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, 17 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • CDKN2A mutation correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • KEAP1 mutation correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • NOTCH1 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • SLC28A1 mutation correlated to 'MRNA_CNMF' and 'MIRSEQ_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, 17 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 0.00025
(0.0102) 		0.00021
(0.0102) 		0.0143
(0.183) 		0.0475
(0.335) 		0.252
(0.844) 		0.738
(1.00) 		2e-05
(0.00204) 		1e-05
(0.00204) 		0.00649
(0.102) 		5e-05
(0.0034) 		0.631
(1.00) 		0.863
(1.00)
TP53 141 (79%) 37 0.0446
(0.335) 		0.0261
(0.253) 		0.00057
(0.0194) 		0.00155
(0.0339) 		1
(1.00) 		0.7
(1.00) 		0.00524
(0.0972) 		0.0228
(0.253) 		0.409
(0.959) 		0.439
(0.968) 		0.0919
(0.478) 		0.063
(0.402)
CDKN2A 26 (15%) 152 0.00126
(0.0321) 		0.00596
(0.101) 		0.0251
(0.253) 		0.542
(0.988) 		0.34
(0.913) 		0.17
(0.694) 		0.379
(0.918) 		0.0906
(0.478) 		0.662
(1.00) 		0.817
(1.00) 		0.843
(1.00) 		0.0298
(0.253)
KEAP1 22 (12%) 156 0.00166
(0.0339) 		0.00069
(0.0201) 		0.119
(0.551) 		0.0624
(0.402) 		0.205
(0.748) 		0.149
(0.644) 		0.188
(0.709) 		0.028
(0.253) 		0.183
(0.709) 		0.445
(0.968) 		0.478
(0.968) 		0.669
(1.00)
SLC28A1 9 (5%) 169 0.0137
(0.183) 		0.0493
(0.335) 		0.0815
(0.465) 		0.0991
(0.493) 		0.321
(0.913) 		0.526
(0.981) 		0.0385
(0.302) 		0.0278
(0.253) 		0.186
(0.709) 		0.0181
(0.218) 		0.816
(1.00) 		0.183
(0.709)
NOTCH1 14 (8%) 164 0.817
(1.00) 		0.602
(0.999) 		0.469
(0.968) 		0.049
(0.335) 		0.589
(0.999) 		0.63
(1.00) 		0.757
(1.00) 		0.392
(0.931) 		0.351
(0.913) 		0.319
(0.913) 		0.0094
(0.137) 		0.0298
(0.253)
PTEN 14 (8%) 164 0.382
(0.918) 		0.324
(0.913) 		0.414
(0.961) 		0.151
(0.644) 		0.724
(1.00) 		0.96
(1.00) 		0.595
(0.999) 		0.515
(0.981) 		0.573
(0.99) 		0.512
(0.981) 		0.2
(0.742) 		1
(1.00)
PIK3CA 27 (15%) 151 0.691
(1.00) 		0.754
(1.00) 		0.294
(0.913) 		0.919
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.343
(0.913) 		0.585
(0.999) 		0.365
(0.913) 		0.375
(0.918) 		0.723
(1.00) 		0.755
(1.00)
MLL2 35 (20%) 143 0.169
(0.694) 		0.467
(0.968) 		0.645
(1.00) 		0.423
(0.968) 		0.696
(1.00) 		0.363
(0.913) 		0.323
(0.913) 		0.857
(1.00) 		0.93
(1.00) 		0.941
(1.00) 		0.744
(1.00) 		1
(1.00)
RB1 12 (7%) 166 0.317
(0.913) 		0.646
(1.00) 		0.522
(0.981) 		0.127
(0.576) 		0.655
(1.00) 		0.482
(0.968) 		0.775
(1.00) 		0.239
(0.837) 		0.322
(0.913) 		0.751
(1.00)
IBTK 5 (3%) 173 0.493
(0.968) 		0.849
(1.00) 		0.737
(1.00) 		0.807
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.611
(1.00)
CYP11B1 15 (8%) 163 0.653
(1.00) 		0.682
(1.00) 		0.659
(1.00) 		0.347
(0.913) 		0.242
(0.837) 		0.0938
(0.478) 		0.57
(0.99) 		0.367
(0.913) 		0.562
(0.99) 		0.977
(1.00)
ASB5 9 (5%) 169 0.493
(0.968) 		0.552
(0.99) 		0.258
(0.85) 		0.474
(0.968) 		1
(1.00) 		0.482
(0.968) 		0.493
(0.968) 		0.252
(0.844) 		0.335
(0.913)
CPS1 25 (14%) 153 0.766
(1.00) 		0.235
(0.837) 		0.272
(0.881) 		1
(1.00) 		0.732
(1.00) 		0.498
(0.968) 		0.99
(1.00) 		0.721
(1.00) 		0.0374
(0.302) 		0.278
(0.886) 		1
(1.00) 		1
(1.00)
EP300 8 (4%) 170 0.15
(0.644) 		0.116
(0.551) 		0.437
(0.968) 		0.359
(0.913) 		1
(1.00) 		0.0829
(0.465) 		0.0844
(0.465) 		0.565
(0.99) 		0.822
(1.00)
ARID1A 12 (7%) 166 0.312
(0.913) 		0.554
(0.99) 		0.453
(0.968) 		0.346
(0.913) 		0.496
(0.968) 		0.6
(0.999) 		0.108
(0.525) 		0.861
(1.00) 		0.534
(0.982) 		0.693
(1.00)
FBXW7 10 (6%) 168 0.491
(0.968) 		0.827
(1.00) 		0.0711
(0.426) 		0.621
(1.00) 		0.789
(1.00) 		0.834
(1.00) 		0.529
(0.981) 		0.961
(1.00) 		0.0657
(0.406)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.34

