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 30 genes and 12 molecular subtypes across 441 patients, 27 significant findings detected with P value < 0.05 and Q value < 0.25.

  • SETD2 mutation correlated to 'METHLYATION_CNMF'.

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

  • PBRM1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • KDM5C mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • VHL mutation correlated to 'MRNA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • FAM200A mutation correlated to 'RPPA_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 30 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, 27 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 44 (10%) 397 0.0041
(0.0624) 		0.00034
(0.0102) 		0.0297
(0.32) 		5e-05
(0.003) 		0.00226
(0.0387) 		0.0304
(0.32) 		1e-05
(9e-04) 		1e-05
(9e-04) 		1e-05
(9e-04) 		3e-05
(0.00216) 		0.161
(0.749) 		0.696
(1.00)
PBRM1 139 (32%) 302 0.119
(0.684) 		0.078
(0.53) 		0.00416
(0.0624) 		1e-05
(9e-04) 		0.00025
(0.009) 		1
(1.00) 		0.00038
(0.0105) 		0.00055
(0.0132) 		0.00063
(0.0142) 		0.00706
(0.102) 		7e-05
(0.00315) 		0.049
(0.412)
VHL 171 (39%) 270 0.00771
(0.107) 		0.0311
(0.32) 		0.355
(1.00) 		0.555
(1.00) 		0.0414
(0.382) 		0.331
(1.00) 		0.00042
(0.0108) 		0.0132
(0.176) 		0.0359
(0.349) 		0.0705
(0.501) 		0.431
(1.00) 		0.635
(1.00)
PTEN 17 (4%) 424 0.3
(0.977) 		0.111
(0.676) 		0.185
(0.758) 		0.176
(0.749) 		0.244
(0.9) 		0.272
(0.949) 		6e-05
(0.00309) 		0.00204
(0.0367) 		0.00406
(0.0624) 		0.171
(0.749) 		0.0527
(0.431) 		1
(1.00)
MTOR 28 (6%) 413 0.561
(1.00) 		0.134
(0.71) 		0.001
(0.0204) 		0.00033
(0.0102) 		0.936
(1.00) 		0.841
(1.00) 		0.362
(1.00) 		0.412
(1.00) 		0.942
(1.00) 		1
(1.00)
SETD2 46 (10%) 395 0.816
(1.00) 		0.134
(0.71) 		0.537
(1.00) 		9e-05
(0.0036) 		0.699
(1.00) 		0.204
(0.809) 		0.37
(1.00) 		0.0306
(0.32) 		0.316
(1.00) 		0.301
(0.977) 		0.392
(1.00) 		0.215
(0.823)
KDM5C 27 (6%) 414 0.166
(0.749) 		0.0649
(0.497) 		0.376
(1.00) 		0.173
(0.749) 		0.048
(0.412) 		0.00115
(0.0218) 		0.02
(0.256) 		0.0327
(0.327) 		1
(1.00) 		1
(1.00)
FAM200A 5 (1%) 436 0.727
(1.00) 		0.00102
(0.0204) 		0.255
(0.907) 		0.177
(0.749) 		0.506
(1.00) 		0.142
(0.719) 		0.378
(1.00)
TP53 12 (3%) 429 0.25
(0.9) 		0.827
(1.00) 		0.349
(1.00) 		0.149
(0.736) 		0.138
(0.717) 		0.0492
(0.412) 		0.164
(0.749) 		0.373
(1.00) 		1
(1.00) 		1
(1.00)
NEFH 5 (1%) 436 0.862
(1.00) 		0.454
(1.00) 		0.979
(1.00) 		0.181
(0.757) 		0.0391
(0.371) 		0.0267
(0.31) 		0.461
(1.00) 		0.913
(1.00) 		0.338
(1.00) 		0.139
(0.717)
PTCH1 7 (2%) 434 1
(1.00) 		0.0206
(0.256) 		0.401
(1.00) 		0.158
(0.749) 		0.885
(1.00) 		0.122
(0.684) 		1
(1.00) 		0.684
(1.00)
NF2 6 (1%) 435 0.0213
(0.256) 		0.347
(1.00) 		0.216
(0.823) 		0.573
(1.00) 		0.12
(0.684) 		0.197
(0.797) 		0.0821
(0.547) 		0.377
(1.00)
CCDC120 4 (1%) 437 0.124
(0.684) 		0.422
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.845
(1.00) 		0.829
(1.00) 		1
(1.00)
PIK3CA 12 (3%) 429 0.422
(1.00) 		0.449
(1.00) 		0.804
(1.00) 		0.337
(1.00) 		0.24
(0.899) 		0.674
(1.00) 		0.872
(1.00) 		0.876
(1.00)
ATM 12 (3%) 429 0.933
(1.00) 		0.471
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.164
(0.749) 		0.351
(1.00) 		0.101
(0.648) 		0.0723
(0.501)
KIAA1751 6 (1%) 435 0.578
(1.00) 		0.456
(1.00) 		0.618
(1.00) 		0.0941
(0.616) 		0.433
(1.00) 		0.665
(1.00) 		0.391
(1.00) 		0.357
(1.00)
GUSB 4 (1%) 437 0.48
(1.00) 		0.31
(0.995) 		0.622
(1.00) 		0.199
(0.797) 		0.301
(0.977) 		0.554
(1.00) 		0.875
(1.00)
ARID1A 11 (2%) 430 0.926
(1.00) 		0.378
(1.00) 		0.97
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.969
(1.00) 		0.545
(1.00) 		0.118
(0.684) 		0.482
(1.00) 		0.298
(0.977)
GPR50 3 (1%) 438 0.103
(0.648) 		0.25
(0.9) 		0.0691
(0.501) 		0.792
(1.00) 		0.803
(1.00) 		0.217
(0.823) 		0.118
(0.684) 		0.436
(1.00)
PCK1 5 (1%) 436 0.387
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.737
(1.00) 		0.744
(1.00) 		0.732
(1.00) 		0.404
(1.00)
DPCR1 6 (1%) 435 0.288
(0.977) 		0.582
(1.00) 		0.212
(0.823) 		1
(1.00) 		0.176
(0.749) 		0.0444
(0.399) 		0.766
(1.00) 		1
(1.00)
NFAT5 6 (1%) 435 0.493
(1.00) 		0.878
(1.00) 		0.246
(0.9) 		0.529
(1.00) 		0.265
(0.935) 		0.406
(1.00) 		0.335
(1.00) 		0.0717
(0.501)
EGFR 7 (2%) 434 0.71
(1.00) 		0.681
(1.00) 		0.747
(1.00) 		0.491
(1.00) 		0.478
(1.00) 		0.942
(1.00) 		1
(1.00) 		0.0714
(0.501)
TRIM6 5 (1%) 436 1
(1.00) 		1
(1.00) 		0.746
(1.00) 		0.0587
(0.469) 		1
(1.00) 		0.173
(0.749) 		0.375
(1.00) 		0.556
(1.00)
RBMX 4 (1%) 437 0.692
(1.00) 		0.618
(1.00) 		0.109
(0.676) 		0.462
(1.00) 		0.428
(1.00) 		0.48
(1.00) 		0.342
(1.00) 		0.164
(0.749)
GPR172B 4 (1%) 437 1
(1.00) 		0.132
(0.71) 		0.792
(1.00) 		0.538
(1.00) 		1
(1.00) 		0.614
(1.00) 		1
(1.00)
FGFR3 4 (1%) 437 0.694
(1.00) 		0.836
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.479
(1.00) 		0.832
(1.00) 		0.287
(0.977)
ARAP3 3 (1%) 438 0.618
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.792
(1.00) 		0.833
(1.00)
OPTC 4 (1%) 437 0.585
(1.00) 		0.185
(0.758) 		1
(1.00) 		0.144
(0.72) 		0.832
(1.00) 		0.29
(0.977)
GOLGA5 5 (1%) 436 0.06
(0.469) 		0.297
(0.977) 		0.73
(1.00) 		0.528
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.517
(1.00)
'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.816 (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 21 17 10
SETD2 MUTATED 2 2 0
SETD2 WILD-TYPE 19 15 10
'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.71

