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 27 genes and 10 molecular subtypes across 221 patients, 38 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • PIK3CA mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • CBWD1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • PGM5 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • APC mutation correlated to 'RPPA_CHIERARCHICAL'.

  • FBXW7 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • HLA-B mutation correlated to 'METHLYATION_CNMF'.

  • CIC mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • ZBTB20 mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • MVK mutation correlated to 'RPPA_CHIERARCHICAL'.

  • CR1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • MLL4 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 27 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 38 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
CBWD1 28 (13%) 193 5e-05
(0.0128) 		1e-05
(0.00265) 		9e-05
(0.0226) 		0.0218
(1.00) 		8e-05
(0.0202) 		1e-05
(0.00265) 		0.00022
(0.0543) 		1e-05
(0.00265) 		0.16
(1.00) 		0.135
(1.00)
TP53 99 (45%) 122 1e-05
(0.00265) 		0.0001
(0.025) 		0.21
(1.00) 		0.554
(1.00) 		0.00023
(0.0566) 		0.00029
(0.0708) 		0.00122
(0.277) 		5e-05
(0.0128) 		0.935
(1.00) 		0.00316
(0.679)
PIK3CA 48 (22%) 173 0.00087
(0.203) 		0.00042
(0.101) 		0.0155
(1.00) 		0.0705
(1.00) 		0.00091
(0.211) 		1e-05
(0.00265) 		0.0568
(1.00) 		0.0166
(1.00) 		0.00642
(1.00) 		0.375
(1.00)
ARID1A 41 (19%) 180 1e-05
(0.00265) 		0.0381
(1.00) 		0.0175
(1.00) 		0.00094
(0.217) 		0.00067
(0.157) 		2e-05
(0.00516) 		0.00222
(0.488) 		0.00285
(0.621) 		0.813
(1.00) 		0.225
(1.00)
PGM5 22 (10%) 199 0.00096
(0.221) 		0.00015
(0.0373) 		0.184
(1.00) 		0.023
(1.00) 		0.00057
(0.135) 		0.00322
(0.689) 		0.00918
(1.00) 		1e-05
(0.00265) 		0.198
(1.00) 		0.19
(1.00)
CR1 20 (9%) 201 0.0589
(1.00) 		8e-05
(0.0202) 		0.0974
(1.00) 		0.104
(1.00) 		0.00052
(0.124) 		3e-05
(0.00771) 		0.00078
(0.183) 		0.0191
(1.00) 		0.371
(1.00) 		0.704
(1.00)
FBXW7 19 (9%) 202 0.0589
(1.00) 		0.0104
(1.00) 		0.00177
(0.398) 		0.014
(1.00) 		0.0145
(1.00) 		7e-05
(0.0178) 		0.0112
(1.00) 		0.00041
(0.0988) 		0.106
(1.00) 		0.0178
(1.00)
ZBTB20 16 (7%) 205 0.0196
(1.00) 		0.00101
(0.231) 		0.149
(1.00) 		0.168
(1.00) 		0.0437
(1.00) 		0.00418
(0.878) 		0.00203
(0.451) 		0.00047
(0.112) 		0.218
(1.00) 		0.134
(1.00)
MLL4 20 (9%) 201 0.0358
(1.00) 		0.00021
(0.0521) 		0.442
(1.00) 		0.0434
(1.00) 		0.0926
(1.00) 		0.00031
(0.0753) 		0.0315
(1.00) 		0.00437
(0.911) 		0.825
(1.00) 		0.131
(1.00)
APC 33 (15%) 188 0.497
(1.00) 		0.0228
(1.00) 		0.076
(1.00) 		0.00052
(0.124) 		0.23
(1.00) 		0.0034
(0.721) 		0.00657
(1.00) 		0.00182
(0.406) 		0.403
(1.00) 		0.183
(1.00)
HLA-B 12 (5%) 209 0.0782
(1.00) 		0.00032
(0.0774) 		0.00499
(1.00) 		0.00178
(0.399) 		0.0209
(1.00) 		0.0408
(1.00) 		0.0249
(1.00) 		0.0553
(1.00) 		0.756
(1.00) 		0.864
(1.00)
CIC 14 (6%) 207 0.0211
(1.00) 		0.00589
(1.00) 		0.0321
(1.00) 		0.0132
(1.00) 		0.664
(1.00) 		0.00505
(1.00) 		0.0104
(1.00) 		0.00023
(0.0566) 		1
(1.00) 		0.0517
(1.00)
MVK 8 (4%) 213 0.255
(1.00) 		0.0395
(1.00) 		0.0431
(1.00) 		0.00106
(0.242) 		0.553
(1.00) 		0.173
(1.00) 		0.0829
(1.00) 		0.00128
(0.289) 		1
(1.00) 		0.306
(1.00)
KRAS 25 (11%) 196 0.0376
(1.00) 		0.699
(1.00) 		0.56
(1.00) 		0.073
(1.00) 		0.238
(1.00) 		0.0523
(1.00) 		0.367
(1.00) 		0.0471
(1.00) 		0.153
(1.00) 		0.726
(1.00)
RHOA 13 (6%) 208 0.0765
(1.00) 		0.385
(1.00) 		0.872
(1.00) 		0.713
(1.00) 		0.542
(1.00) 		0.799
(1.00) 		0.00279
(0.611) 		0.211
(1.00) 		0.136
(1.00) 		0.0815
(1.00)
SMAD4 19 (9%) 202 0.17
(1.00) 		1
(1.00) 		0.0659
(1.00) 		0.332
(1.00) 		0.00214
(0.473) 		0.261
(1.00) 		0.249
(1.00) 		0.497
(1.00) 		0.0956
(1.00) 		0.13
(1.00)
IRF2 14 (6%) 207 0.466
(1.00) 		0.23
(1.00) 		0.0735
(1.00) 		0.35
(1.00) 		0.31
(1.00) 		0.63
(1.00) 		0.0336
(1.00) 		0.0217
(1.00) 		0.614
(1.00) 		0.87
(1.00)
LARP4B 12 (5%) 209 0.0974
(1.00) 		0.0495
(1.00) 		0.00322
(0.689) 		0.0232
(1.00) 		0.153
(1.00) 		0.0834
(1.00) 		0.175
(1.00) 		0.0148
(1.00) 		0.333
(1.00) 		0.137
(1.00)
CDH1 18 (8%) 203 0.0316
(1.00) 		0.338
(1.00) 		0.613
(1.00) 		0.879
(1.00) 		0.126
(1.00) 		0.0492
(1.00) 		0.186
(1.00) 		0.004
(0.844) 		0.12
(1.00) 		0.545
(1.00)
BCOR 16 (7%) 205 0.0029
(0.629) 		0.0508
(1.00) 		0.171
(1.00) 		0.0143
(1.00) 		0.0193
(1.00) 		0.00596
(1.00) 		0.00846
(1.00) 		0.114
(1.00) 		0.791
(1.00) 		1
(1.00)
C13ORF33 6 (3%) 215 0.19
(1.00) 		0.00436
(0.911) 		0.0154
(1.00) 		0.277
(1.00) 		0.123
(1.00) 		0.00291
(0.629) 		1
(1.00) 		0.203
(1.00) 		0.115
(1.00) 		0.217
(1.00)
ACVR1B 10 (5%) 211 0.0637
(1.00) 		0.297
(1.00) 		0.666
(1.00) 		0.157
(1.00) 		0.00535
(1.00) 		0.359
(1.00) 		0.0809
(1.00) 		0.00876
(1.00) 		0.479
(1.00) 		0.199
(1.00)
ERBB2 11 (5%) 210 0.892
(1.00) 		0.433
(1.00) 		0.264
(1.00) 		0.674
(1.00) 		0.762
(1.00) 		0.65
(1.00) 		0.255
(1.00) 		0.436
(1.00) 		0.828
(1.00) 		0.869
(1.00)
C1R 3 (1%) 218 0.556
(1.00) 		0.213
(1.00) 		0.0408
(1.00) 		0.305
(1.00) 		0.225
(1.00)
CTNND1 13 (6%) 208 0.026
(1.00) 		0.0633
(1.00) 		0.284
(1.00) 		0.103
(1.00) 		0.0268
(1.00) 		0.531
(1.00) 		0.0906
(1.00) 		0.0585
(1.00) 		0.373
(1.00) 		0.178
(1.00)
MLXIPL 13 (6%) 208 0.391
(1.00) 		0.346
(1.00) 		0.0306
(1.00) 		0.0123
(1.00) 		0.0757
(1.00) 		0.316
(1.00) 		0.0174
(1.00) 		0.109
(1.00) 		0.894
(1.00) 		0.618
(1.00)
NLK 5 (2%) 216 0.758
(1.00) 		0.314
(1.00) 		0.165
(1.00) 		0.242
(1.00) 		0.414
(1.00) 		0.812
(1.00) 		0.218
(1.00) 		0.456
(1.00) 		0.513
(1.00) 		0.454
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
TP53 MUTATED 41 21 14 18 4
TP53 WILD-TYPE 16 76 8 17 5

