Correlation between gene mutation status and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1057F4M
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1057F4M
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 25 genes and 12 molecular subtypes across 436 patients, 27 significant findings detected with P value < 0.05 and Q value < 0.25.

  • SETD2 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • PBRM1 mutation correlated to 'MRNA_CHIERARCHICAL',  '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 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • NF2 mutation correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • GPR50 mutation correlated to 'RPPA_CNMF'.

  • TFDP2 mutation correlated to 'RPPA_CHIERARCHICAL'.

  • EMG1 mutation correlated to 'MRNA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 25 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
PBRM1 131 (30%) 305 0.0388
(0.342) 		0.00858
(0.143) 		0.00104
(0.0367) 		1e-05
(0.003) 		0.00697
(0.131) 		0.277
(0.892) 		0.00014
(0.0096) 		9e-05
(0.009) 		0.00029
(0.0145) 		0.00375
(0.0937) 		8e-05
(0.009) 		0.049
(0.387)
PTEN 15 (3%) 421 0.447
(1.00) 		0.173
(0.708) 		0.273
(0.892) 		0.0156
(0.187) 		0.00038
(0.0163) 		0.00695
(0.131) 		0.00969
(0.145) 		0.207
(0.768)
VHL 192 (44%) 244 0.0267
(0.276) 		0.0654
(0.456) 		0.155
(0.685) 		0.302
(0.905) 		0.0285
(0.281) 		0.853
(1.00) 		0.00219
(0.0657) 		0.0011
(0.0367) 		0.03
(0.281) 		0.00861
(0.143) 		0.462
(1.00) 		0.556
(1.00)
SETD2 43 (10%) 393 0.603
(1.00) 		0.141
(0.653) 		0.753
(1.00) 		0.00016
(0.0096) 		0.498
(1.00) 		0.0423
(0.352) 		0.62
(1.00) 		0.0141
(0.177) 		0.146
(0.664) 		0.428
(1.00) 		0.392
(1.00) 		0.219
(0.784)
MTOR 28 (6%) 408 0.561
(1.00) 		0.135
(0.653) 		0.0138
(0.177) 		0.00651
(0.131) 		0.936
(1.00) 		0.852
(1.00) 		0.364
(1.00) 		0.427
(1.00) 		0.944
(1.00) 		1
(1.00)
NF2 6 (1%) 430 0.0224
(0.249) 		0.349
(0.986) 		0.226
(0.787) 		0.0122
(0.167) 		0.121
(0.645) 		0.207
(0.768) 		0.0841
(0.549) 		0.379
(1.00)
EMG1 4 (1%) 432 0.00953
(0.145) 		0.051
(0.392) 		0.0915
(0.584) 		0.0256
(0.274) 		0.0106
(0.151) 		0.172
(0.708) 		0.261
(0.891)
KDM5C 25 (6%) 411 0.264
(0.891) 		0.0654
(0.456) 		0.323
(0.949) 		0.193
(0.744) 		0.136
(0.653) 		0.00261
(0.0712) 		0.0568
(0.415) 		0.115
(0.641) 		1
(1.00) 		1
(1.00)
GPR50 3 (1%) 433 0.104
(0.637) 		0.251
(0.866) 		0.00624
(0.131) 		0.879
(1.00) 		0.802
(1.00) 		0.217
(0.784) 		0.117
(0.641) 		0.437
(1.00)
TFDP2 4 (1%) 432 0.818
(1.00) 		0.133
(0.653) 		0.0211
(0.244) 		0.608
(1.00) 		0.699
(1.00) 		0.34
(0.973) 		0.378
(1.00)
TP53 9 (2%) 427 0.352
(0.986) 		0.593
(1.00) 		0.123
(0.645) 		0.137
(0.653) 		0.415
(1.00) 		0.113
(0.641) 		0.42
(1.00) 		0.538
(1.00) 		0.552
(1.00) 		0.668
(1.00)
NEFH 6 (1%) 430 0.772
(1.00) 		0.457
(1.00) 		0.897
(1.00) 		0.0414
(0.352) 		0.177
(0.708) 		0.03
(0.281) 		0.386
(1.00) 		0.758
(1.00) 		0.341
(0.973) 		0.138
(0.653)
ATM 12 (3%) 424 0.565
(1.00) 		0.472
(1.00) 		0.976
(1.00) 		0.951
(1.00) 		0.102
(0.637) 		0.328
(0.956) 		0.0529
(0.396) 		0.117
(0.641)
NUDT11 4 (1%) 432 0.378
(1.00) 		0.833
(1.00) 		0.394
(1.00) 		0.475
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.285
(0.892) 		0.63
(1.00)
PIK3CA 10 (2%) 426 0.14
(0.653) 		0.372
(1.00) 		0.159
(0.693) 		0.67
(1.00) 		0.289
(0.892) 		0.791
(1.00) 		0.714
(1.00) 		0.793
(1.00)
FAM200A 4 (1%) 432 1
(1.00) 		0.0755
(0.514) 		0.315
(0.935) 		0.0842
(0.549) 		0.113
(0.641)
DPCR1 6 (1%) 430 0.292
(0.892) 		0.58
(1.00) 		0.402
(1.00) 		0.775
(1.00) 		0.174
(0.708) 		0.0462
(0.375) 		0.763
(1.00) 		1
(1.00)
EGFR 6 (1%) 430 0.668
(1.00) 		0.793
(1.00) 		0.968
(1.00) 		0.274
(0.892) 		0.658
(1.00) 		1
(1.00) 		0.848
(1.00) 		0.219
(0.784)
SH3KBP1 3 (1%) 433 0.618
(1.00) 		0.875
(1.00) 		0.788
(1.00) 		1
(1.00) 		0.874
(1.00) 		0.792
(1.00) 		0.717
(1.00)
ARID1A 10 (2%) 426 0.847
(1.00) 		0.377
(1.00) 		0.699
(1.00) 		0.828
(1.00) 		0.846
(1.00) 		0.987
(1.00) 		0.66
(1.00) 		0.193
(0.744) 		0.481
(1.00) 		0.294
(0.892)
ARAP3 3 (1%) 433 0.62
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.792
(1.00) 		0.831
(1.00)
SLC16A9 4 (1%) 432 0.292
(0.892) 		0.455
(1.00) 		0.572
(1.00) 		0.201
(0.762) 		0.153
(0.685) 		0.0348
(0.316) 		0.286
(0.892) 		1
(1.00)
PCK1 4 (1%) 432 0.129
(0.653) 		0.281
(0.892) 		1
(1.00) 		0.536
(1.00) 		0.74
(1.00) 		0.224
(0.787) 		0.695
(1.00)
CUL9 7 (2%) 429 0.114
(0.641) 		1
(1.00) 		0.854
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.894
(1.00) 		0.706
(1.00) 		0.491
(1.00) 		1
(1.00) 		0.78
(1.00)
ZDHHC1 4 (1%) 432 0.163
(0.7) 		0.415
(1.00) 		0.177
(0.708) 		0.842
(1.00) 		0.186
(0.735) 		0.683
(1.00) 		0.508
(1.00)
'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.603 (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 17 16 10
SETD2 MUTATED 1 2 0
SETD2 WILD-TYPE 16 14 10
'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.65