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 6 3 10 10 7 8
SETD2 MUTATED 1 2 0 0 1 0 0
SETD2 WILD-TYPE 3 4 3 10 9 7 8
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.537 (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 194 112 132
SETD2 MUTATED 17 13 16
SETD2 WILD-TYPE 177 99 116
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0036

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
SETD2 MUTATED 6 2 22
SETD2 WILD-TYPE 98 60 75

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 = 0.699 (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 97 57 67 67 72 41
SETD2 MUTATED 14 6 8 6 7 2
SETD2 WILD-TYPE 83 51 59 61 65 39
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
SETD2 MUTATED 15 14 14
SETD2 WILD-TYPE 92 164 102
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.37 (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 87 181 171
SETD2 MUTATED 9 15 22
SETD2 WILD-TYPE 78 166 149
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
SETD2 MUTATED 17 3 11 15 0 0
SETD2 WILD-TYPE 85 22 140 101 30 15

Figure S2.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.316 (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 101 175 155
SETD2 MUTATED 7 17 20
SETD2 WILD-TYPE 94 158 135
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
SETD2 MUTATED 8 12 18 6
SETD2 WILD-TYPE 110 103 145 29
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.392 (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 16 20 43 28
SETD2 MUTATED 0 3 7 3
SETD2 WILD-TYPE 16 17 36 25
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
SETD2 MUTATED 0 7 6
SETD2 WILD-TYPE 18 38 38
'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 17 10
BAP1 MUTATED 1 7 0
BAP1 WILD-TYPE 20 10 10

Figure S3.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.01

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 6 3 10 10 7 8
BAP1 MUTATED 0 0 0 7 1 0 0
BAP1 WILD-TYPE 4 6 3 3 9 7 8

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

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
BAP1 MUTATED 12 12 20
BAP1 WILD-TYPE 182 100 112

Figure S5.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.003

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
BAP1 MUTATED 1 8 17
BAP1 WILD-TYPE 103 54 80

Figure S6.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.039

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 97 57 67 67 72 41
BAP1 MUTATED 4 12 8 2 10 2
BAP1 WILD-TYPE 93 45 59 65 62 39

Figure S7.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
BAP1 MUTATED 11 10 17
BAP1 WILD-TYPE 96 168 99

Figure S8.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
BAP1 MUTATED 9 5 30
BAP1 WILD-TYPE 78 176 141

Figure S9.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
BAP1 MUTATED 4 0 4 17 19 0
BAP1 WILD-TYPE 98 25 147 99 11 15

Figure S10.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
BAP1 MUTATED 10 5 29
BAP1 WILD-TYPE 91 170 126

Figure S11.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
BAP1 MUTATED 12 22 4 6
BAP1 WILD-TYPE 106 93 159 29

Figure S12.  Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
BAP1 MUTATED 2 1 1 4
BAP1 WILD-TYPE 14 19 42 24
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.696 (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 18 45 44
BAP1 MUTATED 2 4 2
BAP1 WILD-TYPE 16 41 42
'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.68

