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 29 genes and 12 molecular subtypes across 417 patients, 15 significant findings detected with P value < 0.05 and Q value < 0.25.

  • SETD2 mutation correlated to 'METHLYATION_CNMF'.

  • BAP1 mutation correlated to 'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • PTEN mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • PBRM1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • FAM200A mutation correlated to 'RPPA_CNMF'.

  • MTOR mutation correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 29 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 15 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
BAP1 41 (10%) 376 0.0322
(1.00) 		0.00043
(0.106) 		0.0161
(1.00) 		0.00015
(0.0372) 		0.021
(1.00) 		0.0238
(1.00) 		0.00014
(0.0349) 		6e-05
(0.0151) 		3e-05
(0.00759) 		1e-05
(0.00257) 		0.128
(1.00) 		0.351
(1.00)
PBRM1 136 (33%) 281 0.149
(1.00) 		0.0595
(1.00) 		0.0415
(1.00) 		2e-05
(0.00508) 		0.0013
(0.315) 		0.98
(1.00) 		0.00658
(1.00) 		1e-05
(0.00257) 		0.00369
(0.886) 		0.0309
(1.00) 		0.00013
(0.0325) 		0.0885
(1.00)
PTEN 18 (4%) 399 0.106
(1.00) 		0.0328
(1.00) 		0.099
(1.00) 		0.169
(1.00) 		0.119
(1.00) 		0.307
(1.00) 		3e-05
(0.00759) 		0.00043
(0.106) 		0.00163
(0.393) 		0.114
(1.00) 		0.0737
(1.00) 		1
(1.00)
MTOR 23 (6%) 394 0.726
(1.00) 		0.154
(1.00) 		0.00038
(0.0939) 		0.00096
(0.233) 		0.919
(1.00) 		0.759
(1.00) 		0.256
(1.00) 		0.246
(1.00) 		0.876
(1.00) 		1
(1.00)
SETD2 44 (11%) 373 1
(1.00) 		0.501
(1.00) 		0.449
(1.00) 		1e-05
(0.00257) 		0.664
(1.00) 		0.303
(1.00) 		0.47
(1.00) 		0.0788
(1.00) 		0.402
(1.00) 		0.236
(1.00) 		0.542
(1.00) 		0.358
(1.00)
FAM200A 5 (1%) 412 0.719
(1.00) 		0.00089
(0.217) 		0.254
(1.00) 		0.147
(1.00) 		0.389
(1.00) 		0.207
(1.00) 		0.416
(1.00)
KDM5C 26 (6%) 391 0.275
(1.00) 		0.0882
(1.00) 		0.338
(1.00) 		0.114
(1.00) 		0.0691
(1.00) 		0.102
(1.00) 		0.0104
(1.00) 		0.0414
(1.00) 		1
(1.00) 		1
(1.00)
VHL 166 (40%) 251 0.112
(1.00) 		0.226
(1.00) 		0.423
(1.00) 		0.748
(1.00) 		0.144
(1.00) 		0.333
(1.00) 		0.0077
(1.00) 		0.0505
(1.00) 		0.159
(1.00) 		0.133
(1.00) 		0.437
(1.00) 		0.731
(1.00)
TP53 9 (2%) 408 0.382
(1.00) 		0.515
(1.00) 		0.445
(1.00) 		0.424
(1.00) 		0.446
(1.00) 		0.172
(1.00) 		0.466
(1.00) 		0.517
(1.00) 		1
(1.00) 		1
(1.00)
NEFH 5 (1%) 412 0.858
(1.00) 		0.542
(1.00) 		0.978
(1.00) 		0.177
(1.00) 		0.00981
(1.00) 		0.272
(1.00) 		0.627
(1.00) 		0.83
(1.00) 		0.447
(1.00) 		0.12
(1.00)
CCDC120 4 (1%) 413 0.107
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.668
(1.00) 		0.486
(1.00) 		0.826
(1.00) 		1
(1.00)
GUSB 4 (1%) 413 0.57
(1.00) 		0.312
(1.00) 		0.627
(1.00) 		0.174
(1.00) 		0.702
(1.00) 		0.455
(1.00) 		0.875
(1.00)
PIK3CA 12 (3%) 405 0.523
(1.00) 		0.653
(1.00) 		0.795
(1.00) 		0.284
(1.00) 		0.356
(1.00) 		0.449
(1.00) 		0.751
(1.00) 		0.945
(1.00)
PCK1 5 (1%) 412 0.45
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.85
(1.00) 		0.459
(1.00) 		0.729
(1.00) 		0.386
(1.00)
ARID1A 12 (3%) 405 0.521
(1.00) 		0.259
(1.00) 		0.904
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.252
(1.00) 		0.247
(1.00) 		0.00892
(1.00) 		0.382
(1.00) 		0.193
(1.00)
ATM 11 (3%) 406 0.728
(1.00) 		0.474
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.295
(1.00) 		0.0306
(1.00) 		0.115
(1.00) 		0.091
(1.00)
DPCR1 6 (1%) 411 0.205
(1.00) 		0.51
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.227
(1.00) 		0.335
(1.00) 		0.873
(1.00) 		0.931
(1.00)
FGFR3 4 (1%) 413 0.692
(1.00) 		0.841
(1.00) 		0.956
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.292
(1.00) 		0.825
(1.00) 		0.316
(1.00)
PTCH1 7 (2%) 410 1
(1.00) 		0.0548
(1.00) 		0.409
(1.00) 		0.157
(1.00) 		0.876
(1.00) 		0.332
(1.00) 		0.896
(1.00) 		0.609
(1.00)
RBMX 4 (1%) 413 0.694
(1.00) 		0.618
(1.00) 		0.109
(1.00) 		0.457
(1.00) 		0.4
(1.00) 		0.701
(1.00) 		0.336
(1.00) 		0.126
(1.00)
ARAP3 3 (1%) 414 0.602
(1.00) 		1
(1.00) 		1
(1.00) 		0.775
(1.00) 		1
(1.00) 		0.795
(1.00) 		0.839
(1.00)
GPR172B 4 (1%) 413 1
(1.00) 		0.12
(1.00) 		0.796
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.61
(1.00) 		1
(1.00)
EGFR 7 (2%) 410 0.696
(1.00) 		0.682
(1.00) 		0.738
(1.00) 		0.496
(1.00) 		0.612
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.0948
(1.00)
IL1RAP 4 (1%) 413 0.571
(1.00) 		0.617
(1.00) 		0.26
(1.00) 		0.0918
(1.00) 		0.816
(1.00) 		0.486
(1.00) 		0.558
(1.00) 		0.638
(1.00)
BCL6 5 (1%) 412 0.45
(1.00) 		0.618
(1.00) 		0.812
(1.00) 		0.732
(1.00) 		1
(1.00) 		0.461
(1.00) 		0.727
(1.00) 		0.484
(1.00)
NFAT5 6 (1%) 411 0.367
(1.00) 		0.879
(1.00) 		0.254
(1.00) 		0.531
(1.00) 		0.338
(1.00) 		0.567
(1.00) 		0.282
(1.00) 		0.0957
(1.00)
LARP1 5 (1%) 412 0.449
(1.00) 		0.442
(1.00) 		0.241
(1.00) 		0.528
(1.00) 		0.847
(1.00) 		1
(1.00) 		0.63
(1.00) 		0.321
(1.00)
KIAA1751 6 (1%) 411 0.579
(1.00) 		0.641
(1.00) 		0.614
(1.00) 		0.0747
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.321
(1.00)
INSRR 4 (1%) 413 0.695
(1.00) 		0.123
(1.00) 		0.298
(1.00) 		0.388
(1.00) 		0.397
(1.00) 		0.386
(1.00) 		0.455
(1.00) 		0.787
(1.00)
'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S1.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 21 3
SETD2 MUTATED 2 2 0
SETD2 WILD-TYPE 20 19 3
'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S2.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 10 3 10 10 8 1
SETD2 MUTATED 1 2 0 0 1 0 0
SETD2 WILD-TYPE 3 8 3 10 9 8 1
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
SETD2 MUTATED 17 13 14
SETD2 WILD-TYPE 173 82 116
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S4.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
SETD2 MUTATED 6 0 22
SETD2 WILD-TYPE 90 53 72

