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 19 genes and 12 molecular subtypes across 178 patients, 21 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

  • NOTCH1 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • SLC28A1 mutation correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • POLR2B mutation correlated to 'MIRSEQ_CNMF'.

  • PI16 mutation correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 19 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, 21 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
TP53 145 (81%) 33 0.0636
(0.415) 		0.0222
(0.249) 		0.00023
(0.00874) 		0.00923
(0.14) 		0.122
(0.606) 		0.711
(0.988) 		0.00027
(0.00879) 		0.0038
(0.0788) 		0.00705
(0.115) 		0.365
(0.905) 		0.0293
(0.257) 		0.0501
(0.358)
NFE2L2 27 (15%) 151 0.00016
(0.00866) 		0.00019
(0.00866) 		0.0395
(0.322) 		0.129
(0.606) 		0.12
(0.606) 		0.346
(0.877) 		1e-05
(0.00114) 		1e-05
(0.00114) 		0.0259
(0.253) 		2e-05
(0.00152) 		0.852
(1.00) 		0.686
(0.988)
KEAP1 22 (12%) 156 0.00119
(0.0285) 		0.00084
(0.0239) 		0.515
(0.939) 		0.586
(0.982) 		0.0161
(0.203) 		0.361
(0.903) 		0.0913
(0.534) 		0.0277
(0.253) 		0.0615
(0.412) 		0.442
(0.939) 		0.308
(0.847) 		0.409
(0.932)
CDKN2A 26 (15%) 152 0.00125
(0.0285) 		0.00586
(0.103) 		0.221
(0.75) 		0.646
(0.982) 		0.444
(0.939) 		0.345
(0.877) 		0.406
(0.932) 		0.0893
(0.534) 		0.504
(0.939) 		0.817
(1.00) 		0.211
(0.746) 		0.199
(0.746)
SLC28A1 9 (5%) 169 0.0245
(0.253) 		0.0502
(0.358) 		0.0311
(0.262) 		0.298
(0.847) 		0.413
(0.932) 		0.458
(0.939) 		0.0454
(0.345) 		0.0271
(0.253) 		0.0118
(0.159) 		0.017
(0.204) 		0.287
(0.847) 		0.712
(0.988)
NOTCH1 14 (8%) 164 0.627
(0.982) 		0.604
(0.982) 		0.985
(1.00) 		0.0603
(0.412) 		0.508
(0.939) 		0.587
(0.982) 		0.771
(0.988) 		0.391
(0.92) 		0.397
(0.925) 		0.319
(0.849) 		0.00489
(0.0929) 		0.102
(0.551)
POLR2B 6 (3%) 172 1
(1.00) 		0.791
(1.00) 		0.292
(0.847) 		0.165
(0.682) 		1
(1.00) 		0.202
(0.746) 		0.476
(0.939) 		0.312
(0.847) 		0.0112
(0.159) 		0.451
(0.939) 		0.167
(0.682) 		0.215
(0.746)
PI16 7 (4%) 171 0.235
(0.788) 		0.718
(0.988) 		0.424
(0.939) 		0.023
(0.249) 		0.0446
(0.345) 		0.287
(0.847) 		0.733
(0.988) 		0.883
(1.00) 		0.726
(0.988) 		0.489
(0.939)
MLL2 36 (20%) 142 0.276
(0.847) 		0.464
(0.939) 		0.762
(0.988) 		0.267
(0.847) 		0.982
(1.00) 		0.936
(1.00) 		0.377
(0.905) 		0.74
(0.988) 		0.454
(0.939) 		0.922
(1.00) 		0.718
(0.988) 		0.623
(0.982)
PTEN 14 (8%) 164 0.388
(0.92) 		0.324
(0.85) 		0.445
(0.939) 		0.737
(0.988) 		1
(1.00) 		0.771
(0.988) 		0.626
(0.982) 		0.513
(0.939) 		0.691
(0.988) 		0.511
(0.939) 		0.303
(0.847) 		0.539
(0.967)
PIK3CA 27 (15%) 151 0.76
(0.988) 		0.751
(0.988) 		0.32
(0.849) 		0.614
(0.982) 		0.851
(1.00) 		0.758
(0.988) 		0.562
(0.978) 		0.588
(0.982) 		0.716
(0.988) 		0.373
(0.905) 		1
(1.00) 		0.49
(0.939)
RB1 12 (7%) 166 0.283
(0.847) 		0.643
(0.982) 		0.159
(0.675) 		0.794
(1.00) 		0.097
(0.54) 		0.568
(0.981) 		0.589
(0.982) 		0.24
(0.792) 		0.18
(0.706) 		0.754
(0.988)
CYP11B1 15 (8%) 163 0.307
(0.847) 		0.678
(0.988) 		0.763
(0.988) 		0.602
(0.982) 		0.671
(0.988) 		0.444
(0.939) 		0.685
(0.988) 		0.37
(0.905) 		0.543
(0.967) 		0.977
(1.00)
ASB5 9 (5%) 169 0.592
(0.982) 		0.553
(0.978) 		0.195
(0.746) 		0.453
(0.939) 		1
(1.00) 		0.478
(0.939) 		0.494
(0.939) 		0.216
(0.746) 		0.335
(0.868)
IRF6 6 (3%) 172 0.289
(0.847) 		0.443
(0.939) 		0.632
(0.982) 		0.558
(0.978) 		0.797
(1.00) 		0.143
(0.628) 		0.763
(0.988) 		0.749
(0.988) 		0.125
(0.606) 		0.819
(1.00)
EP300 8 (4%) 170 0.134
(0.609) 		0.117
(0.606) 		0.16
(0.675) 		1
(1.00) 		0.713
(0.988) 		0.0858
(0.529) 		0.0822
(0.521) 		0.213
(0.746) 		0.823
(1.00)
CPS1 24 (13%) 154 0.469
(0.939) 		0.208
(0.746) 		0.501
(0.939) 		1
(1.00) 		0.619
(0.982) 		0.857
(1.00) 		0.959
(1.00) 		0.848
(1.00) 		0.13
(0.606) 		0.128
(0.606) 		0.595
(0.982) 		1
(1.00)
ARID1A 13 (7%) 165 0.309
(0.847) 		0.644
(0.982) 		0.292
(0.847) 		0.638
(0.982) 		0.142
(0.628) 		0.674
(0.988) 		0.177
(0.706) 		0.809
(1.00) 		0.53
(0.959) 		0.503
(0.939)
HRAS 5 (3%) 173 0.829
(1.00) 		0.68
(0.988) 		0.289
(0.847) 		0.931
(1.00) 		1
(1.00) 		0.0972
(0.54) 		0.75
(0.988)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0636 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
TP53 MUTATED 29 42 12 16
TP53 WILD-TYPE 7 4 7 4
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0222 (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 31 48 20
TP53 WILD-TYPE 10 4 8