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
TP53 MUTATED 28 35 19
TP53 WILD-TYPE 40 14 40

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
TP53 MUTATED 33 25 30
TP53 WILD-TYPE 30 43 37
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.554 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
TP53 MUTATED 15 26 20 27
TP53 WILD-TYPE 14 33 20 43
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
TP53 MUTATED 14 12 12 17 30
TP53 WILD-TYPE 34 31 19 13 14

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
TP53 MUTATED 15 1 9 16 21 18 5
TP53 WILD-TYPE 17 14 25 24 11 10 10

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
TP53 MUTATED 43 26 30
TP53 WILD-TYPE 59 49 14

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
TP53 MUTATED 21 26 16 36
TP53 WILD-TYPE 20 57 29 16

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
TP53 MUTATED 12 4 27 14 7 12
TP53 WILD-TYPE 9 4 30 14 7 17
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
TP53 MUTATED 51 10 15
TP53 WILD-TYPE 48 27 6

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.2

Table S11.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
PIK3CA MUTATED 3 31 5 6 3
PIK3CA WILD-TYPE 54 66 17 29 6

Figure S8.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.1

Table S12.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
PIK3CA MUTATED 27 5 10
PIK3CA WILD-TYPE 41 44 49

Figure S9.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
PIK3CA MUTATED 20 8 17
PIK3CA WILD-TYPE 43 60 50

Figure S10.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0705 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
PIK3CA MUTATED 10 11 13 11
PIK3CA WILD-TYPE 19 48 27 59
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.21

Table S15.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
PIK3CA MUTATED 20 8 3 9 4
PIK3CA WILD-TYPE 28 35 28 21 40

Figure S11.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S16.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
PIK3CA MUTATED 4 12 3 10 7 1 7
PIK3CA WILD-TYPE 28 3 31 30 25 27 8

Figure S12.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0568 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
PIK3CA MUTATED 29 14 5
PIK3CA WILD-TYPE 73 61 39
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
PIK3CA MUTATED 12 23 9 4
PIK3CA WILD-TYPE 29 60 36 48

Figure S13.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00642 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
PIK3CA MUTATED 2 2 21 7 0 3
PIK3CA WILD-TYPE 19 6 36 21 14 26