Figure S1.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S5.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
SETD2 MUTATED 14 6 7 5 7 2
SETD2 WILD-TYPE 79 50 60 59 61 36
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
SETD2 MUTATED 14 14 13
SETD2 WILD-TYPE 91 160 94
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
SETD2 MUTATED 8 15 21
SETD2 WILD-TYPE 60 162 149
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0788 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
SETD2 MUTATED 6 24 14
SETD2 WILD-TYPE 108 166 97
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
SETD2 MUTATED 7 17 18
SETD2 WILD-TYPE 88 155 122
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S10.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
SETD2 MUTATED 7 11 18 6
SETD2 WILD-TYPE 105 90 141 29
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S11.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
SETD2 MUTATED 0 3 7 3
SETD2 WILD-TYPE 12 17 35 25
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S12.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
SETD2 MUTATED 0 7 6
SETD2 WILD-TYPE 14 38 37
'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 21 3
BAP1 MUTATED 1 7 0
BAP1 WILD-TYPE 21 14 3

Figure S2.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.11

Table S14.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 10 3 10 10 8 1
BAP1 MUTATED 0 0 0 7 1 0 0
BAP1 WILD-TYPE 4 10 3 3 9 8 1

Figure S3.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
BAP1 MUTATED 11 10 20
BAP1 WILD-TYPE 179 85 110

Figure S4.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S16.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
BAP1 MUTATED 1 6 16
BAP1 WILD-TYPE 95 47 78

Figure S5.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
BAP1 MUTATED 4 10 8 2 9 2
BAP1 WILD-TYPE 89 46 59 62 59 36