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
TP53 MUTATED 13 19 9 22 65 17
TP53 WILD-TYPE 5 15 1 6 5 1

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
TP53 MUTATED 13 21 10 17
TP53 WILD-TYPE 2 1 0 10

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
TP53 MUTATED 24 34 27 4
TP53 WILD-TYPE 8 11 2 2
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.711 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
TP53 MUTATED 17 16 19 23 10 4
TP53 WILD-TYPE 5 4 5 3 4 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0088

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
TP53 MUTATED 29 56 45 15
TP53 WILD-TYPE 8 5 7 13

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0038 (Fisher's exact test), Q value = 0.079

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 67 31
TP53 WILD-TYPE 21 7 5

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00705 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
TP53 MUTATED 81 8 22 26
TP53 WILD-TYPE 11 0 12 2

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.9

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 32 41 47 17
TP53 WILD-TYPE 3 10 7 5
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.26

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
TP53 MUTATED 6 18 11 5
TP53 WILD-TYPE 1 0 6 1

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0501 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
TP53 MUTATED 3 26 11
TP53 WILD-TYPE 0 2 6
'CDKN2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.028

Table S13.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
CDKN2A MUTATED 0 13 2 3
CDKN2A WILD-TYPE 36 33 17 17

Figure S8.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDKN2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00586 (Fisher's exact test), Q value = 0.1

Table S14.  Gene #2: '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 S9.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.75

Table S15.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
CDKN2A MUTATED 2 2 1 2 15 4
CDKN2A WILD-TYPE 16 32 9 26 55 14
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S16.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
CDKN2A MUTATED 3 3 1 2
CDKN2A WILD-TYPE 12 19 9 25
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.94