Figure S14.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
PIK3CA MUTATED 25 5 5
PIK3CA WILD-TYPE 74 32 16
'CBWD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S21.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
CBWD1 MUTATED 0 23 1 3 1
CBWD1 WILD-TYPE 57 74 21 32 8

Figure S15.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CBWD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S22.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
CBWD1 MUTATED 21 0 1
CBWD1 WILD-TYPE 47 49 58

Figure S16.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.023

Table S23.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
CBWD1 MUTATED 18 2 7
CBWD1 WILD-TYPE 45 66 60

Figure S17.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CBWD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
CBWD1 MUTATED 7 7 9 4
CBWD1 WILD-TYPE 22 52 31 66

Figure S18.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.02

Table S25.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
CBWD1 MUTATED 15 4 3 2 0
CBWD1 WILD-TYPE 33 39 28 28 44

Figure S19.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S26.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
CBWD1 MUTATED 5 0 1 6 3 0 9
CBWD1 WILD-TYPE 27 15 33 34 29 28 6

Figure S20.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.054

Table S27.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
CBWD1 MUTATED 23 4 1
CBWD1 WILD-TYPE 79 71 43

Figure S21.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S28.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
CBWD1 MUTATED 15 9 2 2
CBWD1 WILD-TYPE 26 74 43 50

Figure S22.  Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
CBWD1 MUTATED 2 2 7 7 0 2
CBWD1 WILD-TYPE 19 6 50 21 14 27
'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S30.  Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
CBWD1 MUTATED 13 2 5
CBWD1 WILD-TYPE 86 35 16
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
KRAS MUTATED 2 15 2 3 3
KRAS WILD-TYPE 55 82 20 32 6

Figure S23.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
KRAS MUTATED 9 4 5
KRAS WILD-TYPE 59 45 54
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
KRAS MUTATED 10 7 7
KRAS WILD-TYPE 53 61 60
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.073 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
KRAS MUTATED 4 3 9 8
KRAS WILD-TYPE 25 56 31 62
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
KRAS MUTATED 9 4 2 4 2
KRAS WILD-TYPE 39 39 29 26 42
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0523 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
KRAS MUTATED 6 0 1 4 5 1 4
KRAS WILD-TYPE 26 15 33 36 27 27 11
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
KRAS MUTATED 15 7 3
KRAS WILD-TYPE 87 68 41
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
KRAS MUTATED 10 6 5 4
KRAS WILD-TYPE 31 77 40 48

Figure S24.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
KRAS MUTATED 4 1 3 1 3 3
KRAS WILD-TYPE 17 7 54 27 11 26
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
KRAS MUTATED 9 3 3
KRAS WILD-TYPE 90 34 18
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
ARID1A MUTATED 0 33 2 6 0
ARID1A WILD-TYPE 57 64 20 29 9

Figure S25.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
ARID1A MUTATED 18 5 7
ARID1A WILD-TYPE 50 44 52

Figure S26.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
ARID1A MUTATED 19 7 13
ARID1A WILD-TYPE 44 61 54

Figure S27.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
ARID1A MUTATED 6 6 17 10
ARID1A WILD-TYPE 23 53 23 60

Figure S28.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.16

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
ARID1A MUTATED 19 9 4 5 2
ARID1A WILD-TYPE 29 34 27 25 42

Figure S29.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0052

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
ARID1A MUTATED 6 8 3 5 5 2 10
ARID1A WILD-TYPE 26 7 31 35 27 26 5

Figure S30.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
ARID1A MUTATED 28 11 2
ARID1A WILD-TYPE 74 64 42

Figure S31.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00285 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
ARID1A MUTATED 15 17 4 5
ARID1A WILD-TYPE 26 66 41 47

Figure S32.  Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
ARID1A MUTATED 4 1 10 7 2 3
ARID1A WILD-TYPE 17 7 47 21 12 26
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
ARID1A MUTATED 17 4 6
ARID1A WILD-TYPE 82 33 15
'PGM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.22

Table S51.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
PGM5 MUTATED 0 16 3 1 2
PGM5 WILD-TYPE 57 81 19 34 7

Figure S33.  Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PGM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.037

Table S52.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
PGM5 MUTATED 14 1 1
PGM5 WILD-TYPE 54 48 58

Figure S34.  Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PGM5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
PGM5 MUTATED 10 4 6
PGM5 WILD-TYPE 53 64 61
'PGM5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
PGM5 MUTATED 5 4 8 3
PGM5 WILD-TYPE 24 55 32 67

Figure S35.  Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.13

Table S55.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
PGM5 MUTATED 11 2 5 1 0
PGM5 WILD-TYPE 37 41 26 29 44

Figure S36.  Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PGM5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.69

Table S56.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
PGM5 MUTATED 2 0 2 6 3 0 6
PGM5 WILD-TYPE 30 15 32 34 29 28 9

Figure S37.  Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00918 (Fisher's exact test), Q value = 1

Table S57.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
PGM5 MUTATED 17 3 2
PGM5 WILD-TYPE 85 72 42

Figure S38.  Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PGM5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S58.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
PGM5 MUTATED 13 6 2 1
PGM5 WILD-TYPE 28 77 43 51