Figure S6.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S18.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
BAP1 MUTATED 10 9 16
BAP1 WILD-TYPE 95 165 91

Figure S7.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.035

Table S19.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
BAP1 MUTATED 7 6 28
BAP1 WILD-TYPE 61 171 142

Figure S8.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S20.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
BAP1 MUTATED 19 6 16
BAP1 WILD-TYPE 95 184 95

Figure S9.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S21.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
BAP1 MUTATED 9 5 27
BAP1 WILD-TYPE 86 167 113

Figure S10.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
BAP1 MUTATED 11 20 4 6
BAP1 WILD-TYPE 101 81 155 29

Figure S11.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S23.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
BAP1 MUTATED 2 1 1 4
BAP1 WILD-TYPE 10 19 41 24
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.351 (Fisher's exact test), Q value = 1

Table S24.  Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
BAP1 MUTATED 2 4 2
BAP1 WILD-TYPE 12 41 41
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 21 3
PTEN MUTATED 0 4 0
PTEN WILD-TYPE 22 17 3
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 10 3 10 10 8 1
PTEN MUTATED 0 4 0 0 0 0 0
PTEN WILD-TYPE 4 6 3 10 10 8 1

Figure S12.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.099 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
PTEN MUTATED 4 4 9
PTEN WILD-TYPE 186 91 121
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
PTEN MUTATED 1 3 5
PTEN WILD-TYPE 95 50 89
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
PTEN MUTATED 2 7 2 2 4 1
PTEN WILD-TYPE 91 49 65 62 64 37
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
PTEN MUTATED 3 7 8
PTEN WILD-TYPE 102 167 99
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
PTEN MUTATED 2 0 16
PTEN WILD-TYPE 66 177 154

Figure S13.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
PTEN MUTATED 4 2 12
PTEN WILD-TYPE 110 188 99

Figure S14.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
PTEN MUTATED 7 1 10
PTEN WILD-TYPE 88 171 130

Figure S15.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
PTEN MUTATED 7 5 3 3
PTEN WILD-TYPE 105 96 156 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0737 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
PTEN MUTATED 0 0 0 3
PTEN WILD-TYPE 12 20 42 25
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
PTEN MUTATED 0 2 1
PTEN WILD-TYPE 14 43 42
'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S37.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 21 3
PBRM1 MUTATED 10 4 1
PBRM1 WILD-TYPE 12 17 2
'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 10 3 10 10 8 1
PBRM1 MUTATED 2 4 0 0 4 4 1
PBRM1 WILD-TYPE 2 6 3 10 6 4 0
'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
PBRM1 MUTATED 72 22 42
PBRM1 WILD-TYPE 118 73 88

Figure S16.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S40.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
PBRM1 MUTATED 42 6 42
PBRM1 WILD-TYPE 54 47 52

Figure S17.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.31

Table S41.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
PBRM1 MUTATED 47 16 21 19 13 10
PBRM1 WILD-TYPE 46 40 46 45 55 28

Figure S18.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.98 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
PBRM1 MUTATED 35 57 34
PBRM1 WILD-TYPE 70 117 73
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 1

Table S43.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
PBRM1 MUTATED 14 71 50
PBRM1 WILD-TYPE 54 106 120

Figure S19.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S44.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
PBRM1 MUTATED 21 85 29
PBRM1 WILD-TYPE 93 105 82

Figure S20.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.89

Table S45.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
PBRM1 MUTATED 22 71 39
PBRM1 WILD-TYPE 73 101 101

Figure S21.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
PBRM1 MUTATED 28 30 65 9
PBRM1 WILD-TYPE 84 71 94 26

Figure S22.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.032

Table S47.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
PBRM1 MUTATED 4 1 22 4
PBRM1 WILD-TYPE 8 19 20 24

Figure S23.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0885 (Fisher's exact test), Q value = 1

Table S48.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
PBRM1 MUTATED 4 9 18
PBRM1 WILD-TYPE 10 36 25
'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
KDM5C MUTATED 12 3 11
KDM5C WILD-TYPE 178 92 119
'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0882 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
KDM5C MUTATED 4 2 11
KDM5C WILD-TYPE 92 51 83
'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S51.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
KDM5C MUTATED 5 7 5 2 3 1
KDM5C WILD-TYPE 88 49 62 62 65 37
'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S52.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
KDM5C MUTATED 10 6 7
KDM5C WILD-TYPE 95 168 100
'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0691 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
KDM5C MUTATED 2 7 16
KDM5C WILD-TYPE 66 170 154
'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
KDM5C MUTATED 11 7 7
KDM5C WILD-TYPE 103 183 104
'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S55.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
KDM5C MUTATED 2 8 16
KDM5C WILD-TYPE 93 164 124

Figure S24.  Get High-res Image Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 1

Table S56.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
KDM5C MUTATED 4 10 7 5
KDM5C WILD-TYPE 108 91 152 30