Table S17.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
CDKN2A MUTATED 2 8 3 0
CDKN2A WILD-TYPE 30 37 26 6
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 0.88

Table S18.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
CDKN2A MUTATED 2 2 4 1 2 2
CDKN2A WILD-TYPE 20 18 20 25 12 4
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.93

Table S19.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
CDKN2A MUTATED 4 12 5 5
CDKN2A WILD-TYPE 33 49 47 23
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0893 (Fisher's exact test), Q value = 0.53

Table S20.  Gene #2: '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 = 0.504 (Fisher's exact test), Q value = 0.94

Table S21.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
CDKN2A MUTATED 11 2 6 5
CDKN2A WILD-TYPE 81 6 28 23
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22.  Gene #2: '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 = 0.211 (Fisher's exact test), Q value = 0.75

Table S23.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
CDKN2A MUTATED 1 3 0 1
CDKN2A WILD-TYPE 6 15 17 5
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 0.75

Table S24.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
CDKN2A MUTATED 0 5 0
CDKN2A WILD-TYPE 3 23 17
'NFE2L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0087

Table S25.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
NFE2L2 MUTATED 0 14 1 1
NFE2L2 WILD-TYPE 36 32 18 19

Figure S10.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0087

Table S26.  Gene #3: '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 S11.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.32

Table S27.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
NFE2L2 MUTATED 1 3 1 2 19 1
NFE2L2 WILD-TYPE 17 31 9 26 51 17

Figure S12.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.61

Table S28.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
NFE2L2 MUTATED 0 6 2 4
NFE2L2 WILD-TYPE 15 16 8 23
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.61

Table S29.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
NFE2L2 MUTATED 8 4 7 0
NFE2L2 WILD-TYPE 24 41 22 6
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 0.88

Table S30.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
NFE2L2 MUTATED 4 3 1 7 3 1
NFE2L2 WILD-TYPE 18 17 23 19 11 5
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S31.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
NFE2L2 MUTATED 2 21 1 3
NFE2L2 WILD-TYPE 35 40 51 25

Figure S13.  Get High-res Image Gene #3: '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 = 0.0011

Table S32.  Gene #3: '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 S14.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.25

Table S33.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
NFE2L2 MUTATED 12 0 4 10
NFE2L2 WILD-TYPE 80 8 30 18

Figure S15.  Get High-res Image Gene #3: '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 = 0.0015

Table S34.  Gene #3: '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 S16.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
NFE2L2 MUTATED 1 4 3 0
NFE2L2 WILD-TYPE 6 14 14 6
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 0.99

Table S36.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
NFE2L2 MUTATED 0 4 4
NFE2L2 WILD-TYPE 3 24 13
'MLL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 0.85

Table S37.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
MLL2 MUTATED 4 10 6 5
MLL2 WILD-TYPE 32 36 13 15
'MLL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 0.94

Table S38.  Gene #4: '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 = 0.762 (Fisher's exact test), Q value = 0.99

Table S39.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
MLL2 MUTATED 2 7 2 4 18 3
MLL2 WILD-TYPE 16 27 8 24 52 15
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.85

Table S40.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
MLL2 MUTATED 1 7 1 5
MLL2 WILD-TYPE 14 15 9 22
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.982 (Fisher's exact test), Q value = 1

Table S41.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
MLL2 MUTATED 7 9 7 1
MLL2 WILD-TYPE 25 36 22 5
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
MLL2 MUTATED 5 4 6 5 2 2
MLL2 WILD-TYPE 17 16 18 21 12 4
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.9

Table S43.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
MLL2 MUTATED 4 15 12 5
MLL2 WILD-TYPE 33 46 40 23
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 0.99

Table S44.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
MLL2 MUTATED 12 17 7
MLL2 WILD-TYPE 56 57 29
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.94

Table S45.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
MLL2 MUTATED 15 3 7 5
MLL2 WILD-TYPE 77 5 27 23
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.922 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: '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 11 4
MLL2 WILD-TYPE 30 41 43 18
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 0.99

Table S47.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
MLL2 MUTATED 2 4 4 0
MLL2 WILD-TYPE 5 14 13 6
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 0.98