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 = 0.25

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 = 0.00057 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
TP53 MUTATED 36 62 43
TP53 WILD-TYPE 22 7 8

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 = 0.00155 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
TP53 MUTATED 16 29 14
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 = 0.7 (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 = 0.00524 (Fisher's exact test), Q value = 0.097

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
TP53 MUTATED 31 55 41 14
TP53 WILD-TYPE 9 7 9 12

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 = 0.0228 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
TP53 MUTATED 47 65 29
TP53 WILD-TYPE 21 9 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 = 0.409 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
TP53 MUTATED 79 12 14 20 8
TP53 WILD-TYPE 14 2 7 4 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
TP53 MUTATED 31 39 46 17
TP53 WILD-TYPE 4 12 8 5
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0919 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
TP53 MUTATED 10 17 12
TP53 WILD-TYPE 6 2 1
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.063 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
TP53 MUTATED 4 18 17
TP53 WILD-TYPE 0 1 8
'NFE2L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.01

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 = 0.00021 (Fisher's exact test), Q value = 0.01

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 = 0.0143 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
NFE2L2 MUTATED 7 17 3
NFE2L2 WILD-TYPE 51 52 48

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 = 0.0475 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
NFE2L2 MUTATED 4 8 0
NFE2L2 WILD-TYPE 23 22 17

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 = 0.252 (Fisher's exact test), Q value = 0.84

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 = 0.738 (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 = 2e-05 (Fisher's exact test), Q value = 0.002

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
NFE2L2 MUTATED 2 22 1 2
NFE2L2 WILD-TYPE 38 40 49 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 = 0.002

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
NFE2L2 MUTATED 2 24 1
NFE2L2 WILD-TYPE 66 50 35

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 = 0.00649 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
NFE2L2 MUTATED 14 1 1 10 0
NFE2L2 WILD-TYPE 79 13 20 14 10

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 = 5e-05 (Fisher's exact test), Q value = 0.0034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
NFE2L2 MUTATED 15 6 2 3
NFE2L2 WILD-TYPE 20 45 52 19

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 = 0.631 (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 16 19 13
NFE2L2 MUTATED 3 2 3
NFE2L2 WILD-TYPE 13 17 10
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.863 (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
ALL 4 19 25
NFE2L2 MUTATED 0 4 4
NFE2L2 WILD-TYPE 4 15 21
'CDKN2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.032

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 = 0.00596 (Fisher's exact test), Q value = 0.1