Figure S25.  Get High-res Image Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S57.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
KDM5C MUTATED 0 0 2 1
KDM5C WILD-TYPE 12 20 40 27
'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S58.  Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
KDM5C MUTATED 0 2 1
KDM5C WILD-TYPE 14 43 42
'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 21 3
VHL MUTATED 13 6 1
VHL WILD-TYPE 9 15 2
'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 10 3 10 10 8 1
VHL MUTATED 2 2 0 4 6 5 1
VHL WILD-TYPE 2 8 3 6 4 3 0
'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S61.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
VHL MUTATED 80 40 46
VHL WILD-TYPE 110 55 84
'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

Table S62.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
VHL MUTATED 46 23 40
VHL WILD-TYPE 50 30 54
'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 1

Table S63.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
VHL MUTATED 47 21 21 22 26 18
VHL WILD-TYPE 46 35 46 42 42 20
'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S64.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
VHL MUTATED 39 77 39
VHL WILD-TYPE 66 97 68
'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 1

Table S65.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
VHL MUTATED 21 86 59
VHL WILD-TYPE 47 91 111

Figure S26.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0505 (Fisher's exact test), Q value = 1

Table S66.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
VHL MUTATED 38 88 40
VHL WILD-TYPE 76 102 71
'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S67.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
VHL MUTATED 39 76 47
VHL WILD-TYPE 56 96 93
'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S68.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
VHL MUTATED 45 33 73 11
VHL WILD-TYPE 67 68 86 24
'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 1

Table S69.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
VHL MUTATED 5 6 17 15
VHL WILD-TYPE 7 14 25 13
'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S70.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
VHL MUTATED 5 21 17
VHL WILD-TYPE 9 24 26
'FAM200A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S71.  Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
FAM200A MUTATED 2 2 1
FAM200A WILD-TYPE 188 93 129
'FAM200A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.22

Table S72.  Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
FAM200A MUTATED 0 0 0 0 0 3
FAM200A WILD-TYPE 93 56 67 64 68 35

Figure S27.  Get High-res Image Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FAM200A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 1

Table S73.  Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
FAM200A MUTATED 0 3 0
FAM200A WILD-TYPE 105 171 107
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S74.  Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
FAM200A MUTATED 1 4 0
FAM200A WILD-TYPE 67 173 170
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S75.  Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
FAM200A MUTATED 1 4 0
FAM200A WILD-TYPE 113 186 111
'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
FAM200A MUTATED 1 4 0
FAM200A WILD-TYPE 94 168 140
'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S77.  Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
FAM200A MUTATED 1 0 4 0
FAM200A WILD-TYPE 111 101 155 35
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
TP53 MUTATED 3 1 5
TP53 WILD-TYPE 187 94 125
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
TP53 MUTATED 1 2 3
TP53 WILD-TYPE 95 51 91
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
TP53 MUTATED 0 2 2 1 2 1
TP53 WILD-TYPE 93 54 65 63 66 37
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S81.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
TP53 MUTATED 1 3 4
TP53 WILD-TYPE 104 171 103
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S82.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
TP53 MUTATED 2 2 5
TP53 WILD-TYPE 66 175 165
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 1

Table S83.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
TP53 MUTATED 2 2 5
TP53 WILD-TYPE 112 188 106
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S84.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
TP53 MUTATED 3 2 4
TP53 WILD-TYPE 92 170 136
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S85.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
TP53 MUTATED 4 2 2 1
TP53 WILD-TYPE 108 99 157 34
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S86.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
TP53 MUTATED 0 1 2 1
TP53 WILD-TYPE 12 19 40 27
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S87.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
TP53 MUTATED 0 2 2
TP53 WILD-TYPE 14 43 41
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
NEFH MUTATED 3 1 1
NEFH WILD-TYPE 187 94 129
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S89.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
NEFH MUTATED 3 0 1
NEFH WILD-TYPE 93 53 93
'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S90.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
NEFH MUTATED 2 0 1 1 1 0
NEFH WILD-TYPE 91 56 66 63 67 38
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 1

Table S91.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
NEFH MUTATED 0 2 3
NEFH WILD-TYPE 105 172 104
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00981 (Fisher's exact test), Q value = 1

Table S92.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
NEFH MUTATED 3 0 2
NEFH WILD-TYPE 65 177 168

Figure S28.  Get High-res Image Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S93.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
NEFH MUTATED 3 1 1
NEFH WILD-TYPE 111 189 110
'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S94.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
NEFH MUTATED 0 3 2
NEFH WILD-TYPE 95 169 138
'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
NEFH MUTATED 1 2 2 0
NEFH WILD-TYPE 111 99 157 35
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
NEFH MUTATED 0 0 3 0
NEFH WILD-TYPE 12 20 39 28
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S97.  Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
NEFH MUTATED 0 0 3
NEFH WILD-TYPE 14 45 40
'CCDC120 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
CCDC120 MUTATED 0 2 2
CCDC120 WILD-TYPE 190 93 128
'CCDC120 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
CCDC120 MUTATED 1 0 2 0 0 0
CCDC120 WILD-TYPE 92 56 65 64 68 38
'CCDC120 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S100.  Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
CCDC120 MUTATED 1 1 1
CCDC120 WILD-TYPE 104 173 106
'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S101.  Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
CCDC120 MUTATED 1 1 2
CCDC120 WILD-TYPE 67 176 168
'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S102.  Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
CCDC120 MUTATED 0 3 1
CCDC120 WILD-TYPE 114 187 110
'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S103.  Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
CCDC120 MUTATED 1 1 2
CCDC120 WILD-TYPE 94 171 138
'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S104.  Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
CCDC120 MUTATED 1 1 2 0
CCDC120 WILD-TYPE 111 100 157 35
'MTOR MUTATION STATUS' versus 'CN_CNMF'