Table S48.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
MLL2 MUTATED 1 5 4
MLL2 WILD-TYPE 2 23 13
'KEAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.028

Table S49.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
KEAP1 MUTATED 0 12 1 4
KEAP1 WILD-TYPE 36 34 18 16

Figure S17.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.024

Table S50.  Gene #5: '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 S18.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.94

Table S51.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
KEAP1 MUTATED 3 3 1 1 12 2
KEAP1 WILD-TYPE 15 31 9 27 58 16
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 0.98

Table S52.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
KEAP1 MUTATED 2 3 1 1
KEAP1 WILD-TYPE 13 19 9 26
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.2

Table S53.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
KEAP1 MUTATED 1 2 7 1
KEAP1 WILD-TYPE 31 43 22 5

Figure S19.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 0.9

Table S54.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
KEAP1 MUTATED 2 4 1 4 0 0
KEAP1 WILD-TYPE 20 16 23 22 14 6
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0913 (Fisher's exact test), Q value = 0.53

Table S55.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
KEAP1 MUTATED 1 12 6 3
KEAP1 WILD-TYPE 36 49 46 25
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.25

Table S56.  Gene #5: '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 S20.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0615 (Fisher's exact test), Q value = 0.41

Table S57.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
KEAP1 MUTATED 13 1 0 4
KEAP1 WILD-TYPE 79 7 34 24
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.94

Table S58.  Gene #5: '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 = 0.308 (Fisher's exact test), Q value = 0.85

Table S59.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
KEAP1 MUTATED 0 3 0 0
KEAP1 WILD-TYPE 7 15 17 6
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.93

Table S60.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
KEAP1 MUTATED 0 3 0
KEAP1 WILD-TYPE 3 25 17
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
PTEN MUTATED 4 2 0 2
PTEN WILD-TYPE 32 44 19 18
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 0.85

Table S62.  Gene #6: '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 = 0.445 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
PTEN MUTATED 1 3 1 3 3 3
PTEN WILD-TYPE 17 31 9 25 67 15
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
PTEN MUTATED 1 3 0 4
PTEN WILD-TYPE 14 19 10 23
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
PTEN MUTATED 2 4 2 0
PTEN WILD-TYPE 30 41 27 6
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
PTEN MUTATED 1 1 1 3 2 0
PTEN WILD-TYPE 21 19 23 23 12 6
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
PTEN MUTATED 4 3 4 3
PTEN WILD-TYPE 33 58 48 25
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 0.94

Table S68.  Gene #6: '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 = 0.691 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
PTEN MUTATED 7 1 3 1
PTEN WILD-TYPE 85 7 31 27
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 0.94

Table S70.  Gene #6: '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 = 0.303 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
PTEN MUTATED 0 1 4 0
PTEN WILD-TYPE 7 17 13 6
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
PTEN MUTATED 0 2 3
PTEN WILD-TYPE 3 26 14
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.76 (Fisher's exact test), Q value = 0.99

Table S73.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
PIK3CA MUTATED 5 5 3 4
PIK3CA WILD-TYPE 31 41 16 16
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.751 (Fisher's exact test), Q value = 0.99

Table S74.  Gene #7: '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 = 0.32 (Fisher's exact test), Q value = 0.85

Table S75.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
PIK3CA MUTATED 4 7 2 6 7 1
PIK3CA WILD-TYPE 14 27 8 22 63 17
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 0.98

Table S76.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
PIK3CA MUTATED 2 4 0 5
PIK3CA WILD-TYPE 13 18 10 22
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S77.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
PIK3CA MUTATED 6 7 4 0
PIK3CA WILD-TYPE 26 38 25 6
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 0.99

Table S78.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
PIK3CA MUTATED 3 5 4 4 1 0
PIK3CA WILD-TYPE 19 15 20 22 13 6
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.98

Table S79.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
PIK3CA MUTATED 7 7 10 3
PIK3CA WILD-TYPE 30 54 42 25
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 0.98

Table S80.  Gene #7: '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 = 0.716 (Fisher's exact test), Q value = 0.99

Table S81.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
PIK3CA MUTATED 16 0 4 4
PIK3CA WILD-TYPE 76 8 30 24
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.9

Table S82.  Gene #7: '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 = 1 (Fisher's exact test), Q value = 1