Figure S39.  Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
PGM5 MUTATED 3 2 4 4 0 1
PGM5 WILD-TYPE 18 6 53 24 14 28
'PGM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
PGM5 MUTATED 8 2 4
PGM5 WILD-TYPE 91 35 17
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0765 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
RHOA MUTATED 0 10 1 2 0
RHOA WILD-TYPE 57 87 21 33 9
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
RHOA MUTATED 3 2 6
RHOA WILD-TYPE 65 47 53
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
RHOA MUTATED 3 4 5
RHOA WILD-TYPE 60 64 62
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
RHOA MUTATED 2 5 1 4
RHOA WILD-TYPE 27 54 39 66
'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
RHOA MUTATED 2 4 2 3 1
RHOA WILD-TYPE 46 39 29 27 43
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.799 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
RHOA MUTATED 2 0 4 3 2 1 0
RHOA WILD-TYPE 30 15 30 37 30 27 15
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
RHOA MUTATED 3 10 0
RHOA WILD-TYPE 99 65 44

Figure S40.  Get High-res Image Gene #7: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
RHOA MUTATED 1 6 5 1
RHOA WILD-TYPE 40 77 40 51
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
RHOA MUTATED 0 1 3 0 1 4
RHOA WILD-TYPE 21 7 54 28 13 25
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0815 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
RHOA MUTATED 4 5 0
RHOA WILD-TYPE 95 32 21
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S71.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
SMAD4 MUTATED 5 6 1 7 0
SMAD4 WILD-TYPE 52 91 21 28 9
'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S72.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
SMAD4 MUTATED 6 4 5
SMAD4 WILD-TYPE 62 45 54
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0659 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
SMAD4 MUTATED 9 5 2
SMAD4 WILD-TYPE 54 63 65
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
SMAD4 MUTATED 3 2 5 6
SMAD4 WILD-TYPE 26 57 35 64
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.47

Table S75.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
SMAD4 MUTATED 5 1 7 4 0
SMAD4 WILD-TYPE 43 42 24 26 44

Figure S41.  Get High-res Image Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
SMAD4 MUTATED 4 1 1 5 4 0 2
SMAD4 WILD-TYPE 28 14 33 35 28 28 13
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
SMAD4 MUTATED 11 7 1
SMAD4 WILD-TYPE 91 68 43
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S78.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
SMAD4 MUTATED 6 7 3 3
SMAD4 WILD-TYPE 35 76 42 49
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0956 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
SMAD4 MUTATED 1 1 3 6 0 1
SMAD4 WILD-TYPE 20 7 54 22 14 28
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
SMAD4 MUTATED 6 2 4
SMAD4 WILD-TYPE 93 35 17
'IRF2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
IRF2 MUTATED 2 9 1 1 1
IRF2 WILD-TYPE 55 88 21 34 8
'IRF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S82.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
IRF2 MUTATED 6 2 1
IRF2 WILD-TYPE 62 47 58
'IRF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0735 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
IRF2 MUTATED 8 2 3
IRF2 WILD-TYPE 55 66 64
'IRF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
IRF2 MUTATED 2 2 5 4
IRF2 WILD-TYPE 27 57 35 66
'IRF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
IRF2 MUTATED 6 2 1 1 1
IRF2 WILD-TYPE 42 41 30 29 43
'IRF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S86.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
IRF2 MUTATED 3 0 1 3 1 1 2
IRF2 WILD-TYPE 29 15 33 37 31 27 13
'IRF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
IRF2 MUTATED 11 1 2
IRF2 WILD-TYPE 91 74 42

Figure S42.  Get High-res Image Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IRF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
IRF2 MUTATED 7 5 1 1
IRF2 WILD-TYPE 34 78 44 51

Figure S43.  Get High-res Image Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
IRF2 MUTATED 1 0 5 1 1 0
IRF2 WILD-TYPE 20 8 52 27 13 29
'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S90.  Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
IRF2 MUTATED 6 1 1
IRF2 WILD-TYPE 93 36 20
'LARP4B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0974 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
LARP4B MUTATED 1 10 1 0 0
LARP4B WILD-TYPE 56 87 21 35 9
'LARP4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
LARP4B MUTATED 6 3 0
LARP4B WILD-TYPE 62 46 59

Figure S44.  Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'LARP4B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.69

Table S93.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
LARP4B MUTATED 8 0 3
LARP4B WILD-TYPE 55 68 64

Figure S45.  Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'LARP4B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
LARP4B MUTATED 2 2 6 1
LARP4B WILD-TYPE 27 57 34 69

Figure S46.  Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'LARP4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 1

Table S95.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
LARP4B MUTATED 4 0 2 3 1
LARP4B WILD-TYPE 44 43 29 27 43
'LARP4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0834 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
LARP4B MUTATED 2 0 0 1 3 1 3
LARP4B WILD-TYPE 30 15 34 39 29 27 12
'LARP4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S97.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
LARP4B MUTATED 9 2 1
LARP4B WILD-TYPE 93 73 43
'LARP4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
LARP4B MUTATED 6 5 0 1
LARP4B WILD-TYPE 35 78 45 51

Figure S47.  Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'LARP4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
LARP4B MUTATED 3 0 4 2 0 0
LARP4B WILD-TYPE 18 8 53 26 14 29
'LARP4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S100.  Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
LARP4B MUTATED 7 0 2
LARP4B WILD-TYPE 92 37 19
'APC MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
APC MUTATED 10 16 4 2 1
APC WILD-TYPE 47 81 18 33 8
'APC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
APC MUTATED 12 8 2
APC WILD-TYPE 56 41 57

Figure S48.  Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.076 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
APC MUTATED 13 5 11
APC WILD-TYPE 50 63 56
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
APC MUTATED 5 6 14 4
APC WILD-TYPE 24 53 26 66

Figure S49.  Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
APC MUTATED 9 2 5 6 7
APC WILD-TYPE 39 41 26 24 37
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0034 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
APC MUTATED 1 0 2 8 8 4 6
APC WILD-TYPE 31 15 32 32 24 24 9

Figure S50.  Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00657 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
APC MUTATED 22 4 7
APC WILD-TYPE 80 71 37