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

Table S105.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
MTOR MUTATED 9 5 9
MTOR WILD-TYPE 181 90 121
'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S106.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
MTOR MUTATED 5 2 11
MTOR WILD-TYPE 91 51 83
'MTOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.094

Table S107.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
MTOR MUTATED 4 8 8 0 1 0
MTOR WILD-TYPE 89 48 59 64 67 38

Figure S29.  Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.23

Table S108.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
MTOR MUTATED 8 2 11
MTOR WILD-TYPE 97 172 96

Figure S30.  Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S109.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
MTOR MUTATED 4 9 10
MTOR WILD-TYPE 64 168 160
'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S110.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
MTOR MUTATED 7 9 7
MTOR WILD-TYPE 107 181 104
'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S111.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
MTOR MUTATED 6 6 11
MTOR WILD-TYPE 89 166 129
'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S112.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
MTOR MUTATED 7 8 5 3
MTOR WILD-TYPE 105 93 154 32
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S113.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
MTOR MUTATED 1 1 3 1
MTOR WILD-TYPE 11 19 39 27
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S114.  Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
MTOR MUTATED 1 3 2
MTOR WILD-TYPE 13 42 41
'GUSB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
GUSB MUTATED 3 0 1
GUSB WILD-TYPE 187 95 129
'GUSB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
GUSB MUTATED 0 0 1 0 2 0
GUSB WILD-TYPE 93 56 66 64 66 38
'GUSB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
GUSB MUTATED 1 2 0
GUSB WILD-TYPE 104 172 107
'GUSB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 1

Table S118.  Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
GUSB MUTATED 1 0 3
GUSB WILD-TYPE 67 177 167
'GUSB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
GUSB MUTATED 1 1 2
GUSB WILD-TYPE 113 189 109
'GUSB MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S120.  Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
GUSB MUTATED 2 1 1
GUSB WILD-TYPE 93 171 139
'GUSB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S121.  Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
GUSB MUTATED 2 1 1 0
GUSB WILD-TYPE 110 100 158 35
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

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

Table S122.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
PIK3CA MUTATED 7 1 4
PIK3CA WILD-TYPE 183 94 126
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S123.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
PIK3CA MUTATED 3 0 3
PIK3CA WILD-TYPE 93 53 91
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
PIK3CA MUTATED 4 1 1 2 3 0
PIK3CA WILD-TYPE 89 55 66 62 65 38
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S125.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
PIK3CA MUTATED 5 3 3
PIK3CA WILD-TYPE 100 171 104
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S126.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
PIK3CA MUTATED 0 6 6
PIK3CA WILD-TYPE 68 171 164
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
PIK3CA MUTATED 2 5 5
PIK3CA WILD-TYPE 112 185 106
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S128.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
PIK3CA MUTATED 3 4 5
PIK3CA WILD-TYPE 92 168 135
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S129.  Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
PIK3CA MUTATED 4 2 5 1
PIK3CA WILD-TYPE 108 99 154 34
'PCK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S130.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
PCK1 MUTATED 4 0 1
PCK1 WILD-TYPE 186 95 129
'PCK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
PCK1 MUTATED 1 0 2
PCK1 WILD-TYPE 95 53 92
'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S132.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
PCK1 MUTATED 1 0 1 1 1 0
PCK1 WILD-TYPE 92 56 66 63 67 38
'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S133.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
PCK1 MUTATED 1 1 2
PCK1 WILD-TYPE 104 173 105
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S134.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
PCK1 MUTATED 0 3 2
PCK1 WILD-TYPE 68 174 168
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S135.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
PCK1 MUTATED 0 3 2
PCK1 WILD-TYPE 114 187 109
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
PCK1 MUTATED 2 2 1
PCK1 WILD-TYPE 93 170 139
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S137.  Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
PCK1 MUTATED 3 0 2 0
PCK1 WILD-TYPE 109 101 157 35
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S138.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
ARID1A MUTATED 7 1 4
ARID1A WILD-TYPE 183 94 126
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 1

Table S139.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
ARID1A MUTATED 5 1 1
ARID1A WILD-TYPE 91 52 93
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
ARID1A MUTATED 4 1 1 3 2 1
ARID1A WILD-TYPE 89 55 66 61 66 37
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S141.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
ARID1A MUTATED 3 6 3
ARID1A WILD-TYPE 102 168 104
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
ARID1A MUTATED 1 8 3
ARID1A WILD-TYPE 67 169 167
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S143.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
ARID1A MUTATED 1 8 3
ARID1A WILD-TYPE 113 182 108
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
ARID1A MUTATED 1 8 3
ARID1A WILD-TYPE 94 164 137
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 1