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 = 0.0251 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
CDKN2A MUTATED 3 15 8
CDKN2A WILD-TYPE 55 54 43

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 = 0.542 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
CDKN2A MUTATED 2 4 3
CDKN2A WILD-TYPE 25 26 14
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.91

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 = 0.17 (Fisher's exact test), Q value = 0.69

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 = 0.379 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
CDKN2A MUTATED 4 12 5 5
CDKN2A WILD-TYPE 36 50 45 21
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0906 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
CDKN2A MUTATED 6 16 4
CDKN2A WILD-TYPE 62 58 32
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.662 (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 CLUS_5
ALL 93 14 21 24 10
CDKN2A MUTATED 16 1 4 3 0
CDKN2A WILD-TYPE 77 13 17 21 10
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.817 (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 CLUS_4
ALL 35 51 54 22
CDKN2A MUTATED 5 6 10 3
CDKN2A WILD-TYPE 30 45 44 19
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.843 (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 16 19 13
CDKN2A MUTATED 1 2 2
CDKN2A WILD-TYPE 15 17 11
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
CDKN2A MUTATED 1 4 0
CDKN2A WILD-TYPE 3 15 25

Figure S18.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.034

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 S19.  Get High-res Image Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.02

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 S20.  Get High-res Image Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
KEAP1 MUTATED 4 13 5
KEAP1 WILD-TYPE 54 56 46
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0624 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
KEAP1 MUTATED 0 4 3
KEAP1 WILD-TYPE 27 26 14
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.75

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 = 0.149 (Fisher's exact test), Q value = 0.64

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 = 0.188 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
KEAP1 MUTATED 2 12 5 3
KEAP1 WILD-TYPE 38 50 45 23
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
KEAP1 MUTATED 3 13 6
KEAP1 WILD-TYPE 65 61 30

Figure S21.  Get High-res Image Gene #4: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
KEAP1 MUTATED 10 3 0 3 2
KEAP1 WILD-TYPE 83 11 21 21 8
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
KEAP1 MUTATED 5 3 8 2
KEAP1 WILD-TYPE 30 48 46 20
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
KEAP1 MUTATED 0 2 1
KEAP1 WILD-TYPE 16 17 12
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.669 (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
ALL 4 19 25
KEAP1 MUTATED 0 2 1
KEAP1 WILD-TYPE 4 17 24
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.92

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 = 0.91

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 = 0.414 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
PTEN MUTATED 7 4 3
PTEN WILD-TYPE 51 65 48
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
PTEN MUTATED 5 3 0
PTEN WILD-TYPE 22 27 17
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.724 (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 = 0.595 (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 40 62 50 26
PTEN MUTATED 4 3 4 3
PTEN WILD-TYPE 36 59 46 23
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.515 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
PTEN MUTATED 6 4 4
PTEN WILD-TYPE 62 70 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
PTEN MUTATED 7 0 3 1 1
PTEN WILD-TYPE 86 14 18 23 9
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
PTEN MUTATED 1 3 6 2
PTEN WILD-TYPE 34 48 48 20
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
PTEN MUTATED 1 4 0
PTEN WILD-TYPE 15 15 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL 4 19 25
PTEN MUTATED 0 2 3
PTEN WILD-TYPE 4 17 22
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.691 (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 = 0.294 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
PIK3CA MUTATED 10 7 10
PIK3CA WILD-TYPE 48 62 41
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.919 (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 30 17
PIK3CA MUTATED 4 4 3
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 = 0.666 (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 = 0.343 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
PIK3CA MUTATED 8 7 10 2
PIK3CA WILD-TYPE 32 55 40 24
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.585 (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 68 74 36
PIK3CA MUTATED 11 9 7
PIK3CA WILD-TYPE 57 65 29
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
PIK3CA MUTATED 15 4 3 2 0
PIK3CA WILD-TYPE 78 10 18 22 10
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
PIK3CA MUTATED 3 11 8 2
PIK3CA WILD-TYPE 32 40 46 20
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.723 (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 16 19 13
PIK3CA MUTATED 2 4 3
PIK3CA WILD-TYPE 14 15 10
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.755 (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
ALL 4 19 25
PIK3CA MUTATED 1 4 4
PIK3CA WILD-TYPE 3 15 21
'MLL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.69

