
CDKN2A MUTATED 3 14 9
CDKN2A WILD-TYPE 59 55 38

Figure S17.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
CDKN2A MUTATED 2 4 3
CDKN2A WILD-TYPE 25 25 15
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
CDKN2A MUTATED 2 8 3
CDKN2A WILD-TYPE 32 39 28
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
CDKN2A MUTATED 2 5 5 1
CDKN2A WILD-TYPE 27 17 29 26
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S31.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
CDKN2A MUTATED 4 12 5 5
CDKN2A WILD-TYPE 35 49 46 22
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S32.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
CDKN2A MUTATED 10 12 4
CDKN2A WILD-TYPE 71 50 31
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S33.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
CDKN2A MUTATED 15 3 2 4
CDKN2A WILD-TYPE 85 13 21 19
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S34.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
CDKN2A MUTATED 4 9 11
CDKN2A WILD-TYPE 27 65 46
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S35.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
CDKN2A MUTATED 2 2 3
CDKN2A WILD-TYPE 13 16 16
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.974 (Fisher's exact test), Q value = 1

Table S36.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
CDKN2A MUTATED 1 0 0 1 2 1 1 0 1
CDKN2A WILD-TYPE 4 3 3 12 8 6 4 2 3
'KEAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.27

Table S37.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
KEAP1 MUTATED 0 12 1 4
KEAP1 WILD-TYPE 37 36 16 15

Figure S18.  Get High-res Image Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.088

Table S38.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
KEAP1 MUTATED 0 13 4
KEAP1 WILD-TYPE 41 39 24

Figure S19.  Get High-res Image Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
KEAP1 MUTATED 4 12 6
KEAP1 WILD-TYPE 58 57 41
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0758 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
KEAP1 MUTATED 0 4 3
KEAP1 WILD-TYPE 27 25 15
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S41.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
KEAP1 MUTATED 5 2 4
KEAP1 WILD-TYPE 29 45 27
'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
KEAP1 MUTATED 4 1 1 5
KEAP1 WILD-TYPE 25 21 33 22
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0733 (Fisher's exact test), Q value = 1

Table S43.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
KEAP1 MUTATED 1 12 6 3
KEAP1 WILD-TYPE 38 49 45 24
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 1

Table S44.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
KEAP1 MUTATED 4 11 7
KEAP1 WILD-TYPE 77 51 28

Figure S20.  Get High-res Image Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
KEAP1 MUTATED 13 1 1 3
KEAP1 WILD-TYPE 87 15 22 20
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
KEAP1 MUTATED 4 5 9
KEAP1 WILD-TYPE 27 69 48
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00522 (Fisher's exact test), Q value = 0.91

Table S47.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
KEAP1 MUTATED 4 0 0
KEAP1 WILD-TYPE 11 18 19

Figure S21.  Get High-res Image Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S48.  Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
KEAP1 MUTATED 1 0 0 1 2 0 0 0 0
KEAP1 WILD-TYPE 4 3 3 12 8 7 5 2 4
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
PTEN MUTATED 4 2 0 2
PTEN WILD-TYPE 33 46 17 17
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
PTEN MUTATED 5 2 1
PTEN WILD-TYPE 36 50 27
'PTEN MUTATION STATUS' versus 'CN_CNMF'