Table S25.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 17 10
PBRM1 MUTATED 9 3 1
PBRM1 WILD-TYPE 12 14 9
'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.078 (Fisher's exact test), Q value = 0.53

Table S26.  Gene #3: '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 6 3 10 10 7 8
PBRM1 MUTATED 2 3 0 0 4 3 1
PBRM1 WILD-TYPE 2 3 3 10 6 4 7
'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.062

Table S27.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
PBRM1 MUTATED 75 23 41
PBRM1 WILD-TYPE 119 89 91

Figure S13.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9e-04

Table S28.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
PBRM1 MUTATED 45 6 44
PBRM1 WILD-TYPE 59 56 53

Figure S14.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.009

Table S29.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
PBRM1 MUTATED 50 16 21 18 13 11
PBRM1 WILD-TYPE 47 41 46 49 59 30

Figure S15.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S30.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
PBRM1 MUTATED 34 58 37
PBRM1 WILD-TYPE 73 120 79
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.011

Table S31.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
PBRM1 MUTATED 15 74 49
PBRM1 WILD-TYPE 72 107 122

Figure S16.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.013

Table S32.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
PBRM1 MUTATED 40 5 59 30 3 1
PBRM1 WILD-TYPE 62 20 92 86 27 14

Figure S17.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.014

Table S33.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
PBRM1 MUTATED 23 73 39
PBRM1 WILD-TYPE 78 102 116

Figure S18.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00706 (Fisher's exact test), Q value = 0.1

Table S34.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
PBRM1 MUTATED 27 32 67 9
PBRM1 WILD-TYPE 91 83 96 26

Figure S19.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0031

Table S35.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
PBRM1 MUTATED 4 1 23 4
PBRM1 WILD-TYPE 12 19 20 24

Figure S20.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.41

Table S36.  Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
PBRM1 MUTATED 4 9 19
PBRM1 WILD-TYPE 14 36 25

Figure S21.  Get High-res Image Gene #3: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.75

Table S37.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
KDM5C MUTATED 13 3 11
KDM5C WILD-TYPE 181 109 121
'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0649 (Fisher's exact test), Q value = 0.5

Table S38.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
KDM5C MUTATED 4 2 11
KDM5C WILD-TYPE 100 60 86
'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
KDM5C MUTATED 5 7 5 2 3 2
KDM5C WILD-TYPE 92 50 62 65 69 39
'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.75

Table S40.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
KDM5C MUTATED 10 7 7
KDM5C WILD-TYPE 97 171 109
'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.41

Table S41.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
KDM5C MUTATED 2 8 16
KDM5C WILD-TYPE 85 173 155

Figure S22.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.022

Table S42.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
KDM5C MUTATED 14 1 2 9 0 0
KDM5C WILD-TYPE 88 24 149 107 30 15

Figure S23.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.26

Table S43.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
KDM5C MUTATED 2 9 16
KDM5C WILD-TYPE 99 166 139

Figure S24.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.33

Table S44.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
KDM5C MUTATED 4 11 7 5
KDM5C WILD-TYPE 114 104 156 30

Figure S25.  Get High-res Image Gene #4: '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 S45.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
KDM5C MUTATED 0 0 2 1
KDM5C WILD-TYPE 16 20 41 27
'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S46.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
KDM5C MUTATED 0 2 1
KDM5C WILD-TYPE 18 43 43
'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00771 (Fisher's exact test), Q value = 0.11

Table S47.  Gene #5: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 17 10
VHL MUTATED 13 4 1
VHL WILD-TYPE 8 13 9

Figure S26.  Get High-res Image Gene #5: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.32

Table S48.  Gene #5: '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 6 3 10 10 7 8
VHL MUTATED 2 0 0 4 6 5 1
VHL WILD-TYPE 2 6 3 6 4 2 7

Figure S27.  Get High-res Image Gene #5: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
VHL MUTATED 83 40 48
VHL WILD-TYPE 111 72 84
'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
VHL MUTATED 49 24 41
VHL WILD-TYPE 55 38 56
'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.38

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
VHL MUTATED 50 20 22 20 28 20
VHL WILD-TYPE 47 37 45 47 44 21

Figure S28.  Get High-res Image Gene #5: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
VHL MUTATED 41 78 41
VHL WILD-TYPE 66 100 75
'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
VHL MUTATED 22 89 60
VHL WILD-TYPE 65 92 111

Figure S29.  Get High-res Image Gene #5: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
VHL MUTATED 43 6 70 41 10 1
VHL WILD-TYPE 59 19 81 75 20 14

Figure S30.  Get High-res Image Gene #5: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
VHL MUTATED 41 78 48
VHL WILD-TYPE 60 97 107

Figure S31.  Get High-res Image Gene #5: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0705 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
VHL MUTATED 45 36 75 11
VHL WILD-TYPE 73 79 88 24
'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
VHL MUTATED 6 6 18 15
VHL WILD-TYPE 10 14 25 13
'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
VHL MUTATED 6 21 18
VHL WILD-TYPE 12 24 26
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 17 10
PTEN MUTATED 0 2 1
PTEN WILD-TYPE 21 15 9
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.68

Table S60.  Gene #6: '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 6 3 10 10 7 8
PTEN MUTATED 0 2 0 0 0 0 1
PTEN WILD-TYPE 4 4 3 10 10 7 7
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.76