Figure S51.  Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
APC MUTATED 13 8 2 10
APC WILD-TYPE 28 75 43 42

Figure S52.  Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
APC MUTATED 3 2 8 2 1 1
APC WILD-TYPE 18 6 49 26 13 28
'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
APC MUTATED 13 1 3
APC WILD-TYPE 86 36 18
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0589 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
FBXW7 MUTATED 2 15 1 1 0
FBXW7 WILD-TYPE 55 82 21 34 9
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
FBXW7 MUTATED 11 3 1
FBXW7 WILD-TYPE 57 46 58

Figure S53.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.4

Table S113.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
FBXW7 MUTATED 12 1 5
FBXW7 WILD-TYPE 51 67 62

Figure S54.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
FBXW7 MUTATED 4 4 8 2
FBXW7 WILD-TYPE 25 55 32 68

Figure S55.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
FBXW7 MUTATED 10 1 1 2 2
FBXW7 WILD-TYPE 38 42 30 28 42

Figure S56.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.018

Table S116.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
FBXW7 MUTATED 4 0 0 1 2 2 7
FBXW7 WILD-TYPE 28 15 34 39 30 26 8

Figure S57.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
FBXW7 MUTATED 15 2 2
FBXW7 WILD-TYPE 87 73 42

Figure S58.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.099

Table S118.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
FBXW7 MUTATED 11 5 1 2
FBXW7 WILD-TYPE 30 78 44 50

Figure S59.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
FBXW7 MUTATED 4 0 6 4 0 0
FBXW7 WILD-TYPE 17 8 51 24 14 29
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 1

Table S120.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
FBXW7 MUTATED 10 0 4
FBXW7 WILD-TYPE 89 37 17

Figure S60.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 1

Table S121.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
CDH1 MUTATED 0 12 2 3 0
CDH1 WILD-TYPE 57 85 20 32 9

Figure S61.  Get High-res Image Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S122.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
CDH1 MUTATED 5 2 7
CDH1 WILD-TYPE 63 47 52
'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S123.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
CDH1 MUTATED 4 8 6
CDH1 WILD-TYPE 59 60 61
'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
CDH1 MUTATED 2 7 3 6
CDH1 WILD-TYPE 27 52 37 64
'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S125.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
CDH1 MUTATED 2 7 1 4 2
CDH1 WILD-TYPE 46 36 30 26 42
'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0492 (Fisher's exact test), Q value = 1

Table S126.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
CDH1 MUTATED 1 0 8 3 3 1 0
CDH1 WILD-TYPE 31 15 26 37 29 27 15

Figure S62.  Get High-res Image Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
CDH1 MUTATED 8 9 1
CDH1 WILD-TYPE 94 66 43
'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.004 (Fisher's exact test), Q value = 0.84

Table S128.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
CDH1 MUTATED 6 3 8 1
CDH1 WILD-TYPE 35 80 37 51

Figure S63.  Get High-res Image Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S129.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
CDH1 MUTATED 0 0 5 1 2 6
CDH1 WILD-TYPE 21 8 52 27 12 23
'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.545 (Fisher's exact test), Q value = 1

Table S130.  Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
CDH1 MUTATED 8 5 1
CDH1 WILD-TYPE 91 32 20
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0782 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
HLA-B MUTATED 0 9 2 1 0
HLA-B WILD-TYPE 57 88 20 34 9
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.077

Table S132.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
HLA-B MUTATED 9 0 0
HLA-B WILD-TYPE 59 49 59

Figure S64.  Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
HLA-B MUTATED 9 1 2
HLA-B WILD-TYPE 54 67 65

Figure S65.  Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.4

Table S134.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
HLA-B MUTATED 3 1 7 1
HLA-B WILD-TYPE 26 58 33 69

Figure S66.  Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 1

Table S135.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
HLA-B MUTATED 5 0 2 3 0
HLA-B WILD-TYPE 43 43 29 27 44

Figure S67.  Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
HLA-B MUTATED 3 1 0 1 2 0 3
HLA-B WILD-TYPE 29 14 34 39 30 28 12

Figure S68.  Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 1

Table S137.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
HLA-B MUTATED 10 2 0
HLA-B WILD-TYPE 92 73 44

Figure S69.  Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0553 (Fisher's exact test), Q value = 1

Table S138.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
HLA-B MUTATED 5 5 2 0
HLA-B WILD-TYPE 36 78 43 52
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S139.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
HLA-B MUTATED 0 0 5 1 0 1
HLA-B WILD-TYPE 21 8 52 27 14 28
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S140.  Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
HLA-B MUTATED 4 2 1
HLA-B WILD-TYPE 95 35 20
'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
BCOR MUTATED 0 13 2 0 1
BCOR WILD-TYPE 57 84 20 35 8

Figure S70.  Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0508 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
BCOR MUTATED 7 0 3
BCOR WILD-TYPE 61 49 56
'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
BCOR MUTATED 7 2 5
BCOR WILD-TYPE 56 66 62
'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
BCOR MUTATED 2 4 7 1
BCOR WILD-TYPE 27 55 33 69

Figure S71.  Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
BCOR MUTATED 8 2 1 2 0
BCOR WILD-TYPE 40 41 30 28 44

Figure S72.  Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00596 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
BCOR MUTATED 4 3 0 1 2 0 3
BCOR WILD-TYPE 28 12 34 39 30 28 12

Figure S73.  Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00846 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
BCOR MUTATED 13 3 0
BCOR WILD-TYPE 89 72 44