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 3 5 3 10 10 4 8
SETD2 MUTATED 0 2 0 0 1 0 0
SETD2 WILD-TYPE 3 3 3 10 9 4 8
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.753 (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 190 112 131
SETD2 MUTATED 17 11 15
SETD2 WILD-TYPE 173 101 116
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0096

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 = 0.498 (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 69 74 78 69 78 29
SETD2 MUTATED 5 8 10 10 6 1
SETD2 WILD-TYPE 64 66 68 59 72 28
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
SETD2 MUTATED 7 16 9 8
SETD2 WILD-TYPE 102 79 63 113

Figure S2.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.62 (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 86 178 170
SETD2 MUTATED 7 16 20
SETD2 WILD-TYPE 79 162 150
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.18

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 99 25 150 115 30 15
SETD2 MUTATED 18 3 10 12 0 0
SETD2 WILD-TYPE 81 22 140 103 30 15

Figure S3.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
SETD2 MUTATED 5 17 19
SETD2 WILD-TYPE 95 156 135
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.428 (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 117 114 161 35
SETD2 MUTATED 7 13 17 4
SETD2 WILD-TYPE 110 101 144 31
'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 = 0.219 (Fisher's exact test), Q value = 0.78

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
'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.34

Table S13.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 16 10
PBRM1 MUTATED 9 3 1
PBRM1 WILD-TYPE 8 13 9

Figure S4.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00858 (Fisher's exact test), Q value = 0.14

Table S14.  Gene #2: '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 3 5 3 10 10 4 8
PBRM1 MUTATED 2 3 0 0 4 3 1
PBRM1 WILD-TYPE 1 2 3 10 6 1 7

Figure S5.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.037

Table S15.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
PBRM1 MUTATED 72 20 39
PBRM1 WILD-TYPE 118 92 92