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
PTEN MUTATED 4 4 8
PTEN WILD-TYPE 190 108 124
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
PTEN MUTATED 1 3 5
PTEN WILD-TYPE 103 59 92
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
PTEN MUTATED 2 6 2 2 4 1
PTEN WILD-TYPE 95 51 65 65 68 40
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
PTEN MUTATED 3 6 8
PTEN WILD-TYPE 104 172 108
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0031

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
PTEN MUTATED 3 0 14
PTEN WILD-TYPE 84 181 157

Figure S32.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.037

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
PTEN MUTATED 5 1 0 10 0 1
PTEN WILD-TYPE 97 24 151 106 30 14

Figure S33.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
PTEN MUTATED 6 1 10
PTEN WILD-TYPE 95 174 145

Figure S34.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
PTEN MUTATED 6 5 3 3
PTEN WILD-TYPE 112 110 160 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0527 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
PTEN MUTATED 0 0 0 3
PTEN WILD-TYPE 16 20 43 25
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
PTEN MUTATED 0 2 1
PTEN WILD-TYPE 18 43 43
'MTOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
MTOR MUTATED 11 6 11
MTOR WILD-TYPE 183 106 121
'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.71

Table S72.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
MTOR MUTATED 7 3 13
MTOR WILD-TYPE 97 59 84
'MTOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.02

Table S73.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
MTOR MUTATED 7 8 9 1 1 0
MTOR WILD-TYPE 90 49 58 66 71 41

Figure S35.  Get High-res Image Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.01

Table S74.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
MTOR MUTATED 8 3 15
MTOR WILD-TYPE 99 175 101

Figure S36.  Get High-res Image Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S75.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
MTOR MUTATED 5 11 12
MTOR WILD-TYPE 82 170 159
'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
MTOR MUTATED 5 2 9 10 1 1
MTOR WILD-TYPE 97 23 142 106 29 14
'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S77.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
MTOR MUTATED 7 8 13
MTOR WILD-TYPE 94 167 142
'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
MTOR MUTATED 8 10 7 3
MTOR WILD-TYPE 110 105 156 32
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.942 (Fisher's exact test), Q value = 1

Table S79.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
MTOR MUTATED 1 1 4 1
MTOR WILD-TYPE 15 19 39 27
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S80.  Gene #7: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
MTOR MUTATED 1 3 3
MTOR WILD-TYPE 17 42 41
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 0.9

Table S81.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
TP53 MUTATED 3 3 6
TP53 WILD-TYPE 191 109 126
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S82.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
TP53 MUTATED 3 3 3
TP53 WILD-TYPE 101 59 94
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S83.  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 97 57 67 67 72 41
TP53 MUTATED 0 2 2 3 2 1
TP53 WILD-TYPE 97 55 65 64 70 40
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.74

Table S84.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
TP53 MUTATED 1 3 6
TP53 WILD-TYPE 106 175 110
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.72

Table S85.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
TP53 MUTATED 4 2 6
TP53 WILD-TYPE 83 179 165
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0492 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
TP53 MUTATED 1 0 2 6 1 2
TP53 WILD-TYPE 101 25 149 110 29 13

Figure S37.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.75

Table S87.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
TP53 MUTATED 3 2 7
TP53 WILD-TYPE 98 173 148
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
TP53 MUTATED 5 4 2 1
TP53 WILD-TYPE 113 111 161 34
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S89.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
TP53 MUTATED 1 1 2 1
TP53 WILD-TYPE 15 19 41 27
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S90.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
TP53 MUTATED 1 2 2
TP53 WILD-TYPE 17 43 42
'FAM200A MUTATION STATUS' versus 'CN_CNMF'

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

Table S91.  Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
FAM200A MUTATED 2 2 1
FAM200A WILD-TYPE 192 110 131
'FAM200A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.02

Table S92.  Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
FAM200A MUTATED 0 0 0 0 0 3
FAM200A WILD-TYPE 97 57 67 67 72 38

Figure S38.  Get High-res Image Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FAM200A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.91

Table S93.  Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
FAM200A MUTATED 0 3 0
FAM200A WILD-TYPE 107 175 116
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.75

Table S94.  Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
FAM200A MUTATED 1 4 0
FAM200A WILD-TYPE 86 177 171
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
FAM200A MUTATED 1 0 4 0 0 0
FAM200A WILD-TYPE 101 25 147 116 30 15
'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.72

Table S96.  Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
FAM200A MUTATED 1 4 0
FAM200A WILD-TYPE 100 171 155
'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S97.  Gene #9: 'FAM200A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
FAM200A MUTATED 1 0 4 0
FAM200A WILD-TYPE 117 115 159 35
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.862 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
NEFH MUTATED 3 1 1
NEFH WILD-TYPE 191 111 131
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
NEFH MUTATED 3 0 1
NEFH WILD-TYPE 101 62 96
'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S100.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
NEFH MUTATED 2 0 1 1 1 0
NEFH WILD-TYPE 95 57 66 66 71 41
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 0.76

Table S101.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
NEFH MUTATED 0 2 3
NEFH WILD-TYPE 107 176 113
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.37

Table S102.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
NEFH MUTATED 3 0 2
NEFH WILD-TYPE 84 181 169

Figure S39.  Get High-res Image Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.31

Table S103.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
NEFH MUTATED 1 2 0 1 1 0
NEFH WILD-TYPE 101 23 151 115 29 15

Figure S40.  Get High-res Image Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S104.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
NEFH MUTATED 0 3 2
NEFH WILD-TYPE 101 172 153
'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S105.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
NEFH MUTATED 1 2 2 0
NEFH WILD-TYPE 117 113 161 35
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S106.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
NEFH MUTATED 0 0 3 0
NEFH WILD-TYPE 16 20 40 28
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.72