Table S83.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
PIK3CA MUTATED 1 4 3 1
PIK3CA WILD-TYPE 6 14 14 5
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 0.94

Table S84.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
PIK3CA MUTATED 1 6 2
PIK3CA WILD-TYPE 2 22 15
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
RB1 MUTATED 2 5 0 3
RB1 WILD-TYPE 34 41 19 17
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 0.98

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 = 0.159 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
RB1 MUTATED 2 1 0 5 4 0
RB1 WILD-TYPE 16 33 10 23 66 18
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.794 (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 CLUS_4
ALL 15 22 10 27
RB1 MUTATED 1 2 1 1
RB1 WILD-TYPE 14 20 9 26
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.097 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
RB1 MUTATED 0 2 3 1
RB1 WILD-TYPE 32 43 26 5
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
RB1 MUTATED 0 1 2 3 0 0
RB1 WILD-TYPE 22 19 22 23 14 6
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
RB1 MUTATED 1 4 4 3
RB1 WILD-TYPE 36 57 48 25
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 0.79

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 = 0.18 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
RB1 MUTATED 9 1 0 2
RB1 WILD-TYPE 83 7 34 26
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 0.99

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
'CYP11B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.85

Table S95.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
CYP11B1 MUTATED 2 5 4 1
CYP11B1 WILD-TYPE 34 41 15 19
'CYP11B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 0.99

Table S96.  Gene #9: '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 = 0.763 (Fisher's exact test), Q value = 0.99

Table S97.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
CYP11B1 MUTATED 1 3 0 3 5 3
CYP11B1 WILD-TYPE 17 31 10 25 65 15
'CYP11B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 0.98

Table S98.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
CYP11B1 MUTATED 0 1 0 3
CYP11B1 WILD-TYPE 15 21 10 24
'CYP11B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 0.99

Table S99.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
CYP11B1 MUTATED 2 3 4 0
CYP11B1 WILD-TYPE 30 42 25 6
'CYP11B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.94

Table S100.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
CYP11B1 MUTATED 2 4 1 2 0 0
CYP11B1 WILD-TYPE 20 16 23 24 14 6
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.99

Table S101.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
CYP11B1 MUTATED 2 4 6 3
CYP11B1 WILD-TYPE 35 57 46 25
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.9

Table S102.  Gene #9: '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 = 0.543 (Fisher's exact test), Q value = 0.97

Table S103.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
CYP11B1 MUTATED 9 0 1 3
CYP11B1 WILD-TYPE 83 8 33 25
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.977 (Fisher's exact test), Q value = 1

Table S104.  Gene #9: '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 = 0.627 (Fisher's exact test), Q value = 0.98

Table S105.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
NOTCH1 MUTATED 1 3 2 1
NOTCH1 WILD-TYPE 35 43 17 19
'NOTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.604 (Fisher's exact test), Q value = 0.98

Table S106.  Gene #10: '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 = 0.985 (Fisher's exact test), Q value = 1

Table S107.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
NOTCH1 MUTATED 2 3 0 2 6 1
NOTCH1 WILD-TYPE 16 31 10 26 64 17
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0603 (Fisher's exact test), Q value = 0.41

Table S108.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
NOTCH1 MUTATED 2 4 2 0
NOTCH1 WILD-TYPE 13 18 8 27
'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.94

Table S109.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
NOTCH1 MUTATED 3 3 1 1
NOTCH1 WILD-TYPE 29 42 28 5
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 0.98

Table S110.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
NOTCH1 MUTATED 1 2 1 4 0 0
NOTCH1 WILD-TYPE 21 18 23 22 14 6
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 0.99

Table S111.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
NOTCH1 MUTATED 2 6 5 1
NOTCH1 WILD-TYPE 35 55 47 27
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.92

Table S112.  Gene #10: '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 = 0.397 (Fisher's exact test), Q value = 0.92

Table S113.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
NOTCH1 MUTATED 8 0 1 4
NOTCH1 WILD-TYPE 84 8 33 24
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.85

Table S114.  Gene #10: '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 = 0.00489 (Fisher's exact test), Q value = 0.093

Table S115.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
NOTCH1 MUTATED 1 1 0 3
NOTCH1 WILD-TYPE 6 17 17 3

Figure S21.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 0.55

Table S116.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
NOTCH1 MUTATED 1 4 0
NOTCH1 WILD-TYPE 2 24 17
'ASB5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 0.98