Figure S6.  Get High-res Image Gene #2: '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 = 0.003

Table S16.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
PBRM1 MUTATED 45 6 40
PBRM1 WILD-TYPE 59 56 57

Figure S7.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00697 (Fisher's exact test), Q value = 0.13

Table S17.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
PBRM1 MUTATED 19 36 20 23 19 5
PBRM1 WILD-TYPE 50 38 58 46 59 24

Figure S8.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.89

Table S18.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
PBRM1 MUTATED 30 33 17 42
PBRM1 WILD-TYPE 79 62 55 79
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0096

Table S19.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
PBRM1 MUTATED 14 72 44
PBRM1 WILD-TYPE 72 106 126

Figure S9.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.009

Table S20.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
PBRM1 MUTATED 39 5 57 26 2 1
PBRM1 WILD-TYPE 60 20 93 89 28 14

Figure S10.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.014

Table S21.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
PBRM1 MUTATED 21 70 36
PBRM1 WILD-TYPE 79 103 118

Figure S11.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.094

Table S22.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
PBRM1 MUTATED 25 31 64 7
PBRM1 WILD-TYPE 92 83 97 28

Figure S12.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.009

Table S23.  Gene #2: '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 S13.  Get High-res Image Gene #2: '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 = 0.39

Table S24.  Gene #2: '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 S14.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.89

Table S25.  Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
KDM5C MUTATED 13 3 9
KDM5C WILD-TYPE 177 109 122
'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0654 (Fisher's exact test), Q value = 0.46

Table S26.  Gene #3: '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 = 0.323 (Fisher's exact test), Q value = 0.95

Table S27.  Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
KDM5C MUTATED 2 3 7 6 2 2
KDM5C WILD-TYPE 67 71 71 63 76 27
'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.74

Table S28.  Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
KDM5C MUTATED 2 7 5 8
KDM5C WILD-TYPE 107 88 67 113
'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.65

Table S29.  Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
KDM5C MUTATED 2 8 14
KDM5C WILD-TYPE 84 170 156
'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00261 (Fisher's exact test), Q value = 0.071

Table S30.  Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
KDM5C MUTATED 13 1 2 8 0 0
KDM5C WILD-TYPE 86 24 148 107 30 15

Figure S15.  Get High-res Image Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0568 (Fisher's exact test), Q value = 0.42

Table S31.  Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
KDM5C MUTATED 2 9 14
KDM5C WILD-TYPE 98 164 140
'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.64

Table S32.  Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
KDM5C MUTATED 4 10 7 4
KDM5C WILD-TYPE 113 104 154 31
'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S33.  Gene #3: '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 S34.  Gene #3: '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 = 0.0267 (Fisher's exact test), Q value = 0.28

Table S35.  Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 16 10
VHL MUTATED 10 4 1
VHL WILD-TYPE 7 12 9

Figure S16.  Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0654 (Fisher's exact test), Q value = 0.46

Table S36.  Gene #4: '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 3 5 3 10 10 4 8
VHL MUTATED 1 0 0 4 6 3 1
VHL WILD-TYPE 2 5 3 6 4 1 7
'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
VHL MUTATED 94 44 54
VHL WILD-TYPE 96 68 77
'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
VHL MUTATED 51 23 46
VHL WILD-TYPE 53 39 51
'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
VHL MUTATED 27 43 31 23 41 13
VHL WILD-TYPE 42 31 47 46 37 16

Figure S17.  Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
VHL MUTATED 48 42 30 58
VHL WILD-TYPE 61 53 42 63
'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.066

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
VHL MUTATED 29 96 67
VHL WILD-TYPE 57 82 103

Figure S18.  Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.037

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
VHL MUTATED 45 6 81 48 11 1
VHL WILD-TYPE 54 19 69 67 19 14

Figure S19.  Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
VHL MUTATED 47 86 55
VHL WILD-TYPE 53 87 99

Figure S20.  Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00861 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
VHL MUTATED 53 36 84 15
VHL WILD-TYPE 64 78 77 20

Figure S21.  Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S45.  Gene #4: '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 7 7 18 16
VHL WILD-TYPE 9 13 25 12
'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
VHL MUTATED 7 23 18
VHL WILD-TYPE 11 22 26
'MTOR MUTATION STATUS' versus 'CN_CNMF'

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

Table S47.  Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
MTOR MUTATED 11 6 11
MTOR WILD-TYPE 179 106 120
'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.65

Table S48.  Gene #5: '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 = 0.0138 (Fisher's exact test), Q value = 0.18