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 = 0.467 (Fisher's exact test), Q value = 0.97

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 = 0.645 (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 58 69 51
MLL2 MUTATED 9 15 11
MLL2 WILD-TYPE 49 54 40
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
MLL2 MUTATED 6 6 1
MLL2 WILD-TYPE 21 24 16
'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 = 0.363 (Fisher's exact test), Q value = 0.91

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 = 0.323 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
MLL2 MUTATED 4 15 11 5
MLL2 WILD-TYPE 36 47 39 21
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.857 (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 68 74 36
MLL2 MUTATED 12 16 7
MLL2 WILD-TYPE 56 58 29
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.93 (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 CLUS_5
ALL 93 14 21 24 10
MLL2 MUTATED 17 2 5 4 1
MLL2 WILD-TYPE 76 12 16 20 9
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.941 (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 CLUS_4
ALL 35 51 54 22
MLL2 MUTATED 5 10 10 4
MLL2 WILD-TYPE 30 41 44 18
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.744 (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 16 19 13
MLL2 MUTATED 4 3 3
MLL2 WILD-TYPE 12 16 10
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL 4 19 25
MLL2 MUTATED 1 4 5
MLL2 WILD-TYPE 3 15 20
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.91

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 = 0.646 (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 = 0.522 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
RB1 MUTATED 4 3 5
RB1 WILD-TYPE 54 66 46
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
RB1 MUTATED 0 4 1
RB1 WILD-TYPE 27 26 16
'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 = 0.482 (Fisher's exact test), Q value = 0.97

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 = 0.775 (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 40 62 50 26
RB1 MUTATED 2 4 3 3
RB1 WILD-TYPE 38 58 47 23
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
RB1 MUTATED 2 6 4
RB1 WILD-TYPE 66 68 32
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
RB1 MUTATED 7 1 0 2 2
RB1 WILD-TYPE 86 13 21 22 8
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.751 (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 CLUS_4
ALL 35 51 54 22
RB1 MUTATED 2 3 6 1
RB1 WILD-TYPE 33 48 48 21
'IBTK MUTATION STATUS' versus 'MRNA_CNMF'

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

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 = 0.849 (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 = 0.737 (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 58 69 51
IBTK MUTATED 1 3 1
IBTK WILD-TYPE 57 66 50
'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 40 62 50 26
IBTK MUTATED 1 3 1 0
IBTK WILD-TYPE 39 59 49 26
'IBTK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.843 (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 68 74 36
IBTK MUTATED 1 3 1
IBTK WILD-TYPE 67 71 35
'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 CLUS_5
ALL 93 14 21 24 10
IBTK MUTATED 4 0 0 1 0
IBTK WILD-TYPE 89 14 21 23 10
'IBTK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.611 (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 CLUS_4
ALL 35 51 54 22
IBTK MUTATED 1 3 1 0
IBTK WILD-TYPE 34 48 53 22
'CYP11B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.653 (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 = 0.682 (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 = 0.659 (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 58 69 51
CYP11B1 MUTATED 4 5 6
CYP11B1 WILD-TYPE 54 64 45
'CYP11B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
CYP11B1 MUTATED 3 1 0
CYP11B1 WILD-TYPE 24 29 17
'CYP11B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.84

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 = 0.0938 (Fisher's exact test), Q value = 0.48

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 = 0.57 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
CYP11B1 MUTATED 2 4 6 3
CYP11B1 WILD-TYPE 38 58 44 23
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
CYP11B1 MUTATED 4 6 5
CYP11B1 WILD-TYPE 64 68 31
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
CYP11B1 MUTATED 6 2 1 3 1
CYP11B1 WILD-TYPE 87 12 20 21 9
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.977 (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 CLUS_4
ALL 35 51 54 22
CYP11B1 MUTATED 3 4 5 1
CYP11B1 WILD-TYPE 32 47 49 21
'NOTCH1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S112.  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 = 0.602 (Fisher's exact test), Q value = 1

Table S113.  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 = 0.469 (Fisher's exact test), Q value = 0.97