Table S107.  Gene #10: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
NEFH MUTATED 0 0 3
NEFH WILD-TYPE 18 45 41
'PTCH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S108.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
PTCH1 MUTATED 3 2 2
PTCH1 WILD-TYPE 191 110 130
'PTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.26

Table S109.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
PTCH1 MUTATED 0 0 4
PTCH1 WILD-TYPE 104 62 93

Figure S41.  Get High-res Image Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S110.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
PTCH1 MUTATED 2 3 0 1 1 0
PTCH1 WILD-TYPE 95 54 67 66 71 41
'PTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.75

Table S111.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
PTCH1 MUTATED 2 1 4
PTCH1 WILD-TYPE 105 177 112
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S112.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
PTCH1 MUTATED 1 4 2
PTCH1 WILD-TYPE 86 177 169
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.68

Table S113.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
PTCH1 MUTATED 3 0 2 0 2 0
PTCH1 WILD-TYPE 99 25 149 116 28 15
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S114.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
PTCH1 MUTATED 1 3 3
PTCH1 WILD-TYPE 100 172 152
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S115.  Gene #11: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
PTCH1 MUTATED 1 3 3 0
PTCH1 WILD-TYPE 117 112 160 35
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.26

Table S116.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
NF2 MUTATED 1 0 5
NF2 WILD-TYPE 193 112 127

Figure S42.  Get High-res Image Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
NF2 MUTATED 0 1 2
NF2 WILD-TYPE 104 61 95
'NF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.82

Table S118.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
NF2 MUTATED 1 1 0 3 0 1
NF2 WILD-TYPE 96 56 67 64 72 40
'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
NF2 MUTATED 1 2 3
NF2 WILD-TYPE 106 176 113
'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.68

Table S120.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
NF2 MUTATED 0 1 5
NF2 WILD-TYPE 87 180 166
'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.8

Table S121.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
NF2 MUTATED 0 0 1 4 1 0
NF2 WILD-TYPE 102 25 150 112 29 15
'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0821 (Fisher's exact test), Q value = 0.55

Table S122.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
NF2 MUTATED 0 1 5
NF2 WILD-TYPE 101 174 150
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 1

Table S123.  Gene #12: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
NF2 MUTATED 3 1 1 1
NF2 WILD-TYPE 115 114 162 34
'CCDC120 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.68

Table S124.  Gene #13: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
CCDC120 MUTATED 0 2 2
CCDC120 WILD-TYPE 194 110 130
'CCDC120 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
CCDC120 MUTATED 1 0 2 0 0 0
CCDC120 WILD-TYPE 96 57 65 67 72 41
'CCDC120 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S126.  Gene #13: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
CCDC120 MUTATED 1 1 1
CCDC120 WILD-TYPE 106 177 115
'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
CCDC120 MUTATED 1 1 2
CCDC120 WILD-TYPE 86 180 169
'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S128.  Gene #13: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
CCDC120 MUTATED 2 0 1 1 0 0
CCDC120 WILD-TYPE 100 25 150 115 30 15
'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S129.  Gene #13: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
CCDC120 MUTATED 1 1 2
CCDC120 WILD-TYPE 100 174 153
'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S130.  Gene #13: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
CCDC120 MUTATED 1 1 2 0
CCDC120 WILD-TYPE 117 114 161 35
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
PIK3CA MUTATED 7 1 4
PIK3CA WILD-TYPE 187 111 128
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S132.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
PIK3CA MUTATED 3 0 3
PIK3CA WILD-TYPE 101 62 94
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
PIK3CA MUTATED 4 1 1 2 3 0
PIK3CA WILD-TYPE 93 56 66 65 69 41
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S134.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
PIK3CA MUTATED 5 3 3
PIK3CA WILD-TYPE 102 175 113
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.9

Table S135.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
PIK3CA MUTATED 0 6 6
PIK3CA WILD-TYPE 87 175 165
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S136.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
PIK3CA MUTATED 1 0 5 5 1 0
PIK3CA WILD-TYPE 101 25 146 111 29 15
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S137.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
PIK3CA MUTATED 3 4 5
PIK3CA WILD-TYPE 98 171 150
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S138.  Gene #14: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
PIK3CA MUTATED 4 2 5 1
PIK3CA WILD-TYPE 114 113 158 34
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S139.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
ATM MUTATED 6 3 3
ATM WILD-TYPE 188 109 129
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
ATM MUTATED 5 1 2
ATM WILD-TYPE 99 61 95
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
ATM MUTATED 3 1 0 3 3 1
ATM WILD-TYPE 94 56 67 64 69 40
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S142.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
ATM MUTATED 3 5 3
ATM WILD-TYPE 104 173 113
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.75

Table S143.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
ATM MUTATED 0 7 5
ATM WILD-TYPE 87 174 166
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S144.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
ATM MUTATED 1 0 8 2 1 0
ATM WILD-TYPE 101 25 143 114 29 15
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.65

Table S145.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
ATM MUTATED 0 7 4
ATM WILD-TYPE 101 168 151
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0723 (Fisher's exact test), Q value = 0.5

Table S146.  Gene #15: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
ATM MUTATED 0 4 5 2
ATM WILD-TYPE 118 111 158 33
'KIAA1751 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S147.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
KIAA1751 MUTATED 2 1 3
KIAA1751 WILD-TYPE 192 111 129
'KIAA1751 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S148.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
KIAA1751 MUTATED 3 0 2
KIAA1751 WILD-TYPE 101 62 95
'KIAA1751 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S149.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
KIAA1751 MUTATED 2 0 1 2 0 0
KIAA1751 WILD-TYPE 95 57 66 65 72 41
'KIAA1751 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0941 (Fisher's exact test), Q value = 0.62