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

Table S51.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
PTEN MUTATED 7 4 3
PTEN WILD-TYPE 55 65 44
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S52.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
PTEN MUTATED 5 3 0
PTEN WILD-TYPE 22 26 18
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
PTEN MUTATED 3 4 1
PTEN WILD-TYPE 31 43 30
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
PTEN MUTATED 2 2 2 2
PTEN WILD-TYPE 27 20 32 25
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S55.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
PTEN MUTATED 4 3 4 3
PTEN WILD-TYPE 35 58 47 24
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S56.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
PTEN MUTATED 7 3 4
PTEN WILD-TYPE 74 59 31
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S57.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
PTEN MUTATED 9 1 2 0
PTEN WILD-TYPE 91 15 21 23
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
PTEN MUTATED 1 5 6
PTEN WILD-TYPE 30 69 51
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S59.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
PTEN MUTATED 0 2 3
PTEN WILD-TYPE 15 16 16
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
PTEN MUTATED 0 0 0 1 2 2 0 0 0
PTEN WILD-TYPE 5 3 3 12 8 5 5 2 4
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S61.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
PIK3CA MUTATED 4 6 3 4
PIK3CA WILD-TYPE 33 42 14 15
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S62.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
PIK3CA MUTATED 7 6 4
PIK3CA WILD-TYPE 34 46 24
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S63.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
PIK3CA MUTATED 12 8 7
PIK3CA WILD-TYPE 50 61 40
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S64.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
PIK3CA MUTATED 4 3 4
PIK3CA WILD-TYPE 23 26 14
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S65.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
PIK3CA MUTATED 5 7 5
PIK3CA WILD-TYPE 29 40 26
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
PIK3CA MUTATED 5 2 7 3
PIK3CA WILD-TYPE 24 20 27 24
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
PIK3CA MUTATED 8 7 10 2
PIK3CA WILD-TYPE 31 54 41 25
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S68.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
PIK3CA MUTATED 11 8 8
PIK3CA WILD-TYPE 70 54 27
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.613 (Fisher's exact test), Q value = 1

Table S69.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
PIK3CA MUTATED 18 2 2 2
PIK3CA WILD-TYPE 82 14 21 21
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S70.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
PIK3CA MUTATED 3 13 8
PIK3CA WILD-TYPE 28 61 49
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S71.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
PIK3CA MUTATED 4 4 2
PIK3CA WILD-TYPE 11 14 17
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S72.  Gene #6: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
PIK3CA MUTATED 1 1 0 2 2 1 1 1 1
PIK3CA WILD-TYPE 4 2 3 11 8 6 4 1 3
'MLL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S73.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
MLL2 MUTATED 4 10 6 5
MLL2 WILD-TYPE 33 38 11 14
'MLL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S74.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
MLL2 MUTATED 6 13 6
MLL2 WILD-TYPE 35 39 22
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 1

Table S75.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
MLL2 MUTATED 8 16 11
MLL2 WILD-TYPE 54 53 36
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
MLL2 MUTATED 6 6 1
MLL2 WILD-TYPE 21 23 17
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S77.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
MLL2 MUTATED 6 9 8
MLL2 WILD-TYPE 28 38 23
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
MLL2 MUTATED 6 7 7 3
MLL2 WILD-TYPE 23 15 27 24
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S79.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
MLL2 MUTATED 4 15 11 5
MLL2 WILD-TYPE 35 46 40 22
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
MLL2 MUTATED 12 15 8
MLL2 WILD-TYPE 69 47 27
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.948 (Fisher's exact test), Q value = 1

Table S81.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
MLL2 MUTATED 17 3 4 5
MLL2 WILD-TYPE 83 13 19 18
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S82.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
MLL2 MUTATED 5 14 10
MLL2 WILD-TYPE 26 60 47
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S83.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
MLL2 MUTATED 2 5 3
MLL2 WILD-TYPE 13 13 16
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S84.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
MLL2 MUTATED 0 2 0 3 1 1 3 0 0
MLL2 WILD-TYPE 5 1 3 10 9 6 2 2 4
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S85.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
RB1 MUTATED 2 5 0 3
RB1 WILD-TYPE 35 43 17 16
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S86.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
RB1 MUTATED 2 5 3
RB1 WILD-TYPE 39 47 25
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S87.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
RB1 MUTATED 4 3 5
RB1 WILD-TYPE 58 66 42
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
RB1 MUTATED 0 4 1
RB1 WILD-TYPE 27 25 17
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S89.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
RB1 MUTATED 3 2 1
RB1 WILD-TYPE 31 45 30
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S90.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
RB1 MUTATED 1 0 2 3
RB1 WILD-TYPE 28 22 32 24
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S91.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
RB1 MUTATED 1 4 4 3
RB1 WILD-TYPE 38 57 47 24
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S92.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
RB1 MUTATED 4 4 4
RB1 WILD-TYPE 77 58 31
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S93.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
RB1 MUTATED 9 1 0 2
RB1 WILD-TYPE 91 15 23 21
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S94.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
RB1 MUTATED 2 4 6
RB1 WILD-TYPE 29 70 51
'IBTK MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S95.  Gene #9: 'IBTK MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
IBTK MUTATED 1 2 0 2
IBTK WILD-TYPE 36 46 17 17
'IBTK MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'IBTK MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
IBTK MUTATED 1 3 1
IBTK WILD-TYPE 40 49 27
'IBTK MUTATION STATUS' versus 'CN_CNMF'