Table S117.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
ASB5 MUTATED 1 4 2 2
ASB5 WILD-TYPE 35 42 17 18
'ASB5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 0.98

Table S118.  Gene #11: '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 = 0.195 (Fisher's exact test), Q value = 0.75

Table S119.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
ASB5 MUTATED 1 0 2 1 4 1
ASB5 WILD-TYPE 17 34 8 27 66 17
'ASB5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.94

Table S120.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
ASB5 MUTATED 0 1 2 0
ASB5 WILD-TYPE 32 44 27 6
'ASB5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S121.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
ASB5 MUTATED 1 0 1 1 0 0
ASB5 WILD-TYPE 21 20 23 25 14 6
'ASB5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.94

Table S122.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
ASB5 MUTATED 1 4 4 0
ASB5 WILD-TYPE 36 57 48 28
'ASB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.94

Table S123.  Gene #11: '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 = 0.216 (Fisher's exact test), Q value = 0.75

Table S124.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
ASB5 MUTATED 7 0 0 0
ASB5 WILD-TYPE 85 8 34 28
'ASB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 0.87

Table S125.  Gene #11: '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
'IRF6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.85

Table S126.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
IRF6 MUTATED 1 1 2 0
IRF6 WILD-TYPE 35 45 17 20
'IRF6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 0.94

Table S127.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
IRF6 MUTATED 1 1 2
IRF6 WILD-TYPE 40 51 26
'IRF6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.98

Table S128.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
IRF6 MUTATED 0 3 0 1 2 0
IRF6 WILD-TYPE 18 31 10 27 68 18
'IRF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.98

Table S129.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
IRF6 MUTATED 1 0 0 2
IRF6 WILD-TYPE 14 22 10 25
'IRF6 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S130.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
IRF6 MUTATED 1 2 2 0
IRF6 WILD-TYPE 31 43 27 6
'IRF6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.63

Table S131.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
IRF6 MUTATED 0 3 1 0 1 0
IRF6 WILD-TYPE 22 17 23 26 13 6
'IRF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 0.99

Table S132.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
IRF6 MUTATED 2 1 2 1
IRF6 WILD-TYPE 35 60 50 27
'IRF6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 0.99

Table S133.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
IRF6 MUTATED 2 2 2
IRF6 WILD-TYPE 66 72 34
'IRF6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.61

Table S134.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
IRF6 MUTATED 1 1 1 1
IRF6 WILD-TYPE 91 7 33 27
'IRF6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S135.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
IRF6 MUTATED 1 1 1 1
IRF6 WILD-TYPE 34 50 53 21
'EP300 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.61

Table S136.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
EP300 MUTATED 5 2 0 0
EP300 WILD-TYPE 31 44 19 20
'EP300 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.61

Table S137.  Gene #13: '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 = 0.16 (Fisher's exact test), Q value = 0.67

Table S138.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
EP300 MUTATED 3 0 0 1 3 1
EP300 WILD-TYPE 15 34 10 27 67 17
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S139.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
EP300 MUTATED 1 1 1 0
EP300 WILD-TYPE 31 44 28 6
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 0.99

Table S140.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
EP300 MUTATED 0 0 1 2 0 0
EP300 WILD-TYPE 22 20 23 24 14 6
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0858 (Fisher's exact test), Q value = 0.53

Table S141.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
EP300 MUTATED 3 0 3 2
EP300 WILD-TYPE 34 61 49 26
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0822 (Fisher's exact test), Q value = 0.52

Table S142.  Gene #13: '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 = 0.213 (Fisher's exact test), Q value = 0.75

Table S143.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
EP300 MUTATED 7 0 0 0
EP300 WILD-TYPE 85 8 34 28
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S144.  Gene #13: '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
'CPS1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.94

Table S145.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
CPS1 MUTATED 4 6 5 3
CPS1 WILD-TYPE 32 40 14 17
'CPS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 0.75

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 7 7
CPS1 WILD-TYPE 37 45 21
'CPS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
CPS1 MUTATED 2 3 3 5 10 1
CPS1 WILD-TYPE 16 31 7 23 60 17
'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 CLUS_4
ALL 15 22 10 27
CPS1 MUTATED 1 2 1 3
CPS1 WILD-TYPE 14 20 9 24
'CPS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 0.98