Table S150.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
KIAA1751 MUTATED 2 0 3
KIAA1751 WILD-TYPE 105 178 113
'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S151.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
KIAA1751 MUTATED 2 2 1
KIAA1751 WILD-TYPE 85 179 170
'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S152.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
KIAA1751 MUTATED 3 0 1 1 0 0
KIAA1751 WILD-TYPE 99 25 150 115 30 15
'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S153.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
KIAA1751 MUTATED 0 4 2
KIAA1751 WILD-TYPE 101 171 153
'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S154.  Gene #16: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
KIAA1751 MUTATED 0 3 3 0
KIAA1751 WILD-TYPE 118 112 160 35
'GUSB MUTATION STATUS' versus 'CN_CNMF'

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

Table S155.  Gene #17: 'GUSB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
GUSB MUTATED 3 0 1
GUSB WILD-TYPE 191 112 131
'GUSB MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S156.  Gene #17: 'GUSB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
GUSB MUTATED 0 0 1 0 2 0
GUSB WILD-TYPE 97 57 66 67 70 41
'GUSB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S157.  Gene #17: 'GUSB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
GUSB MUTATED 1 2 0
GUSB WILD-TYPE 106 176 116
'GUSB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.8

Table S158.  Gene #17: 'GUSB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
GUSB MUTATED 1 0 3
GUSB WILD-TYPE 86 181 168
'GUSB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.98

Table S159.  Gene #17: 'GUSB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
GUSB MUTATED 1 0 0 2 1 0
GUSB WILD-TYPE 101 25 151 114 29 15
'GUSB MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S160.  Gene #17: 'GUSB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
GUSB MUTATED 2 1 1
GUSB WILD-TYPE 99 174 154
'GUSB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S161.  Gene #17: 'GUSB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
GUSB MUTATED 2 1 1 0
GUSB WILD-TYPE 116 114 162 35
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S162.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
ARID1A MUTATED 5 2 4
ARID1A WILD-TYPE 189 110 128
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S163.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
ARID1A MUTATED 5 2 1
ARID1A WILD-TYPE 99 60 96
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.97 (Fisher's exact test), Q value = 1

Table S164.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
ARID1A MUTATED 3 1 1 2 3 1
ARID1A WILD-TYPE 94 56 66 65 69 40
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S165.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
ARID1A MUTATED 3 5 3
ARID1A WILD-TYPE 104 173 113
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S166.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
ARID1A MUTATED 1 6 4
ARID1A WILD-TYPE 86 175 167
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.969 (Fisher's exact test), Q value = 1

Table S167.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
ARID1A MUTATED 2 0 5 3 1 0
ARID1A WILD-TYPE 100 25 146 113 29 15
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S168.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
ARID1A MUTATED 1 6 4
ARID1A WILD-TYPE 100 169 151
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 0.68

Table S169.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
ARID1A MUTATED 1 1 8 1
ARID1A WILD-TYPE 117 114 155 34
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S170.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
ARID1A MUTATED 1 0 2 0
ARID1A WILD-TYPE 15 20 41 28
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.98

Table S171.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
ARID1A MUTATED 1 0 2
ARID1A WILD-TYPE 17 45 42
'GPR50 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.65

Table S172.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
GPR50 MUTATED 0 2 1
GPR50 WILD-TYPE 194 110 131
'GPR50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 0.9

Table S173.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
GPR50 MUTATED 1 2 0
GPR50 WILD-TYPE 103 60 97
'GPR50 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0691 (Fisher's exact test), Q value = 0.5

Table S174.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
GPR50 MUTATED 0 0 0 2 0 1
GPR50 WILD-TYPE 97 57 67 65 72 40
'GPR50 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S175.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
GPR50 MUTATED 0 2 1
GPR50 WILD-TYPE 107 176 115
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S176.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
GPR50 MUTATED 1 1 1
GPR50 WILD-TYPE 86 180 170
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.82

Table S177.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
GPR50 MUTATED 0 0 1 1 0 1
GPR50 WILD-TYPE 102 25 150 115 30 14
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.68

Table S178.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
GPR50 MUTATED 2 0 1
GPR50 WILD-TYPE 99 175 154
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S179.  Gene #19: 'GPR50 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
GPR50 MUTATED 2 1 0 0
GPR50 WILD-TYPE 116 114 163 35
'PCK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S180.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
PCK1 MUTATED 4 0 1
PCK1 WILD-TYPE 190 112 131
'PCK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S181.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
PCK1 MUTATED 1 0 2
PCK1 WILD-TYPE 103 62 95
'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S182.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
PCK1 MUTATED 1 0 1 1 1 0
PCK1 WILD-TYPE 96 57 66 66 71 41
'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S183.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
PCK1 MUTATED 1 1 2
PCK1 WILD-TYPE 106 177 114
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S184.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
PCK1 MUTATED 0 3 2
PCK1 WILD-TYPE 87 178 169
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S185.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
PCK1 MUTATED 0 0 3 2 0 0
PCK1 WILD-TYPE 102 25 148 114 30 15
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S186.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
PCK1 MUTATED 2 2 1
PCK1 WILD-TYPE 99 173 154
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 1

Table S187.  Gene #20: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
PCK1 MUTATED 3 0 2 0
PCK1 WILD-TYPE 115 115 161 35
'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.98

Table S188.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
DPCR1 MUTATED 1 3 2
DPCR1 WILD-TYPE 193 109 130
'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S189.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
DPCR1 MUTATED 1 2 3
DPCR1 WILD-TYPE 103 60 94
'DPCR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.82