Figure S74.  Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
BCOR MUTATED 6 7 2 1
BCOR WILD-TYPE 35 76 43 51
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
BCOR MUTATED 0 0 5 2 0 2
BCOR WILD-TYPE 21 8 52 26 14 27
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
BCOR MUTATED 6 2 1
BCOR WILD-TYPE 93 35 20
'C13ORF33 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
C13ORF33 MUTATED 0 3 1 1 1
C13ORF33 WILD-TYPE 57 94 21 34 8
'C13ORF33 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.91

Table S152.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
C13ORF33 MUTATED 6 0 0
C13ORF33 WILD-TYPE 62 49 59

Figure S75.  Get High-res Image Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'C13ORF33 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 1

Table S153.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
C13ORF33 MUTATED 5 1 0
C13ORF33 WILD-TYPE 58 67 67

Figure S76.  Get High-res Image Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'C13ORF33 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
C13ORF33 MUTATED 1 1 3 1
C13ORF33 WILD-TYPE 28 58 37 69
'C13ORF33 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S155.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
C13ORF33 MUTATED 3 0 1 0 0
C13ORF33 WILD-TYPE 45 43 30 30 44
'C13ORF33 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.63

Table S156.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
C13ORF33 MUTATED 0 0 0 1 0 0 3
C13ORF33 WILD-TYPE 32 15 34 39 32 28 12

Figure S77.  Get High-res Image Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S157.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
C13ORF33 MUTATED 3 2 1
C13ORF33 WILD-TYPE 99 73 43
'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S158.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
C13ORF33 MUTATED 3 2 1 0
C13ORF33 WILD-TYPE 38 81 44 52
'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S159.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
C13ORF33 MUTATED 1 0 0 3 0 1
C13ORF33 WILD-TYPE 20 8 57 25 14 28
'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 1

Table S160.  Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
C13ORF33 MUTATED 2 1 2
C13ORF33 WILD-TYPE 97 36 19
'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
CIC MUTATED 0 11 0 2 1
CIC WILD-TYPE 57 86 22 33 8

Figure S78.  Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00589 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
CIC MUTATED 8 0 1
CIC WILD-TYPE 60 49 58

Figure S79.  Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
CIC MUTATED 9 2 3
CIC WILD-TYPE 54 66 64

Figure S80.  Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
CIC MUTATED 4 3 6 1
CIC WILD-TYPE 25 56 34 69

Figure S81.  Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
CIC MUTATED 3 2 1 3 1
CIC WILD-TYPE 45 41 30 27 43
'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
CIC MUTATED 4 0 0 0 4 0 2
CIC WILD-TYPE 28 15 34 40 28 28 13

Figure S82.  Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
CIC MUTATED 12 1 1
CIC WILD-TYPE 90 74 43

Figure S83.  Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
CIC MUTATED 9 4 1 0
CIC WILD-TYPE 32 79 44 52

Figure S84.  Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
CIC MUTATED 1 0 3 1 0 1
CIC WILD-TYPE 20 8 54 27 14 28
'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0517 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
CIC MUTATED 2 1 3
CIC WILD-TYPE 97 36 18
'ACVR1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0637 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
ACVR1B MUTATED 0 8 0 1 1
ACVR1B WILD-TYPE 57 89 22 34 8
'ACVR1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S172.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
ACVR1B MUTATED 5 1 1
ACVR1B WILD-TYPE 63 48 58
'ACVR1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S173.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
ACVR1B MUTATED 4 2 4
ACVR1B WILD-TYPE 59 66 63
'ACVR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 1

Table S174.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
ACVR1B MUTATED 1 2 5 2
ACVR1B WILD-TYPE 28 57 35 68
'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 1

Table S175.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
ACVR1B MUTATED 3 0 0 4 0
ACVR1B WILD-TYPE 45 43 31 26 44

Figure S85.  Get High-res Image Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
ACVR1B MUTATED 2 0 0 2 3 0 0
ACVR1B WILD-TYPE 30 15 34 38 29 28 15
'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0809 (Fisher's exact test), Q value = 1

Table S177.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
ACVR1B MUTATED 8 2 0
ACVR1B WILD-TYPE 94 73 44
'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00876 (Fisher's exact test), Q value = 1

Table S178.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
ACVR1B MUTATED 6 3 1 0
ACVR1B WILD-TYPE 35 80 44 52

Figure S86.  Get High-res Image Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S179.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
ACVR1B MUTATED 1 1 3 2 0 0
ACVR1B WILD-TYPE 20 7 54 26 14 29
'ACVR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S180.  Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
ACVR1B MUTATED 5 0 2
ACVR1B WILD-TYPE 94 37 19
'ZBTB20 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
ZBTB20 MUTATED 0 13 1 2 0
ZBTB20 WILD-TYPE 57 84 21 33 9

Figure S87.  Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ZBTB20 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.23

Table S182.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
ZBTB20 MUTATED 10 0 1
ZBTB20 WILD-TYPE 58 49 58

Figure S88.  Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZBTB20 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S183.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
ZBTB20 MUTATED 7 2 6
ZBTB20 WILD-TYPE 56 66 61
'ZBTB20 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
ZBTB20 MUTATED 3 3 6 3
ZBTB20 WILD-TYPE 26 56 34 67
'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 1

Table S185.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
ZBTB20 MUTATED 6 1 1 5 1
ZBTB20 WILD-TYPE 42 42 30 25 43

Figure S89.  Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00418 (Fisher's exact test), Q value = 0.88

Table S186.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
ZBTB20 MUTATED 3 0 0 2 5 0 4
ZBTB20 WILD-TYPE 29 15 34 38 27 28 11

Figure S90.  Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.45

Table S187.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
ZBTB20 MUTATED 14 2 0
ZBTB20 WILD-TYPE 88 73 44

Figure S91.  Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.11

Table S188.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
ZBTB20 MUTATED 9 6 1 0
ZBTB20 WILD-TYPE 32 77 44 52