Table S49.  Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
MTOR MUTATED 2 6 10 7 1 0
MTOR WILD-TYPE 67 68 68 62 77 29

Figure S22.  Get High-res Image Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00651 (Fisher's exact test), Q value = 0.13

Table S50.  Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
MTOR MUTATED 3 14 3 6
MTOR WILD-TYPE 106 81 69 115

Figure S23.  Get High-res Image Gene #5: '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 S51.  Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
MTOR MUTATED 5 11 12
MTOR WILD-TYPE 81 167 158
'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S52.  Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
MTOR MUTATED 5 2 9 10 1 1
MTOR WILD-TYPE 94 23 141 105 29 14
'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
MTOR MUTATED 7 8 13
MTOR WILD-TYPE 93 165 141
'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
MTOR MUTATED 8 10 7 3
MTOR WILD-TYPE 109 104 154 32
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S55.  Gene #5: '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 S56.  Gene #5: '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 = 0.352 (Fisher's exact test), Q value = 0.99

Table S57.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
TP53 MUTATED 2 3 4
TP53 WILD-TYPE 188 109 127
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
TP53 MUTATED 3 3 2
TP53 WILD-TYPE 101 59 95
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.64

Table S59.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
TP53 MUTATED 2 0 4 1 0 0
TP53 WILD-TYPE 67 74 74 68 78 29
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.65

Table S60.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
TP53 MUTATED 0 1 3 3
TP53 WILD-TYPE 109 94 69 118
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 1

Table S61.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
TP53 MUTATED 3 2 4
TP53 WILD-TYPE 83 176 166
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.64

Table S62.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
TP53 MUTATED 1 0 2 3 1 2
TP53 WILD-TYPE 98 25 148 112 29 13
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 1

Table S63.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
TP53 MUTATED 2 2 5
TP53 WILD-TYPE 98 171 149
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S64.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
TP53 MUTATED 3 4 2 0
TP53 WILD-TYPE 114 110 159 35
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 1

Table S65.  Gene #6: '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 0
TP53 WILD-TYPE 15 19 41 28
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S66.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S67.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
PTEN MUTATED 4 4 6
PTEN WILD-TYPE 186 108 125
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.71

Table S68.  Gene #7: '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 = 0.273 (Fisher's exact test), Q value = 0.89

Table S69.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
PTEN MUTATED 2 1 7 2 2 1
PTEN WILD-TYPE 67 73 71 67 76 28
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.19

Table S70.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
PTEN MUTATED 1 8 4 2
PTEN WILD-TYPE 108 87 68 119

Figure S24.  Get High-res Image Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.016

Table S71.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
PTEN MUTATED 3 0 12
PTEN WILD-TYPE 83 178 158

Figure S25.  Get High-res Image Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00695 (Fisher's exact test), Q value = 0.13

Table S72.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
PTEN MUTATED 5 1 0 8 0 1
PTEN WILD-TYPE 94 24 150 107 30 14

Figure S26.  Get High-res Image Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00969 (Fisher's exact test), Q value = 0.15

Table S73.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
PTEN MUTATED 5 1 9
PTEN WILD-TYPE 95 172 145

Figure S27.  Get High-res Image Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.77

Table S74.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
PTEN MUTATED 4 5 3 3
PTEN WILD-TYPE 113 109 158 32
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
NEFH MUTATED 3 2 1
NEFH WILD-TYPE 187 110 130
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S76.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.897 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
NEFH MUTATED 1 2 2 0 1 0
NEFH WILD-TYPE 68 72 76 69 77 29
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.35

Table S78.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
NEFH MUTATED 2 4 0 0
NEFH WILD-TYPE 107 91 72 121

Figure S28.  Get High-res Image Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S79.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
NEFH MUTATED 3 1 2
NEFH WILD-TYPE 83 177 168
'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.28

Table S80.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
NEFH MUTATED 2 2 0 1 1 0
NEFH WILD-TYPE 97 23 150 114 29 15

Figure S29.  Get High-res Image Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S81.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
NEFH MUTATED 0 4 2
NEFH WILD-TYPE 100 169 152
'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S82.  Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
NEFH MUTATED 1 3 2 0
NEFH WILD-TYPE 116 111 159 35
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.97

Table S83.  Gene #8: '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 = 0.138 (Fisher's exact test), Q value = 0.65

Table S84.  Gene #8: '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
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.25

Table S85.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
NF2 MUTATED 1 0 5
NF2 WILD-TYPE 189 112 126

Figure S30.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 0.99

Table S86.  Gene #9: '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 = 0.226 (Fisher's exact test), Q value = 0.79