Table S114.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
NOTCH1 MUTATED 3 5 6
NOTCH1 WILD-TYPE 55 64 45
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.34

Table S115.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
NOTCH1 MUTATED 0 5 3
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 = 0.589 (Fisher's exact test), Q value = 1

Table S116.  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 = 0.63 (Fisher's exact test), Q value = 1

Table S117.  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 = 0.757 (Fisher's exact test), Q value = 1

Table S118.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
NOTCH1 MUTATED 2 6 5 1
NOTCH1 WILD-TYPE 38 56 45 25
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 0.93

Table S119.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
NOTCH1 MUTATED 3 8 3
NOTCH1 WILD-TYPE 65 66 33
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 0.91

Table S120.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
NOTCH1 MUTATED 7 2 0 3 1
NOTCH1 WILD-TYPE 86 12 21 21 9
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.91

Table S121.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
NOTCH1 MUTATED 4 3 6 0
NOTCH1 WILD-TYPE 31 48 48 22
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0094 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
NOTCH1 MUTATED 1 0 4
NOTCH1 WILD-TYPE 15 19 9

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

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.25

Table S123.  Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
NOTCH1 MUTATED 1 4 0
NOTCH1 WILD-TYPE 3 15 25

Figure S24.  Get High-res Image Gene #11: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.18

Table S124.  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 S25.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.34

Table S125.  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 S26.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0815 (Fisher's exact test), Q value = 0.47

Table S126.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
SLC28A1 MUTATED 6 1 2
SLC28A1 WILD-TYPE 52 68 49
'SLC28A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0991 (Fisher's exact test), Q value = 0.49

Table S127.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
SLC28A1 MUTATED 3 0 2
SLC28A1 WILD-TYPE 24 30 15
'SLC28A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.91

Table S128.  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 = 0.526 (Fisher's exact test), Q value = 0.98

Table S129.  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 = 0.0385 (Fisher's exact test), Q value = 0.3

Table S130.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
SLC28A1 MUTATED 3 0 5 1
SLC28A1 WILD-TYPE 37 62 45 25

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 = 0.0278 (Fisher's exact test), Q value = 0.25

Table S131.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
SLC28A1 MUTATED 3 1 5
SLC28A1 WILD-TYPE 65 73 31

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 = 0.186 (Fisher's exact test), Q value = 0.71

Table S132.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
SLC28A1 MUTATED 4 1 3 0 0
SLC28A1 WILD-TYPE 89 13 18 24 10
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.22

Table S133.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
SLC28A1 MUTATED 0 1 3 4
SLC28A1 WILD-TYPE 35 50 51 18

Figure S29.  Get High-res Image Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
SLC28A1 MUTATED 2 1 1
SLC28A1 WILD-TYPE 14 18 12
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
SLC28A1 MUTATED 0 0 4
SLC28A1 WILD-TYPE 4 19 21
'ASB5 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S136.  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 = 0.99

Table S137.  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 = 0.258 (Fisher's exact test), Q value = 0.85

Table S138.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
ASB5 MUTATED 2 6 1
ASB5 WILD-TYPE 56 63 50
'ASB5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.97

Table S139.  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 S140.  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 = 0.482 (Fisher's exact test), Q value = 0.97

Table S141.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
ASB5 MUTATED 1 4 4 0
ASB5 WILD-TYPE 39 58 46 26
'ASB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S142.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
ASB5 MUTATED 2 4 3
ASB5 WILD-TYPE 66 70 33
'ASB5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.84

Table S143.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
ASB5 MUTATED 5 2 0 0 0
ASB5 WILD-TYPE 88 12 21 24 10
'ASB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 0.91

Table S144.  Gene #13: 'ASB5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
ASB5 MUTATED 0 4 2 1
ASB5 WILD-TYPE 35 47 52 21
'CPS1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S145.  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 = 0.235 (Fisher's exact test), Q value = 0.84

Table S146.  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 = 0.272 (Fisher's exact test), Q value = 0.88

Table S147.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
CPS1 MUTATED 5 10 10
CPS1 WILD-TYPE 53 59 41
'CPS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S148.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
CPS1 MUTATED 3 3 1
CPS1 WILD-TYPE 24 27 16
'CPS1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S149.  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 = 0.498 (Fisher's exact test), Q value = 0.97