Table S149.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
CPS1 MUTATED 5 7 2 1
CPS1 WILD-TYPE 27 38 27 5
'CPS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S150.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
CPS1 MUTATED 2 3 5 3 2 0
CPS1 WILD-TYPE 20 17 19 23 12 6
'CPS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.959 (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 37 61 52 28
CPS1 MUTATED 4 9 7 4
CPS1 WILD-TYPE 33 52 45 24
'CPS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.848 (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 11 5
CPS1 WILD-TYPE 60 63 31
'CPS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
CPS1 MUTATED 6 1 6 5
CPS1 WILD-TYPE 86 7 28 23
'CPS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.61

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 2 6 4
CPS1 WILD-TYPE 29 49 48 18
'CPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.595 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
CPS1 MUTATED 1 3 1 0
CPS1 WILD-TYPE 6 15 16 6
'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 3 28 17
CPS1 MUTATED 0 3 2
CPS1 WILD-TYPE 3 25 15
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.85

Table S157.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
ARID1A MUTATED 1 5 1 3
ARID1A WILD-TYPE 35 41 18 17
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.98

Table S158.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
ARID1A MUTATED 2 5 3
ARID1A WILD-TYPE 39 47 25
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.85

Table S159.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
ARID1A MUTATED 0 4 1 0 6 2
ARID1A WILD-TYPE 18 30 9 28 64 16
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 0.98

Table S160.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
ARID1A MUTATED 0 2 0 3
ARID1A WILD-TYPE 15 20 10 24
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.63

Table S161.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
ARID1A MUTATED 4 1 1 1
ARID1A WILD-TYPE 28 44 28 5
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 0.99

Table S162.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
ARID1A MUTATED 1 3 1 2 0 0
ARID1A WILD-TYPE 21 17 23 24 14 6
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.71

Table S163.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
ARID1A MUTATED 0 5 6 2
ARID1A WILD-TYPE 37 56 46 26
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S164.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
ARID1A MUTATED 4 6 3
ARID1A WILD-TYPE 64 68 33
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 0.96

Table S165.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
ARID1A MUTATED 5 0 4 2
ARID1A WILD-TYPE 87 8 30 26
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 0.94

Table S166.  Gene #15: '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 4 2 3 2
ARID1A WILD-TYPE 31 49 51 20
'SLC28A1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.25

Table S167.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
SLC28A1 MUTATED 0 1 3 0
SLC28A1 WILD-TYPE 36 45 16 20

Figure S22.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0502 (Fisher's exact test), Q value = 0.36

Table S168.  Gene #16: '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
'SLC28A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.26

Table S169.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
SLC28A1 MUTATED 1 4 1 2 0 1
SLC28A1 WILD-TYPE 17 30 9 26 70 17

Figure S23.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SLC28A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 0.85

Table S170.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
SLC28A1 MUTATED 2 0 1 2
SLC28A1 WILD-TYPE 13 22 9 25
'SLC28A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 0.93

Table S171.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
SLC28A1 MUTATED 2 4 0 0
SLC28A1 WILD-TYPE 30 41 29 6
'SLC28A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.94

Table S172.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
SLC28A1 MUTATED 1 1 2 0 2 0
SLC28A1 WILD-TYPE 21 19 22 26 12 6
'SLC28A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.35

Table S173.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
SLC28A1 MUTATED 3 0 5 1
SLC28A1 WILD-TYPE 34 61 47 27

Figure S24.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.25

Table S174.  Gene #16: '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 S25.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.16

Table S175.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
SLC28A1 MUTATED 2 1 5 0
SLC28A1 WILD-TYPE 90 7 29 28

Figure S26.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.2

Table S176.  Gene #16: '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 S27.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.85

Table S177.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
SLC28A1 MUTATED 1 0 2 1
SLC28A1 WILD-TYPE 6 18 15 5
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.712 (Fisher's exact test), Q value = 0.99

Table S178.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
SLC28A1 MUTATED 0 2 2
SLC28A1 WILD-TYPE 3 26 15
'POLR2B MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S179.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
POLR2B MUTATED 1 2 0 0
POLR2B WILD-TYPE 35 44 19 20
'POLR2B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S180.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
POLR2B MUTATED 1 2 0
POLR2B WILD-TYPE 40 50 28
'POLR2B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.85