Table S145.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
ARID1A MUTATED 0 1 10 1
ARID1A WILD-TYPE 112 100 149 34

Figure S31.  Get High-res Image Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 20 42 28
ARID1A MUTATED 1 0 2 0
ARID1A WILD-TYPE 11 20 40 28
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S147.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 45 43
ARID1A MUTATED 1 0 2
ARID1A WILD-TYPE 13 45 41
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S148.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
ATM MUTATED 6 3 2
ATM WILD-TYPE 184 92 128
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S149.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
ATM MUTATED 5 1 2
ATM WILD-TYPE 91 52 92
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S150.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
ATM MUTATED 3 1 0 3 2 1
ATM WILD-TYPE 90 55 67 61 66 37
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S151.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
ATM MUTATED 3 4 3
ATM WILD-TYPE 102 170 104
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S152.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
ATM MUTATED 0 7 4
ATM WILD-TYPE 68 170 166
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 1

Table S153.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
ATM MUTATED 0 9 2
ATM WILD-TYPE 114 181 109

Figure S32.  Get High-res Image Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S154.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
ATM MUTATED 0 7 3
ATM WILD-TYPE 95 165 137
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.091 (Fisher's exact test), Q value = 1

Table S155.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
ATM MUTATED 0 3 5 2
ATM WILD-TYPE 112 98 154 33
'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S156.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
DPCR1 MUTATED 1 3 2
DPCR1 WILD-TYPE 189 92 128
'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S157.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
DPCR1 MUTATED 1 2 3
DPCR1 WILD-TYPE 95 51 91
'DPCR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

Table S158.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
DPCR1 MUTATED 0 2 2 0 1 1
DPCR1 WILD-TYPE 93 54 65 64 67 37
'DPCR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S159.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
DPCR1 MUTATED 1 3 2
DPCR1 WILD-TYPE 104 171 105
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S160.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
DPCR1 MUTATED 2 1 3
DPCR1 WILD-TYPE 66 176 167
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 1

Table S161.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
DPCR1 MUTATED 3 1 2
DPCR1 WILD-TYPE 111 189 109
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S162.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
DPCR1 MUTATED 2 2 2
DPCR1 WILD-TYPE 93 170 138
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S163.  Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
DPCR1 MUTATED 2 2 2 0
DPCR1 WILD-TYPE 110 99 157 35
'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S164.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
FGFR3 MUTATED 2 0 2
FGFR3 WILD-TYPE 188 95 128
'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S165.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
FGFR3 MUTATED 1 1 2
FGFR3 WILD-TYPE 95 52 92
'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S166.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
FGFR3 MUTATED 1 0 0 1 1 0
FGFR3 WILD-TYPE 92 56 67 63 67 38
'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S167.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
FGFR3 MUTATED 1 1 1
FGFR3 WILD-TYPE 104 173 106
'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S168.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
FGFR3 MUTATED 1 2 1
FGFR3 WILD-TYPE 67 175 169
'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S169.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
FGFR3 MUTATED 0 2 2
FGFR3 WILD-TYPE 114 188 109
'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S170.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
FGFR3 MUTATED 1 1 2
FGFR3 WILD-TYPE 94 171 138
'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
FGFR3 MUTATED 3 0 1 0
FGFR3 WILD-TYPE 109 101 158 35
'PTCH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S172.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
PTCH1 MUTATED 3 2 2
PTCH1 WILD-TYPE 187 93 128
'PTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0548 (Fisher's exact test), Q value = 1

Table S173.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
PTCH1 MUTATED 0 0 4
PTCH1 WILD-TYPE 96 53 90
'PTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S174.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
PTCH1 MUTATED 2 3 0 1 1 0
PTCH1 WILD-TYPE 91 53 67 63 67 38
'PTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S175.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
PTCH1 MUTATED 2 1 4
PTCH1 WILD-TYPE 103 173 103
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S176.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
PTCH1 MUTATED 1 4 2
PTCH1 WILD-TYPE 67 173 168
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S177.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
PTCH1 MUTATED 3 4 0
PTCH1 WILD-TYPE 111 186 111
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S178.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
PTCH1 MUTATED 1 3 3
PTCH1 WILD-TYPE 94 169 137
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S179.  Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
PTCH1 MUTATED 1 3 3 0
PTCH1 WILD-TYPE 111 98 156 35
'RBMX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S180.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
RBMX MUTATED 2 0 2
RBMX WILD-TYPE 188 95 128
'RBMX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S181.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
RBMX MUTATED 1 0 2
RBMX WILD-TYPE 95 53 92
'RBMX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 1