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

Table S97.  Gene #9: 'IBTK MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
IBTK MUTATED 1 3 1
IBTK WILD-TYPE 61 66 46
'IBTK MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S98.  Gene #9: 'IBTK MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
IBTK MUTATED 1 3 1 0
IBTK WILD-TYPE 38 58 50 27
'IBTK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.43 (Fisher's exact test), Q value = 1

Table S99.  Gene #9: 'IBTK MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
IBTK MUTATED 1 3 1
IBTK WILD-TYPE 80 59 34
'IBTK MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S100.  Gene #9: 'IBTK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
IBTK MUTATED 4 0 0 1
IBTK WILD-TYPE 96 16 23 22
'IBTK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S101.  Gene #9: 'IBTK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
IBTK MUTATED 1 3 1
IBTK WILD-TYPE 30 71 56
'CYP11B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S102.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
CYP11B1 MUTATED 3 5 3 1
CYP11B1 WILD-TYPE 34 43 14 18
'CYP11B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S103.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
CYP11B1 MUTATED 3 5 4
CYP11B1 WILD-TYPE 38 47 24
'CYP11B1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S104.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
CYP11B1 MUTATED 5 6 4
CYP11B1 WILD-TYPE 57 63 43
'CYP11B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S105.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
CYP11B1 MUTATED 3 0 1
CYP11B1 WILD-TYPE 24 29 17
'CYP11B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S106.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
CYP11B1 MUTATED 5 2 2
CYP11B1 WILD-TYPE 29 45 29
'CYP11B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0951 (Fisher's exact test), Q value = 1

Table S107.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
CYP11B1 MUTATED 4 0 1 4
CYP11B1 WILD-TYPE 25 22 33 23
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S108.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
CYP11B1 MUTATED 2 4 6 3
CYP11B1 WILD-TYPE 37 57 45 24
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S109.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
CYP11B1 MUTATED 6 4 5
CYP11B1 WILD-TYPE 75 58 30
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S110.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
CYP11B1 MUTATED 7 2 1 3
CYP11B1 WILD-TYPE 93 14 22 20
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S111.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
CYP11B1 MUTATED 3 5 5
CYP11B1 WILD-TYPE 28 69 52
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S112.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
CYP11B1 MUTATED 2 1 0
CYP11B1 WILD-TYPE 13 17 19
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S113.  Gene #10: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
CYP11B1 MUTATED 1 0 0 1 0 0 0 0 1
CYP11B1 WILD-TYPE 4 3 3 12 10 7 5 2 3
'NOTCH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S114.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
NOTCH1 MUTATED 1 4 1 1
NOTCH1 WILD-TYPE 36 44 16 18
'NOTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S115.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
NOTCH1 MUTATED 1 4 2
NOTCH1 WILD-TYPE 40 48 26
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S116.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
NOTCH1 MUTATED 3 7 4
NOTCH1 WILD-TYPE 59 62 43
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 1

Table S117.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
NOTCH1 MUTATED 0 4 4
NOTCH1 WILD-TYPE 27 25 14

Figure S22.  Get High-res Image Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S118.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
NOTCH1 MUTATED 1 4 3
NOTCH1 WILD-TYPE 33 43 28
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S119.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
NOTCH1 MUTATED 2 3 2 1
NOTCH1 WILD-TYPE 27 19 32 26
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S120.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
NOTCH1 MUTATED 2 6 5 1
NOTCH1 WILD-TYPE 37 55 46 26
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S121.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
NOTCH1 MUTATED 4 7 3
NOTCH1 WILD-TYPE 77 55 32
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S122.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
NOTCH1 MUTATED 8 3 0 2
NOTCH1 WILD-TYPE 92 13 23 21
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S123.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
NOTCH1 MUTATED 4 3 6
NOTCH1 WILD-TYPE 27 71 51
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 1

Table S124.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
NOTCH1 MUTATED 3 1 2
NOTCH1 WILD-TYPE 12 17 17
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 1