Table S190.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
DPCR1 MUTATED 0 2 2 0 1 1
DPCR1 WILD-TYPE 97 55 65 67 71 40
'DPCR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S191.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
DPCR1 MUTATED 1 3 2
DPCR1 WILD-TYPE 106 175 114
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.75

Table S192.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
DPCR1 MUTATED 3 1 2
DPCR1 WILD-TYPE 84 180 169
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.4

Table S193.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
DPCR1 MUTATED 1 1 0 2 1 1
DPCR1 WILD-TYPE 101 24 151 114 29 14

Figure S43.  Get High-res Image Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S194.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
DPCR1 MUTATED 2 2 2
DPCR1 WILD-TYPE 99 173 153
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S195.  Gene #21: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
DPCR1 MUTATED 2 2 2 0
DPCR1 WILD-TYPE 116 113 161 35
'NFAT5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S196.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
NFAT5 MUTATED 2 3 1
NFAT5 WILD-TYPE 192 109 131
'NFAT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S197.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
NFAT5 MUTATED 2 1 3
NFAT5 WILD-TYPE 102 61 94
'NFAT5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.9

Table S198.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
NFAT5 MUTATED 0 2 1 0 1 1
NFAT5 WILD-TYPE 97 55 66 67 71 40
'NFAT5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S199.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
NFAT5 MUTATED 0 3 2
NFAT5 WILD-TYPE 107 175 114
'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.93

Table S200.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
NFAT5 MUTATED 1 1 4
NFAT5 WILD-TYPE 86 180 167
'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.406 (Fisher's exact test), Q value = 1

Table S201.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
NFAT5 MUTATED 4 0 1 1 0 0
NFAT5 WILD-TYPE 98 25 150 115 30 15
'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S202.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
NFAT5 MUTATED 1 1 4
NFAT5 WILD-TYPE 100 174 151
'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0717 (Fisher's exact test), Q value = 0.5

Table S203.  Gene #22: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
NFAT5 MUTATED 0 1 3 2
NFAT5 WILD-TYPE 118 114 160 33
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S204.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
EGFR MUTATED 4 2 1
EGFR WILD-TYPE 190 110 131
'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S205.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
EGFR MUTATED 2 0 2
EGFR WILD-TYPE 102 62 95
'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S206.  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 97 57 67 67 72 41
EGFR MUTATED 2 2 0 1 1 1
EGFR WILD-TYPE 95 55 67 66 71 40
'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S207.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
EGFR MUTATED 3 2 2
EGFR WILD-TYPE 104 176 114
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 1

Table S208.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
EGFR MUTATED 0 3 4
EGFR WILD-TYPE 87 178 167
'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.942 (Fisher's exact test), Q value = 1

Table S209.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
EGFR MUTATED 1 0 3 3 0 0
EGFR WILD-TYPE 101 25 148 113 30 15
'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S210.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
EGFR MUTATED 1 3 2
EGFR WILD-TYPE 100 172 153
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0714 (Fisher's exact test), Q value = 0.5

Table S211.  Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
EGFR MUTATED 0 1 3 2
EGFR WILD-TYPE 118 114 160 33
'TRIM6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S212.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
TRIM6 MUTATED 2 1 1
TRIM6 WILD-TYPE 192 111 131
'TRIM6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S213.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
TRIM6 MUTATED 2 1 1
TRIM6 WILD-TYPE 102 61 96
'TRIM6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S214.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
TRIM6 MUTATED 2 1 0 1 0 0
TRIM6 WILD-TYPE 95 56 67 66 72 41
'TRIM6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0587 (Fisher's exact test), Q value = 0.47

Table S215.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
TRIM6 MUTATED 1 0 3
TRIM6 WILD-TYPE 106 178 113
'TRIM6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S216.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
TRIM6 MUTATED 1 2 2
TRIM6 WILD-TYPE 86 179 169
'TRIM6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.75

Table S217.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
TRIM6 MUTATED 0 0 2 1 1 1
TRIM6 WILD-TYPE 102 25 149 115 29 14
'TRIM6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S218.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
TRIM6 MUTATED 0 2 3
TRIM6 WILD-TYPE 101 173 152
'TRIM6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S219.  Gene #24: 'TRIM6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
TRIM6 MUTATED 1 3 1 0
TRIM6 WILD-TYPE 117 112 162 35
'RBMX MUTATION STATUS' versus 'CN_CNMF'

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

Table S220.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
RBMX MUTATED 2 0 2
RBMX WILD-TYPE 192 112 130
'RBMX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S221.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
RBMX MUTATED 1 0 2
RBMX WILD-TYPE 103 62 95
'RBMX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.68

Table S222.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
RBMX MUTATED 0 2 0 0 1 0
RBMX WILD-TYPE 97 55 67 67 71 41
'RBMX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S223.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
RBMX MUTATED 0 1 2
RBMX WILD-TYPE 107 177 114
'RBMX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S224.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
RBMX MUTATED 0 1 3
RBMX WILD-TYPE 87 180 168
'RBMX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S225.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
RBMX MUTATED 2 0 0 2 0 0
RBMX WILD-TYPE 100 25 151 114 30 15
'RBMX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S226.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
RBMX MUTATED 1 0 2
RBMX WILD-TYPE 100 175 153
'RBMX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.75

Table S227.  Gene #25: 'RBMX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
RBMX MUTATED 1 1 0 1
RBMX WILD-TYPE 117 114 163 34
'GPR172B MUTATION STATUS' versus 'CN_CNMF'