Table S87.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
NF2 MUTATED 1 1 3 0 0 1
NF2 WILD-TYPE 68 73 75 69 78 28
'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.17

Table S88.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
NF2 MUTATED 0 3 3 0
NF2 WILD-TYPE 109 92 69 121

Figure S31.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.64

Table S89.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
NF2 MUTATED 0 1 5
NF2 WILD-TYPE 86 177 165
'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.77

Table S90.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
NF2 MUTATED 0 0 1 4 1 0
NF2 WILD-TYPE 99 25 149 111 29 15
'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0841 (Fisher's exact test), Q value = 0.55

Table S91.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
NF2 MUTATED 0 1 5
NF2 WILD-TYPE 100 172 149
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S92.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
NF2 MUTATED 3 1 1 1
NF2 WILD-TYPE 114 113 160 34
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
ATM MUTATED 6 4 2
ATM WILD-TYPE 184 108 129
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: '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 = 0.976 (Fisher's exact test), Q value = 1

Table S95.  Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
ATM MUTATED 2 2 2 1 3 1
ATM WILD-TYPE 67 72 76 68 75 28
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.951 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
ATM MUTATED 4 2 2 3
ATM WILD-TYPE 105 93 70 118
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.64

Table S97.  Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
ATM MUTATED 0 8 4
ATM WILD-TYPE 86 170 166
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 0.96

Table S98.  Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
ATM MUTATED 2 0 8 1 1 0
ATM WILD-TYPE 97 25 142 114 29 15
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0529 (Fisher's exact test), Q value = 0.4

Table S99.  Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
ATM MUTATED 0 8 3
ATM WILD-TYPE 100 165 151
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.64

Table S100.  Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
ATM MUTATED 0 5 5 1
ATM WILD-TYPE 117 109 156 34
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S101.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
NUDT11 MUTATED 3 1 0
NUDT11 WILD-TYPE 187 111 131
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S102.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
NUDT11 MUTATED 1 1 2
NUDT11 WILD-TYPE 103 61 95
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S103.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
NUDT11 MUTATED 0 1 1 1 0 1
NUDT11 WILD-TYPE 69 73 77 68 78 28
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.475 (Fisher's exact test), Q value = 1

Table S104.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
NUDT11 MUTATED 0 2 1 1
NUDT11 WILD-TYPE 109 93 71 120
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S105.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
NUDT11 MUTATED 1 2 1
NUDT11 WILD-TYPE 85 176 169
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S106.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
NUDT11 MUTATED 1 0 2 0 1 0
NUDT11 WILD-TYPE 98 25 148 115 29 15
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.89

Table S107.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
NUDT11 MUTATED 1 3 0
NUDT11 WILD-TYPE 99 170 154
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S108.  Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
NUDT11 MUTATED 0 2 2 0
NUDT11 WILD-TYPE 117 112 159 35
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.65

Table S109.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
PIK3CA MUTATED 6 0 4
PIK3CA WILD-TYPE 184 112 127
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S110.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
PIK3CA MUTATED 2 0 3
PIK3CA WILD-TYPE 102 62 94
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.69

Table S111.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
PIK3CA MUTATED 3 0 3 2 0 1
PIK3CA WILD-TYPE 66 74 75 67 78 28
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
PIK3CA MUTATED 1 2 2 4
PIK3CA WILD-TYPE 108 93 70 117
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.89

Table S113.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
PIK3CA MUTATED 0 5 5
PIK3CA WILD-TYPE 86 173 165
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S114.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
PIK3CA MUTATED 1 0 4 4 1 0
PIK3CA WILD-TYPE 98 25 146 111 29 15
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
PIK3CA MUTATED 2 3 5
PIK3CA WILD-TYPE 98 170 149
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
PIK3CA MUTATED 4 2 4 0
PIK3CA WILD-TYPE 113 112 157 35
'GPR50 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.64

Table S117.  Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
GPR50 MUTATED 0 2 1
GPR50 WILD-TYPE 190 110 130
'GPR50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.87

Table S118.  Gene #13: '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 = 0.00624 (Fisher's exact test), Q value = 0.13

Table S119.  Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
GPR50 MUTATED 1 0 0 0 0 2
GPR50 WILD-TYPE 68 74 78 69 78 27

Figure S32.  Get High-res Image Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'GPR50 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S120.  Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
GPR50 MUTATED 1 0 1 1
GPR50 WILD-TYPE 108 95 71 120
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S121.  Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
GPR50 MUTATED 1 1 1
GPR50 WILD-TYPE 85 177 169
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.78