Table S125.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
NOTCH1 MUTATED 2 1 0 0 1 0 0 0 2
NOTCH1 WILD-TYPE 3 2 3 13 9 7 5 2 2

Figure S23.  Get High-res Image Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 1

Table S126.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
SLC28A1 MUTATED 0 1 3 0
SLC28A1 WILD-TYPE 37 47 14 19

Figure S24.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 1

Table S127.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
SLC28A1 MUTATED 0 1 3
SLC28A1 WILD-TYPE 41 51 25

Figure S25.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 1

Table S128.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
SLC28A1 MUTATED 7 1 1
SLC28A1 WILD-TYPE 55 68 46

Figure S26.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SLC28A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S129.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
SLC28A1 MUTATED 3 0 2
SLC28A1 WILD-TYPE 24 29 16
'SLC28A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S130.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
SLC28A1 MUTATED 2 4 0
SLC28A1 WILD-TYPE 32 43 31
'SLC28A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S131.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
SLC28A1 MUTATED 2 1 3 0
SLC28A1 WILD-TYPE 27 21 31 27
'SLC28A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 1

Table S132.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
SLC28A1 MUTATED 3 0 5 1
SLC28A1 WILD-TYPE 36 61 46 26

Figure S27.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00807 (Fisher's exact test), Q value = 1

Table S133.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
SLC28A1 MUTATED 4 0 5
SLC28A1 WILD-TYPE 77 62 30

Figure S28.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
SLC28A1 MUTATED 3 1 3 1
SLC28A1 WILD-TYPE 97 15 20 22
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.505 (Fisher's exact test), Q value = 1

Table S135.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
SLC28A1 MUTATED 0 5 3
SLC28A1 WILD-TYPE 31 69 54
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S136.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
SLC28A1 MUTATED 0 2 2
SLC28A1 WILD-TYPE 15 16 17
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 1

Table S137.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
SLC28A1 MUTATED 0 1 1 2 0 0 0 0 0
SLC28A1 WILD-TYPE 5 2 2 11 10 7 5 2 4
'ASB5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 1

Table S138.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
ASB5 MUTATED 1 4 2 2
ASB5 WILD-TYPE 36 44 15 17
'ASB5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 1

Table S139.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
ASB5 MUTATED 2 4 3
ASB5 WILD-TYPE 39 48 25
'ASB5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S140.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
ASB5 MUTATED 2 6 1
ASB5 WILD-TYPE 60 63 46
'ASB5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S141.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
ASB5 MUTATED 2 1 0
ASB5 WILD-TYPE 32 46 31
'ASB5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S142.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
ASB5 MUTATED 1 0 1 1
ASB5 WILD-TYPE 28 22 33 26
'ASB5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 1

Table S143.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
ASB5 MUTATED 1 4 4 0
ASB5 WILD-TYPE 38 57 47 27
'ASB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S144.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
ASB5 MUTATED 4 2 3
ASB5 WILD-TYPE 77 60 32
'ASB5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

Table S145.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
ASB5 MUTATED 7 0 0 0
ASB5 WILD-TYPE 93 16 23 23
'ASB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S146.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
ASB5 MUTATED 0 5 2
ASB5 WILD-TYPE 31 69 55
'CPS1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S147.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
CPS1 MUTATED 5 8 4 2
CPS1 WILD-TYPE 32 40 13 17
'CPS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 1

Table S148.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
CPS1 MUTATED 4 8 7
CPS1 WILD-TYPE 37 44 21
'CPS1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S149.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
CPS1 MUTATED 7 9 9
CPS1 WILD-TYPE 55 60 38
'CPS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S150.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
CPS1 MUTATED 3 3 1
CPS1 WILD-TYPE 24 26 17
'CPS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S151.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
CPS1 MUTATED 4 8 3
CPS1 WILD-TYPE 30 39 28
'CPS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S152.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
CPS1 MUTATED 4 2 7 2
CPS1 WILD-TYPE 25 20 27 25
'CPS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S153.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
CPS1 MUTATED 5 9 7 4
CPS1 WILD-TYPE 34 52 44 23
'CPS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S154.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
CPS1 MUTATED 10 10 5
CPS1 WILD-TYPE 71 52 30
'CPS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0723 (Fisher's exact test), Q value = 1