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

Table S228.  Gene #26: 'GPR172B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
GPR172B MUTATED 2 1 1
GPR172B WILD-TYPE 192 111 131
'GPR172B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.71

Table S229.  Gene #26: 'GPR172B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
GPR172B MUTATED 0 1 0 2 0 0
GPR172B WILD-TYPE 97 56 67 65 72 41
'GPR172B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S230.  Gene #26: 'GPR172B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
GPR172B MUTATED 0 2 1
GPR172B WILD-TYPE 107 176 115
'GPR172B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S231.  Gene #26: 'GPR172B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
GPR172B MUTATED 0 3 1
GPR172B WILD-TYPE 87 178 170
'GPR172B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S232.  Gene #26: 'GPR172B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
GPR172B MUTATED 1 0 2 1 0 0
GPR172B WILD-TYPE 101 25 149 115 30 15
'GPR172B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S233.  Gene #26: 'GPR172B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
GPR172B MUTATED 0 1 2
GPR172B WILD-TYPE 101 174 153
'GPR172B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S234.  Gene #26: 'GPR172B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
GPR172B MUTATED 1 1 1 0
GPR172B WILD-TYPE 117 114 162 35
'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S235.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
FGFR3 MUTATED 2 0 2
FGFR3 WILD-TYPE 192 112 130
'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S236.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
FGFR3 MUTATED 1 1 2
FGFR3 WILD-TYPE 103 61 95
'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S237.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
FGFR3 MUTATED 1 0 0 1 1 0
FGFR3 WILD-TYPE 96 57 67 66 71 41
'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S238.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
FGFR3 MUTATED 1 1 1
FGFR3 WILD-TYPE 106 177 115
'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S239.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
FGFR3 MUTATED 1 2 1
FGFR3 WILD-TYPE 86 179 170
'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S240.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
FGFR3 MUTATED 2 0 0 2 0 0
FGFR3 WILD-TYPE 100 25 151 114 30 15
'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S241.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
FGFR3 MUTATED 1 1 2
FGFR3 WILD-TYPE 100 174 153
'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.98

Table S242.  Gene #27: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
FGFR3 MUTATED 3 0 1 0
FGFR3 WILD-TYPE 115 115 162 35
'ARAP3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S243.  Gene #28: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
ARAP3 MUTATED 2 1 0
ARAP3 WILD-TYPE 192 111 132
'ARAP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S244.  Gene #28: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
ARAP3 MUTATED 1 0 1 0 1 0
ARAP3 WILD-TYPE 96 57 66 67 71 41
'ARAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S245.  Gene #28: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
ARAP3 MUTATED 1 1 1
ARAP3 WILD-TYPE 106 177 115
'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S246.  Gene #28: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
ARAP3 MUTATED 0 1 2
ARAP3 WILD-TYPE 87 180 169
'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S247.  Gene #28: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
ARAP3 MUTATED 1 0 1 1 0 0
ARAP3 WILD-TYPE 101 25 150 115 30 15
'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S248.  Gene #28: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
ARAP3 MUTATED 0 2 1
ARAP3 WILD-TYPE 101 173 154
'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S249.  Gene #28: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
ARAP3 MUTATED 1 0 2 0
ARAP3 WILD-TYPE 117 115 161 35
'OPTC MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
OPTC MUTATED 1 2 1
OPTC WILD-TYPE 193 110 131
'OPTC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.76

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
OPTC MUTATED 0 2 1
OPTC WILD-TYPE 104 60 96
'OPTC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S252.  Gene #29: 'OPTC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
OPTC MUTATED 1 2 1
OPTC WILD-TYPE 86 179 170
'OPTC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.72

Table S253.  Gene #29: 'OPTC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
OPTC MUTATED 2 0 0 1 0 1
OPTC WILD-TYPE 100 25 151 115 30 14
'OPTC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S254.  Gene #29: 'OPTC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
OPTC MUTATED 1 1 2
OPTC WILD-TYPE 100 174 153
'OPTC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.98

Table S255.  Gene #29: 'OPTC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
OPTC MUTATED 3 0 1 0
OPTC WILD-TYPE 115 115 162 35
'GOLGA5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.06 (Fisher's exact test), Q value = 0.47

Table S256.  Gene #30: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 112 132
GOLGA5 MUTATED 5 0 0
GOLGA5 WILD-TYPE 189 112 132
'GOLGA5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.98

Table S257.  Gene #30: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 97 57 67 67 72 41
GOLGA5 MUTATED 0 0 2 2 1 0
GOLGA5 WILD-TYPE 97 57 65 65 71 41
'GOLGA5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S258.  Gene #30: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 178 116
GOLGA5 MUTATED 2 2 1
GOLGA5 WILD-TYPE 105 176 115
'GOLGA5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S259.  Gene #30: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 181 171
GOLGA5 MUTATED 1 1 3
GOLGA5 WILD-TYPE 86 180 168
'GOLGA5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S260.  Gene #30: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 102 25 151 116 30 15
GOLGA5 MUTATED 2 0 1 1 1 0
GOLGA5 WILD-TYPE 100 25 150 115 29 15
'GOLGA5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S261.  Gene #30: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 175 155
GOLGA5 MUTATED 1 2 2
GOLGA5 WILD-TYPE 100 173 153
'GOLGA5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S262.  Gene #30: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 115 163 35
GOLGA5 MUTATED 0 2 3 0
GOLGA5 WILD-TYPE 118 113 160 35
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/15182431/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/15107132/KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 441

  • Number of significantly mutated genes = 30

  • 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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