Table S122.  Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
GPR50 MUTATED 0 0 1 1 0 1
GPR50 WILD-TYPE 99 25 149 114 30 14
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.64

Table S123.  Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
GPR50 MUTATED 2 0 1
GPR50 WILD-TYPE 98 173 153
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S124.  Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
GPR50 MUTATED 2 1 0 0
GPR50 WILD-TYPE 115 113 161 35
'TFDP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S125.  Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
TFDP2 MUTATED 1 1 2
TFDP2 WILD-TYPE 189 111 129
'TFDP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.65

Table S126.  Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
TFDP2 MUTATED 1 0 3 0 0 0
TFDP2 WILD-TYPE 68 74 75 69 78 29
'TFDP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.24

Table S127.  Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
TFDP2 MUTATED 1 0 3 0
TFDP2 WILD-TYPE 108 95 69 121

Figure S33.  Get High-res Image Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TFDP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S128.  Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
TFDP2 MUTATED 0 1 2
TFDP2 WILD-TYPE 86 177 168
'TFDP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S129.  Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
TFDP2 MUTATED 0 0 1 2 0 0
TFDP2 WILD-TYPE 99 25 149 113 30 15
'TFDP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.97

Table S130.  Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
TFDP2 MUTATED 1 0 2
TFDP2 WILD-TYPE 99 173 152
'TFDP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S131.  Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
TFDP2 MUTATED 1 2 0 0
TFDP2 WILD-TYPE 116 112 161 35
'FAM200A MUTATION STATUS' versus 'CN_CNMF'

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

Table S132.  Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
FAM200A MUTATED 2 1 1
FAM200A WILD-TYPE 188 111 130
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 0.51

Table S133.  Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
FAM200A MUTATED 0 4 0
FAM200A WILD-TYPE 86 174 170
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 0.93

Table S134.  Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
FAM200A MUTATED 0 0 4 0 0 0
FAM200A WILD-TYPE 99 25 146 115 30 15
'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0842 (Fisher's exact test), Q value = 0.55

Table S135.  Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
FAM200A MUTATED 0 4 0
FAM200A WILD-TYPE 100 169 154
'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.64

Table S136.  Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
FAM200A MUTATED 0 0 4 0
FAM200A WILD-TYPE 117 114 157 35
'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.89

Table S137.  Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
DPCR1 MUTATED 1 3 2
DPCR1 WILD-TYPE 189 109 129
'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S138.  Gene #16: '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 = 0.402 (Fisher's exact test), Q value = 1

Table S139.  Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
DPCR1 MUTATED 0 0 2 2 1 1
DPCR1 WILD-TYPE 69 74 76 67 77 28
'DPCR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S140.  Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
DPCR1 MUTATED 2 2 0 2
DPCR1 WILD-TYPE 107 93 72 119
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.71

Table S141.  Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
DPCR1 MUTATED 3 1 2
DPCR1 WILD-TYPE 83 177 168
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.37

Table S142.  Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
DPCR1 MUTATED 1 1 0 2 1 1
DPCR1 WILD-TYPE 98 24 150 113 29 14

Figure S34.  Get High-res Image Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S143.  Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
DPCR1 MUTATED 2 2 2
DPCR1 WILD-TYPE 98 171 152
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S144.  Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
DPCR1 MUTATED 2 2 2 0
DPCR1 WILD-TYPE 115 112 159 35
'EGFR MUTATION STATUS' versus 'CN_CNMF'

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

Table S145.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
EGFR MUTATED 4 1 1
EGFR WILD-TYPE 186 111 130
'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S146.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
EGFR MUTATED 2 0 1
EGFR WILD-TYPE 102 62 96
'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S147.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
EGFR MUTATED 1 2 1 1 1 0
EGFR WILD-TYPE 68 72 77 68 77 29
'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.89

Table S148.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
EGFR MUTATED 1 0 1 4
EGFR WILD-TYPE 108 95 71 117
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S149.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
EGFR MUTATED 0 3 3
EGFR WILD-TYPE 86 175 167
'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S150.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
EGFR MUTATED 1 0 3 2 0 0
EGFR WILD-TYPE 98 25 147 113 30 15
'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S151.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
EGFR MUTATED 1 3 1
EGFR WILD-TYPE 99 170 153
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.78