Table S155.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
CPS1 MUTATED 7 3 4 5
CPS1 WILD-TYPE 93 13 19 18
'CPS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 1

Table S156.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
CPS1 MUTATED 6 7 6
CPS1 WILD-TYPE 25 67 51
'CPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S157.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
CPS1 MUTATED 2 2 2
CPS1 WILD-TYPE 13 16 17
'CPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 1

Table S158.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 3 3 13 10 7 5 2 4
CPS1 MUTATED 1 0 1 1 0 2 1 0 0
CPS1 WILD-TYPE 4 3 2 12 10 5 4 2 4
'EP300 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S159.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
EP300 MUTATED 5 2 0 0
EP300 WILD-TYPE 32 46 17 19
'EP300 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S160.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
EP300 MUTATED 5 2 0
EP300 WILD-TYPE 36 50 28
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 1

Table S161.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
EP300 MUTATED 2 2 4
EP300 WILD-TYPE 60 67 43
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S162.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
EP300 MUTATED 0 1 2
EP300 WILD-TYPE 34 46 29
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S163.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
EP300 MUTATED 1 0 1 1
EP300 WILD-TYPE 28 22 33 26
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0925 (Fisher's exact test), Q value = 1

Table S164.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
EP300 MUTATED 3 0 3 2
EP300 WILD-TYPE 36 61 48 25
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S165.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
EP300 MUTATED 5 1 2
EP300 WILD-TYPE 76 61 33
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S166.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
EP300 MUTATED 7 0 0 0
EP300 WILD-TYPE 93 16 23 23
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S167.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
EP300 MUTATED 0 3 4
EP300 WILD-TYPE 31 71 53
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S168.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
ARID1A MUTATED 1 4 1 3
ARID1A WILD-TYPE 36 44 16 16
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.55 (Fisher's exact test), Q value = 1

Table S169.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
ARID1A MUTATED 2 4 3
ARID1A WILD-TYPE 39 48 25
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S170.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
ARID1A MUTATED 5 5 2
ARID1A WILD-TYPE 57 64 45
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S171.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
ARID1A MUTATED 3 1 0
ARID1A WILD-TYPE 24 28 18
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S172.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
ARID1A MUTATED 1 2 3
ARID1A WILD-TYPE 33 45 28
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S173.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
ARID1A MUTATED 1 1 1 3
ARID1A WILD-TYPE 28 21 33 24
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S174.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
ARID1A MUTATED 0 4 6 2
ARID1A WILD-TYPE 39 57 45 25
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S175.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
ARID1A MUTATED 4 5 3
ARID1A WILD-TYPE 77 57 32
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S176.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
ARID1A MUTATED 4 2 3 1
ARID1A WILD-TYPE 96 14 20 22
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S177.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
ARID1A MUTATED 3 4 3
ARID1A WILD-TYPE 28 70 54
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S178.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
FBXW7 MUTATED 1 4 2 2
FBXW7 WILD-TYPE 36 44 15 17
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S179.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
FBXW7 MUTATED 2 5 2
FBXW7 WILD-TYPE 39 47 26
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S180.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 69 47
FBXW7 MUTATED 4 5 1
FBXW7 WILD-TYPE 58 64 46
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S181.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
FBXW7 MUTATED 0 2 1
FBXW7 WILD-TYPE 34 45 30
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S182.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 22 34 27
FBXW7 MUTATED 0 1 1 1
FBXW7 WILD-TYPE 29 21 33 26
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S183.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 61 51 27
FBXW7 MUTATED 2 5 2 1
FBXW7 WILD-TYPE 37 56 49 26
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S184.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 62 35
FBXW7 MUTATED 4 5 1
FBXW7 WILD-TYPE 77 57 34
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.935 (Fisher's exact test), Q value = 1

Table S185.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 100 16 23 23
FBXW7 MUTATED 6 0 1 1
FBXW7 WILD-TYPE 94 16 22 22
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S186.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 74 57
FBXW7 MUTATED 2 5 1
FBXW7 WILD-TYPE 29 69 56
Methods & Data
Input

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

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

  • Number of patients = 178

  • Number of significantly mutated genes = 17

  • Number of Molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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