Table S182.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
RBMX MUTATED 0 2 0 0 1 0
RBMX WILD-TYPE 93 54 67 64 67 38
'RBMX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S183.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
RBMX MUTATED 0 1 2
RBMX WILD-TYPE 105 173 105
'RBMX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S184.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
RBMX MUTATED 0 1 3
RBMX WILD-TYPE 68 176 167
'RBMX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S185.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
RBMX MUTATED 1 1 2
RBMX WILD-TYPE 113 189 109
'RBMX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 1

Table S186.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
RBMX MUTATED 1 0 2
RBMX WILD-TYPE 94 172 138
'RBMX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S187.  Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
RBMX MUTATED 1 1 0 1
RBMX WILD-TYPE 111 100 159 34
'ARAP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S188.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
ARAP3 MUTATED 2 1 0
ARAP3 WILD-TYPE 188 94 130
'ARAP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S189.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
ARAP3 MUTATED 1 0 1 0 1 0
ARAP3 WILD-TYPE 92 56 66 64 67 38
'ARAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S190.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
ARAP3 MUTATED 1 1 1
ARAP3 WILD-TYPE 104 173 106
'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S191.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
ARAP3 MUTATED 0 1 2
ARAP3 WILD-TYPE 68 176 168
'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S192.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
ARAP3 MUTATED 1 1 1
ARAP3 WILD-TYPE 113 189 110
'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S193.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
ARAP3 MUTATED 0 2 1
ARAP3 WILD-TYPE 95 170 139
'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S194.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
ARAP3 MUTATED 1 0 2 0
ARAP3 WILD-TYPE 111 101 157 35
'GPR172B MUTATION STATUS' versus 'CN_CNMF'

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

Table S195.  Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
GPR172B MUTATED 2 1 1
GPR172B WILD-TYPE 188 94 129
'GPR172B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S196.  Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
GPR172B MUTATED 0 1 0 2 0 0
GPR172B WILD-TYPE 93 55 67 62 68 38
'GPR172B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S197.  Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
GPR172B MUTATED 0 2 1
GPR172B WILD-TYPE 105 172 106
'GPR172B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S198.  Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
GPR172B MUTATED 0 3 1
GPR172B WILD-TYPE 68 174 169
'GPR172B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S199.  Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
GPR172B MUTATED 1 2 1
GPR172B WILD-TYPE 113 188 110
'GPR172B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S200.  Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
GPR172B MUTATED 0 1 2
GPR172B WILD-TYPE 95 171 138
'GPR172B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S201.  Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
GPR172B MUTATED 1 1 1 0
GPR172B WILD-TYPE 111 100 158 35
'EGFR MUTATION STATUS' versus 'CN_CNMF'

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

Table S202.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
EGFR MUTATED 4 2 1
EGFR WILD-TYPE 186 93 129
'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S203.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
EGFR MUTATED 2 0 2
EGFR WILD-TYPE 94 53 92
'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S204.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
EGFR MUTATED 2 2 0 1 1 1
EGFR WILD-TYPE 91 54 67 63 67 37
'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S205.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
EGFR MUTATED 3 2 2
EGFR WILD-TYPE 102 172 105
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S206.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
EGFR MUTATED 0 3 4
EGFR WILD-TYPE 68 174 166
'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S207.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
EGFR MUTATED 0 4 3
EGFR WILD-TYPE 114 186 108
'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S208.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
EGFR MUTATED 1 3 2
EGFR WILD-TYPE 94 169 138
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0948 (Fisher's exact test), Q value = 1

Table S209.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
EGFR MUTATED 0 1 3 2
EGFR WILD-TYPE 112 100 156 33
'IL1RAP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S210.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
IL1RAP MUTATED 3 0 1
IL1RAP WILD-TYPE 187 95 129
'IL1RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S211.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
IL1RAP MUTATED 1 0 2
IL1RAP WILD-TYPE 95 53 92
'IL1RAP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S212.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
IL1RAP MUTATED 3 1 0 0 0 0
IL1RAP WILD-TYPE 90 55 67 64 68 38
'IL1RAP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0918 (Fisher's exact test), Q value = 1

Table S213.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
IL1RAP MUTATED 2 0 2
IL1RAP WILD-TYPE 103 174 105
'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S214.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
IL1RAP MUTATED 1 2 1
IL1RAP WILD-TYPE 67 175 169
'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S215.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
IL1RAP MUTATED 0 3 1
IL1RAP WILD-TYPE 114 187 110
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S216.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
IL1RAP MUTATED 0 3 1
IL1RAP WILD-TYPE 95 169 139
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S217.  Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
IL1RAP MUTATED 1 0 3 0
IL1RAP WILD-TYPE 111 101 156 35
'BCL6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S218.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
BCL6 MUTATED 4 0 1
BCL6 WILD-TYPE 186 95 129
'BCL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S219.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
BCL6 MUTATED 1 0 2
BCL6 WILD-TYPE 95 53 92
'BCL6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S220.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
BCL6 MUTATED 1 1 2 0 1 0
BCL6 WILD-TYPE 92 55 65 64 67 38
'BCL6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S221.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
BCL6 MUTATED 2 2 1
BCL6 WILD-TYPE 103 172 106
'BCL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S222.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
BCL6 MUTATED 1 2 2
BCL6 WILD-TYPE 67 175 168
'BCL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 1