Table S152.  Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
EGFR MUTATED 0 1 3 1
EGFR WILD-TYPE 117 113 158 34
'SH3KBP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S153.  Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
SH3KBP1 MUTATED 2 1 0
SH3KBP1 WILD-TYPE 188 111 131
'SH3KBP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S154.  Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
SH3KBP1 MUTATED 0 1 1 1 0 0
SH3KBP1 WILD-TYPE 69 73 77 68 78 29
'SH3KBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S155.  Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
SH3KBP1 MUTATED 0 1 1 1
SH3KBP1 WILD-TYPE 109 94 71 120
'SH3KBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S156.  Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
SH3KBP1 MUTATED 0 2 1
SH3KBP1 WILD-TYPE 86 176 169
'SH3KBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S157.  Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
SH3KBP1 MUTATED 0 0 2 1 0 0
SH3KBP1 WILD-TYPE 99 25 148 114 30 15
'SH3KBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S158.  Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
SH3KBP1 MUTATED 0 2 1
SH3KBP1 WILD-TYPE 100 171 153
'SH3KBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S159.  Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
SH3KBP1 MUTATED 0 1 2 0
SH3KBP1 WILD-TYPE 117 113 159 35
'EMG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00953 (Fisher's exact test), Q value = 0.15

Table S160.  Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 16 10
EMG1 MUTATED 0 0 3
EMG1 WILD-TYPE 17 16 7

Figure S35.  Get High-res Image Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.051 (Fisher's exact test), Q value = 0.39

Table S161.  Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 3 5 3 10 10 4 8
EMG1 MUTATED 0 0 0 0 0 0 3
EMG1 WILD-TYPE 3 5 3 10 10 4 5
'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0915 (Fisher's exact test), Q value = 0.58

Table S162.  Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
EMG1 MUTATED 1 3 0
EMG1 WILD-TYPE 189 109 131
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.27

Table S163.  Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
EMG1 MUTATED 3 1 0
EMG1 WILD-TYPE 83 177 170

Figure S36.  Get High-res Image Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.15

Table S164.  Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
EMG1 MUTATED 0 0 2 0 0 2
EMG1 WILD-TYPE 99 25 148 115 30 13

Figure S37.  Get High-res Image Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.71

Table S165.  Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
EMG1 MUTATED 1 0 3
EMG1 WILD-TYPE 99 173 151
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.89

Table S166.  Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
EMG1 MUTATED 0 3 1 0
EMG1 WILD-TYPE 117 111 160 35
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S167.  Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
ARID1A MUTATED 4 2 4
ARID1A WILD-TYPE 186 110 127
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S168.  Gene #20: '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 = 0.699 (Fisher's exact test), Q value = 1

Table S169.  Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
ARID1A MUTATED 2 1 4 2 1 0
ARID1A WILD-TYPE 67 73 74 67 77 29
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S170.  Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
ARID1A MUTATED 2 3 1 4
ARID1A WILD-TYPE 107 92 71 117
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S171.  Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
ARID1A MUTATED 1 5 4
ARID1A WILD-TYPE 85 173 166
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.987 (Fisher's exact test), Q value = 1

Table S172.  Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
ARID1A MUTATED 2 0 4 3 1 0
ARID1A WILD-TYPE 97 25 146 112 29 15
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S173.  Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
ARID1A MUTATED 1 5 4
ARID1A WILD-TYPE 99 168 150
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.74

Table S174.  Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
ARID1A MUTATED 1 1 7 1
ARID1A WILD-TYPE 116 113 154 34
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S175.  Gene #20: '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 = 0.294 (Fisher's exact test), Q value = 0.89

Table S176.  Gene #20: '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
'ARAP3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S177.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
ARAP3 MUTATED 2 1 0
ARAP3 WILD-TYPE 188 111 131
'ARAP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S178.  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 69 74 78 69 78 29
ARAP3 MUTATED 0 1 0 1 1 0
ARAP3 WILD-TYPE 69 73 78 68 77 29
'ARAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S179.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
ARAP3 MUTATED 1 1 0 1
ARAP3 WILD-TYPE 108 94 72 120
'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S180.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
ARAP3 MUTATED 0 1 2
ARAP3 WILD-TYPE 86 177 168
'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S181.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
ARAP3 MUTATED 1 0 1 1 0 0
ARAP3 WILD-TYPE 98 25 149 114 30 15
'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S182.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
ARAP3 MUTATED 0 2 1
ARAP3 WILD-TYPE 100 171 153
'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S183.  Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
ARAP3 MUTATED 1 0 2 0
ARAP3 WILD-TYPE 116 114 159 35
'SLC16A9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.89

Table S184.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
SLC16A9 MUTATED 2 2 0
SLC16A9 WILD-TYPE 188 110 131
'SLC16A9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S185.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
SLC16A9 MUTATED 2 1 0
SLC16A9 WILD-TYPE 102 61 97
'SLC16A9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S186.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
SLC16A9 MUTATED 2 1 0 0 1 0
SLC16A9 WILD-TYPE 67 73 78 69 77 29
'SLC16A9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.76