Figure S92.  Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 1

Table S189.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
ZBTB20 MUTATED 1 1 4 4 0 0
ZBTB20 WILD-TYPE 20 7 53 24 14 29
'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S190.  Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
ZBTB20 MUTATED 8 0 2
ZBTB20 WILD-TYPE 91 37 19
'MVK MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
MVK MUTATED 0 6 0 2 0
MVK WILD-TYPE 57 91 22 33 9
'MVK MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
MVK MUTATED 4 0 0
MVK WILD-TYPE 64 49 59

Figure S93.  Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MVK MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
MVK MUTATED 5 0 3
MVK WILD-TYPE 58 68 64

Figure S94.  Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MVK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.24

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
MVK MUTATED 1 1 6 0
MVK WILD-TYPE 28 58 34 70

Figure S95.  Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MVK MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
MVK MUTATED 3 1 1 1 0
MVK WILD-TYPE 45 42 30 29 44
'MVK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
MVK MUTATED 1 1 0 1 1 0 2
MVK WILD-TYPE 31 14 34 39 31 28 13
'MVK MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0829 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
MVK MUTATED 7 1 0
MVK WILD-TYPE 95 74 44
'MVK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
MVK MUTATED 6 1 1 0
MVK WILD-TYPE 35 82 44 52

Figure S96.  Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MVK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
MVK MUTATED 0 0 1 1 0 1
MVK WILD-TYPE 21 8 56 27 14 28
'MVK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
MVK MUTATED 1 1 1
MVK WILD-TYPE 98 36 20
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S201.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
ERBB2 MUTATED 2 7 1 1 0
ERBB2 WILD-TYPE 55 90 21 34 9
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
ERBB2 MUTATED 5 1 2
ERBB2 WILD-TYPE 63 48 57
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 1

Table S203.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
ERBB2 MUTATED 6 2 3
ERBB2 WILD-TYPE 57 66 64
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S204.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
ERBB2 MUTATED 3 3 2 3
ERBB2 WILD-TYPE 26 56 38 67
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S205.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
ERBB2 MUTATED 4 2 1 2 1
ERBB2 WILD-TYPE 44 41 30 28 43
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.65 (Fisher's exact test), Q value = 1

Table S206.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
ERBB2 MUTATED 2 0 1 3 3 0 1
ERBB2 WILD-TYPE 30 15 33 37 29 28 14
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S207.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
ERBB2 MUTATED 8 2 1
ERBB2 WILD-TYPE 94 73 43
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S208.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
ERBB2 MUTATED 4 4 2 1
ERBB2 WILD-TYPE 37 79 43 51
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S209.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
ERBB2 MUTATED 1 0 3 3 0 1
ERBB2 WILD-TYPE 20 8 54 25 14 28
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S210.  Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
ERBB2 MUTATED 6 1 1
ERBB2 WILD-TYPE 93 36 20
'CR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0589 (Fisher's exact test), Q value = 1

Table S211.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
CR1 MUTATED 2 13 0 3 2
CR1 WILD-TYPE 55 84 22 32 7
'CR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.02

Table S212.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
CR1 MUTATED 12 1 0
CR1 WILD-TYPE 56 48 59

Figure S97.  Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0974 (Fisher's exact test), Q value = 1

Table S213.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
CR1 MUTATED 10 3 6
CR1 WILD-TYPE 53 65 61
'CR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 1

Table S214.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
CR1 MUTATED 5 5 6 3
CR1 WILD-TYPE 24 54 34 67
'CR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.12

Table S215.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
CR1 MUTATED 11 1 2 4 0
CR1 WILD-TYPE 37 42 29 26 44

Figure S98.  Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0077

Table S216.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
CR1 MUTATED 2 1 0 6 2 0 7
CR1 WILD-TYPE 30 14 34 34 30 28 8

Figure S99.  Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.18

Table S217.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
CR1 MUTATED 17 3 0
CR1 WILD-TYPE 85 72 44

Figure S100.  Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 1

Table S218.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
CR1 MUTATED 8 9 2 1
CR1 WILD-TYPE 33 74 43 51

Figure S101.  Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S219.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
CR1 MUTATED 0 0 5 4 0 1
CR1 WILD-TYPE 21 8 52 24 14 28
'CR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S220.  Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
CR1 MUTATED 8 1 1
CR1 WILD-TYPE 91 36 20
'C1R MUTATION STATUS' versus 'CN_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 1

Table S221.  Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
C1R MUTATED 0 3 0 0 0
C1R WILD-TYPE 57 94 22 35 9
'C1R MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
C1R MUTATED 2 0 1
C1R WILD-TYPE 61 68 66
'C1R MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 1

Table S223.  Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
C1R MUTATED 1 0 2 0
C1R WILD-TYPE 28 59 38 70

Figure S102.  Get High-res Image Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'C1R MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
C1R MUTATED 3 0 0
C1R WILD-TYPE 99 75 44
'C1R MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S225.  Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
C1R MUTATED 2 1 0 0
C1R WILD-TYPE 39 82 45 52
'CTNND1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 1

Table S226.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
CTNND1 MUTATED 1 11 0 0 1
CTNND1 WILD-TYPE 56 86 22 35 8

Figure S103.  Get High-res Image Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTNND1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0633 (Fisher's exact test), Q value = 1

Table S227.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
CTNND1 MUTATED 8 2 1
CTNND1 WILD-TYPE 60 47 58
'CTNND1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 1

Table S228.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
CTNND1 MUTATED 6 2 5
CTNND1 WILD-TYPE 57 66 62
'CTNND1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S229.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
CTNND1 MUTATED 2 3 6 2
CTNND1 WILD-TYPE 27 56 34 68
'CTNND1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 1