Table S223.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
BCL6 MUTATED 0 3 2
BCL6 WILD-TYPE 114 187 109
'BCL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S224.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
BCL6 MUTATED 2 2 1
BCL6 WILD-TYPE 93 170 139
'BCL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S225.  Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
BCL6 MUTATED 1 2 1 1
BCL6 WILD-TYPE 111 99 158 34
'NFAT5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S226.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
NFAT5 MUTATED 2 3 1
NFAT5 WILD-TYPE 188 92 129
'NFAT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S227.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
NFAT5 MUTATED 2 1 3
NFAT5 WILD-TYPE 94 52 91
'NFAT5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 1

Table S228.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
NFAT5 MUTATED 0 2 1 0 1 1
NFAT5 WILD-TYPE 93 54 66 64 67 37
'NFAT5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S229.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
NFAT5 MUTATED 0 3 2
NFAT5 WILD-TYPE 105 171 105
'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S230.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
NFAT5 MUTATED 1 1 4
NFAT5 WILD-TYPE 67 176 166
'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S231.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
NFAT5 MUTATED 3 2 1
NFAT5 WILD-TYPE 111 188 110
'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S232.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
NFAT5 MUTATED 1 1 4
NFAT5 WILD-TYPE 94 171 136
'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0957 (Fisher's exact test), Q value = 1

Table S233.  Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
NFAT5 MUTATED 0 1 3 2
NFAT5 WILD-TYPE 112 100 156 33
'LARP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S234.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
LARP1 MUTATED 4 0 1
LARP1 WILD-TYPE 186 95 129
'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S235.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
LARP1 MUTATED 2 1 0
LARP1 WILD-TYPE 94 52 94
'LARP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 1

Table S236.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
LARP1 MUTATED 1 0 1 3 0 0
LARP1 WILD-TYPE 92 56 66 61 68 38
'LARP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S237.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
LARP1 MUTATED 0 3 2
LARP1 WILD-TYPE 105 171 105
'LARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S238.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
LARP1 MUTATED 0 3 2
LARP1 WILD-TYPE 68 174 168
'LARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S239.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
LARP1 MUTATED 1 3 1
LARP1 WILD-TYPE 113 187 110
'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S240.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
LARP1 MUTATED 0 3 2
LARP1 WILD-TYPE 95 169 138
'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S241.  Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
LARP1 MUTATED 0 1 4 0
LARP1 WILD-TYPE 112 100 155 35
'KIAA1751 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S242.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
KIAA1751 MUTATED 2 1 3
KIAA1751 WILD-TYPE 188 94 127
'KIAA1751 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S243.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
KIAA1751 MUTATED 3 0 2
KIAA1751 WILD-TYPE 93 53 92
'KIAA1751 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S244.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
KIAA1751 MUTATED 2 0 1 2 0 0
KIAA1751 WILD-TYPE 91 56 66 62 68 38
'KIAA1751 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0747 (Fisher's exact test), Q value = 1

Table S245.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
KIAA1751 MUTATED 2 0 3
KIAA1751 WILD-TYPE 103 174 104
'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S246.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
KIAA1751 MUTATED 2 2 1
KIAA1751 WILD-TYPE 66 175 169
'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S247.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
KIAA1751 MUTATED 1 3 1
KIAA1751 WILD-TYPE 113 187 110
'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S248.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
KIAA1751 MUTATED 0 4 2
KIAA1751 WILD-TYPE 95 168 138
'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S249.  Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
KIAA1751 MUTATED 0 3 3 0
KIAA1751 WILD-TYPE 112 98 156 35
'INSRR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S250.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 95 130
INSRR MUTATED 2 0 2
INSRR WILD-TYPE 188 95 128
'INSRR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S251.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 53 94
INSRR MUTATED 0 2 2
INSRR WILD-TYPE 96 51 92
'INSRR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S252.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 93 56 67 64 68 38
INSRR MUTATED 0 1 2 1 0 0
INSRR WILD-TYPE 93 55 65 63 68 38
'INSRR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S253.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 174 107
INSRR MUTATED 0 2 2
INSRR WILD-TYPE 105 172 105
'INSRR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S254.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 177 170
INSRR MUTATED 0 1 3
INSRR WILD-TYPE 68 176 167
'INSRR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S255.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 190 111
INSRR MUTATED 2 2 0
INSRR WILD-TYPE 112 188 111
'INSRR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S256.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 172 140
INSRR MUTATED 2 1 1
INSRR WILD-TYPE 93 171 139
'INSRR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S257.  Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 112 101 159 35
INSRR MUTATED 1 2 1 0
INSRR WILD-TYPE 111 99 158 35
Methods & Data
Input

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

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

  • Number of patients = 417

  • Number of significantly mutated genes = 29

  • Number of Molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

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

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