Table S187.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
SLC16A9 MUTATED 3 0 0 1
SLC16A9 WILD-TYPE 106 95 72 120
'SLC16A9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.68

Table S188.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
SLC16A9 MUTATED 2 2 0
SLC16A9 WILD-TYPE 84 176 170
'SLC16A9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.32

Table S189.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
SLC16A9 MUTATED 0 2 2 0 0 0
SLC16A9 WILD-TYPE 99 23 148 115 30 15

Figure S38.  Get High-res Image Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SLC16A9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.89

Table S190.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
SLC16A9 MUTATED 1 3 0
SLC16A9 WILD-TYPE 99 170 154
'SLC16A9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S191.  Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
SLC16A9 MUTATED 1 1 2 0
SLC16A9 WILD-TYPE 116 113 159 35
'PCK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.65

Table S192.  Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
PCK1 MUTATED 4 0 0
PCK1 WILD-TYPE 186 112 131
'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.89

Table S193.  Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
PCK1 MUTATED 2 1 0 0 0 0
PCK1 WILD-TYPE 67 73 78 69 78 29
'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S194.  Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
PCK1 MUTATED 1 1 0 1
PCK1 WILD-TYPE 108 94 72 120
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S195.  Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
PCK1 MUTATED 0 3 1
PCK1 WILD-TYPE 86 175 169
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S196.  Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
PCK1 MUTATED 0 0 3 1 0 0
PCK1 WILD-TYPE 99 25 147 114 30 15
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.79

Table S197.  Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
PCK1 MUTATED 2 2 0
PCK1 WILD-TYPE 98 171 154
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S198.  Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
PCK1 MUTATED 2 0 2 0
PCK1 WILD-TYPE 115 114 159 35
'CUL9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.64

Table S199.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
CUL9 MUTATED 1 4 2
CUL9 WILD-TYPE 189 108 129
'CUL9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S200.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 62 97
CUL9 MUTATED 3 1 2
CUL9 WILD-TYPE 101 61 95
'CUL9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S201.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
CUL9 MUTATED 2 1 1 0 2 0
CUL9 WILD-TYPE 67 73 77 69 76 29
'CUL9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S202.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
CUL9 MUTATED 2 0 2 2
CUL9 WILD-TYPE 107 95 70 119
'CUL9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S203.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
CUL9 MUTATED 1 3 3
CUL9 WILD-TYPE 85 175 167
'CUL9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S204.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
CUL9 MUTATED 3 0 2 2 0 0
CUL9 WILD-TYPE 96 25 148 113 30 15
'CUL9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S205.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
CUL9 MUTATED 1 4 2
CUL9 WILD-TYPE 99 169 152
'CUL9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S206.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
CUL9 MUTATED 1 1 5 0
CUL9 WILD-TYPE 116 113 156 35
'CUL9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S207.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 20 43 28
CUL9 MUTATED 0 0 2 1
CUL9 WILD-TYPE 16 20 41 27
'CUL9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S208.  Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 45 44
CUL9 MUTATED 0 1 2
CUL9 WILD-TYPE 18 44 42
'ZDHHC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.7

Table S209.  Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 112 131
ZDHHC1 MUTATED 0 2 2
ZDHHC1 WILD-TYPE 190 110 129
'ZDHHC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 1

Table S210.  Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 69 74 78 69 78 29
ZDHHC1 MUTATED 2 1 0 1 0 0
ZDHHC1 WILD-TYPE 67 73 78 68 78 29
'ZDHHC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S211.  Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 95 72 121
ZDHHC1 MUTATED 0 0 1 3
ZDHHC1 WILD-TYPE 109 95 71 118
'ZDHHC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S212.  Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 178 170
ZDHHC1 MUTATED 0 2 2
ZDHHC1 WILD-TYPE 86 176 168
'ZDHHC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 0.74

Table S213.  Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 25 150 115 30 15
ZDHHC1 MUTATED 0 1 3 0 0 0
ZDHHC1 WILD-TYPE 99 24 147 115 30 15
'ZDHHC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S214.  Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 173 154
ZDHHC1 MUTATED 0 2 2
ZDHHC1 WILD-TYPE 100 171 152
'ZDHHC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S215.  Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 117 114 161 35
ZDHHC1 MUTATED 0 1 3 0
ZDHHC1 WILD-TYPE 117 113 158 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/20067280/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/20125734/KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 436

  • Number of significantly mutated genes = 25

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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