Table S230.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
CTNND1 MUTATED 7 1 0 3 1
CTNND1 WILD-TYPE 41 42 31 27 43

Figure S104.  Get High-res Image Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CTNND1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S231.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
CTNND1 MUTATED 1 1 1 2 4 1 2
CTNND1 WILD-TYPE 31 14 33 38 28 27 13
'CTNND1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0906 (Fisher's exact test), Q value = 1

Table S232.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
CTNND1 MUTATED 10 2 1
CTNND1 WILD-TYPE 92 73 43
'CTNND1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0585 (Fisher's exact test), Q value = 1

Table S233.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
CTNND1 MUTATED 6 5 1 1
CTNND1 WILD-TYPE 35 78 44 51
'CTNND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S234.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
CTNND1 MUTATED 2 2 4 2 0 1
CTNND1 WILD-TYPE 19 6 53 26 14 28
'CTNND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S235.  Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
CTNND1 MUTATED 10 1 0
CTNND1 WILD-TYPE 89 36 21
'MLXIPL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S236.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
MLXIPL MUTATED 1 8 1 2 1
MLXIPL WILD-TYPE 56 89 21 33 8
'MLXIPL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S237.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
MLXIPL MUTATED 5 2 1
MLXIPL WILD-TYPE 63 47 58
'MLXIPL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 1

Table S238.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
MLXIPL MUTATED 8 1 4
MLXIPL WILD-TYPE 55 67 63

Figure S105.  Get High-res Image Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MLXIPL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S239.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
MLXIPL MUTATED 2 3 7 1
MLXIPL WILD-TYPE 27 56 33 69

Figure S106.  Get High-res Image Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLXIPL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0757 (Fisher's exact test), Q value = 1

Table S240.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
MLXIPL MUTATED 7 1 2 0 2
MLXIPL WILD-TYPE 41 42 29 30 42
'MLXIPL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S241.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
MLXIPL MUTATED 3 0 0 4 2 1 2
MLXIPL WILD-TYPE 29 15 34 36 30 27 13
'MLXIPL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 1

Table S242.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
MLXIPL MUTATED 11 1 1
MLXIPL WILD-TYPE 91 74 43

Figure S107.  Get High-res Image Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MLXIPL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 1

Table S243.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
MLXIPL MUTATED 6 4 1 2
MLXIPL WILD-TYPE 35 79 44 50
'MLXIPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S244.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
MLXIPL MUTATED 2 0 3 1 0 1
MLXIPL WILD-TYPE 19 8 54 27 14 28
'MLXIPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S245.  Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
MLXIPL MUTATED 6 1 0
MLXIPL WILD-TYPE 93 36 21
'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 1

Table S246.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
MLL4 MUTATED 1 15 1 2 1
MLL4 WILD-TYPE 56 82 21 33 8

Figure S108.  Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.052

Table S247.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
MLL4 MUTATED 12 0 1
MLL4 WILD-TYPE 56 49 58

Figure S109.  Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S248.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
MLL4 MUTATED 9 6 5
MLL4 WILD-TYPE 54 62 62
'MLL4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 1

Table S249.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
MLL4 MUTATED 3 3 9 5
MLL4 WILD-TYPE 26 56 31 65

Figure S110.  Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0926 (Fisher's exact test), Q value = 1

Table S250.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
MLL4 MUTATED 8 2 2 4 1
MLL4 WILD-TYPE 40 41 29 26 43
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.075

Table S251.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
MLL4 MUTATED 2 1 0 3 3 1 7
MLL4 WILD-TYPE 30 14 34 37 29 27 8

Figure S111.  Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MLL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 1

Table S252.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
MLL4 MUTATED 15 3 2
MLL4 WILD-TYPE 87 72 42

Figure S112.  Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MLL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.91

Table S253.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
MLL4 MUTATED 10 6 1 3
MLL4 WILD-TYPE 31 77 44 49

Figure S113.  Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S254.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
MLL4 MUTATED 1 0 6 2 0 1
MLL4 WILD-TYPE 20 8 51 26 14 28
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 1

Table S255.  Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
MLL4 MUTATED 8 0 2
MLL4 WILD-TYPE 91 37 19
'NLK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S256.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 97 22 35 9
NLK MUTATED 1 4 0 0 0
NLK WILD-TYPE 56 93 22 35 9
'NLK MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S257.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 49 59
NLK MUTATED 3 1 0
NLK WILD-TYPE 65 48 59
'NLK MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S258.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 68 67
NLK MUTATED 3 0 2
NLK WILD-TYPE 60 68 65
'NLK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S259.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 59 40 70
NLK MUTATED 0 1 3 1
NLK WILD-TYPE 29 58 37 69
'NLK MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S260.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 48 43 31 30 44
NLK MUTATED 3 0 1 0 1
NLK WILD-TYPE 45 43 30 30 43
'NLK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S261.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 32 15 34 40 32 28 15
NLK MUTATED 1 0 0 1 1 1 1
NLK WILD-TYPE 31 15 34 39 31 27 14
'NLK MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 1

Table S262.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 75 44
NLK MUTATED 4 0 1
NLK WILD-TYPE 98 75 43
'NLK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S263.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 83 45 52
NLK MUTATED 2 2 1 0
NLK WILD-TYPE 39 81 44 52
'NLK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S264.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 21 8 57 28 14 29
NLK MUTATED 1 0 1 1 1 0
NLK WILD-TYPE 20 8 56 27 13 29
'NLK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S265.  Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 37 21
NLK MUTATED 3 0 1
NLK WILD-TYPE 96 37 20
Methods & Data
Input

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

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

  • Number of patients = 221

  • Number of significantly mutated genes = 27

  • Number of Molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

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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