Table S150.  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 = 0.99 (Fisher's exact test), Q value = 1

Table S151.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
CPS1 MUTATED 5 9 7 4
CPS1 WILD-TYPE 35 53 43 22
'CPS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
CPS1 MUTATED 8 12 5
CPS1 WILD-TYPE 60 62 31
'CPS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.3

Table S153.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
CPS1 MUTATED 7 0 5 5 2
CPS1 WILD-TYPE 86 14 16 19 8

Figure S30.  Get High-res Image Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CPS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 0.89

Table S154.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
CPS1 MUTATED 6 3 6 4
CPS1 WILD-TYPE 29 48 48 18
'CPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S155.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
CPS1 MUTATED 2 2 1
CPS1 WILD-TYPE 14 17 12
'CPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S156.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
CPS1 MUTATED 0 2 3
CPS1 WILD-TYPE 4 17 22
'EP300 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S157.  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 = 0.116 (Fisher's exact test), Q value = 0.55

Table S158.  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 = 0.437 (Fisher's exact test), Q value = 0.97

Table S159.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
EP300 MUTATED 2 2 4
EP300 WILD-TYPE 56 67 47
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 0.91

Table S160.  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 S161.  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 = 0.0829 (Fisher's exact test), Q value = 0.47

Table S162.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
EP300 MUTATED 3 0 3 2
EP300 WILD-TYPE 37 62 47 24
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0844 (Fisher's exact test), Q value = 0.47

Table S163.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
EP300 MUTATED 6 1 1
EP300 WILD-TYPE 62 73 35
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.99

Table S164.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
EP300 MUTATED 6 1 0 0 0
EP300 WILD-TYPE 87 13 21 24 10
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S165.  Gene #15: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
EP300 MUTATED 1 3 3 0
EP300 WILD-TYPE 34 48 51 22
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.91

Table S166.  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 = 0.554 (Fisher's exact test), Q value = 0.99

Table S167.  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 = 0.453 (Fisher's exact test), Q value = 0.97

Table S168.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
ARID1A MUTATED 6 4 2
ARID1A WILD-TYPE 52 65 49
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.91

Table S169.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
ARID1A MUTATED 3 1 0
ARID1A WILD-TYPE 24 29 17
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.97

Table S170.  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 = 0.6 (Fisher's exact test), Q value = 1

Table S171.  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 = 0.108 (Fisher's exact test), Q value = 0.52

Table S172.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
ARID1A MUTATED 0 5 6 1
ARID1A WILD-TYPE 40 57 44 25
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S173.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
ARID1A MUTATED 4 5 3
ARID1A WILD-TYPE 64 69 33
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 0.98

Table S174.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
ARID1A MUTATED 4 1 2 2 1
ARID1A WILD-TYPE 89 13 19 22 9
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S175.  Gene #16: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
ARID1A MUTATED 3 2 3 2
ARID1A WILD-TYPE 32 49 51 20
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.97

Table S176.  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 = 0.827 (Fisher's exact test), Q value = 1

Table S177.  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 = 0.0711 (Fisher's exact test), Q value = 0.43

Table S178.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
FBXW7 MUTATED 4 6 0
FBXW7 WILD-TYPE 54 63 51
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S179.  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 S180.  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 = 0.834 (Fisher's exact test), Q value = 1

Table S181.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
FBXW7 MUTATED 2 5 2 1
FBXW7 WILD-TYPE 38 57 48 25
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.529 (Fisher's exact test), Q value = 0.98

Table S182.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
FBXW7 MUTATED 3 6 1
FBXW7 WILD-TYPE 65 68 35
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S183.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
FBXW7 MUTATED 5 1 1 1 0
FBXW7 WILD-TYPE 88 13 20 23 10
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0657 (Fisher's exact test), Q value = 0.41

Table S184.  Gene #17: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
FBXW7 MUTATED 4 3 0 1
FBXW7 WILD-TYPE 31 48 54 21
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/15165188/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/15114194/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)
Made with Nozzle