Table S181.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
POLR2B MUTATED 1 0 1 0 3 1
POLR2B WILD-TYPE 17 34 9 28 67 17
'POLR2B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.68

Table S182.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
POLR2B MUTATED 2 1 0 0
POLR2B WILD-TYPE 13 21 10 27
'POLR2B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S183.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
POLR2B MUTATED 1 2 1 0
POLR2B WILD-TYPE 31 43 28 6
'POLR2B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.75

Table S184.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
POLR2B MUTATED 0 0 2 1 0 1
POLR2B WILD-TYPE 22 20 22 25 14 5
'POLR2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.94

Table S185.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
POLR2B MUTATED 0 2 2 2
POLR2B WILD-TYPE 37 59 50 26
'POLR2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.85

Table S186.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
POLR2B MUTATED 4 2 0
POLR2B WILD-TYPE 64 72 36
'POLR2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.16

Table S187.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
POLR2B MUTATED 1 2 2 0
POLR2B WILD-TYPE 91 6 32 28

Figure S28.  Get High-res Image Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'POLR2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 0.94

Table S188.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
POLR2B MUTATED 0 1 3 1
POLR2B WILD-TYPE 35 50 51 21
'POLR2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.68

Table S189.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 18 17 6
POLR2B MUTATED 1 0 1 1
POLR2B WILD-TYPE 6 18 16 5
'POLR2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.75

Table S190.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 28 17
POLR2B MUTATED 1 1 1
POLR2B WILD-TYPE 2 27 16
'HRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S191.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
HRAS MUTATED 2 2 0 0
HRAS WILD-TYPE 34 44 19 20
'HRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 0.99

Table S192.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
HRAS MUTATED 2 2 0
HRAS WILD-TYPE 39 50 28
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.85

Table S193.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
HRAS MUTATED 0 0 1 0 3 1
HRAS WILD-TYPE 18 34 9 28 67 17
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S194.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
HRAS MUTATED 1 2 2 0
HRAS WILD-TYPE 36 59 50 28
'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S195.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
HRAS MUTATED 2 2 1
HRAS WILD-TYPE 66 72 35
'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0972 (Fisher's exact test), Q value = 0.54

Table S196.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
HRAS MUTATED 2 1 0 2
HRAS WILD-TYPE 90 7 34 26
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.75 (Fisher's exact test), Q value = 0.99

Table S197.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
HRAS MUTATED 2 1 2 0
HRAS WILD-TYPE 33 50 52 22
'PI16 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.79

Table S198.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 46 19 20
PI16 MUTATED 0 2 2 1
PI16 WILD-TYPE 36 44 17 19
'PI16 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 0.99

Table S199.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
PI16 MUTATED 1 2 2
PI16 WILD-TYPE 40 50 26
'PI16 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.94

Table S200.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 34 10 28 70 18
PI16 MUTATED 0 0 0 2 5 0
PI16 WILD-TYPE 18 34 10 26 65 18
'PI16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.25

Table S201.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 22 10 27
PI16 MUTATED 0 4 0 0
PI16 WILD-TYPE 15 18 10 27

Figure S29.  Get High-res Image Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PI16 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.35

Table S202.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
PI16 MUTATED 3 0 1 1
PI16 WILD-TYPE 29 45 28 5

Figure S30.  Get High-res Image Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PI16 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.85

Table S203.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
PI16 MUTATED 1 2 0 1 0 1
PI16 WILD-TYPE 21 18 24 25 14 5
'PI16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 0.99

Table S204.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 52 28
PI16 MUTATED 1 4 1 1
PI16 WILD-TYPE 36 57 51 27
'PI16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S205.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
PI16 MUTATED 2 4 1
PI16 WILD-TYPE 66 70 35
'PI16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.99

Table S206.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 8 34 28
PI16 MUTATED 3 0 1 2
PI16 WILD-TYPE 89 8 33 26
'PI16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.489 (Fisher's exact test), Q value = 0.94

Table S207.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
PI16 MUTATED 1 1 4 0
PI16 WILD-TYPE 34 50 50 22
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/22595684/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/22552638/LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 178

  • Number of significantly mutated genes = 19

  • 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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