Correlation between gene mutation status and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1GM86QJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1GM86QJ
Overview
Introduction

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

Summary

Testing the association between mutation status of 21 genes and 14 molecular subtypes across 466 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 21 genes and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
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 Fisher's exact test Fisher's exact test
TP53 385 (83%) 81 0.654
(1.00) 		0.219
(1.00) 		0.512
(1.00) 		0.313
(1.00) 		0.0484
(0.835) 		0.0442
(0.811) 		0.303
(1.00) 		0.237
(1.00) 		0.744
(1.00) 		0.564
(1.00) 		0.455
(1.00) 		0.914
(1.00)
RB1 15 (3%) 451 0.144
(0.969) 		0.285
(1.00) 		0.792
(1.00) 		0.931
(1.00) 		0.138
(0.969) 		0.879
(1.00) 		0.819
(1.00) 		0.279
(1.00) 		0.233
(1.00) 		0.767
(1.00) 		0.264
(1.00) 		0.269
(1.00)
BRCA1 18 (4%) 448 0.31
(1.00) 		0.533
(1.00) 		0.322
(1.00) 		0.993
(1.00) 		0.0169
(0.597) 		0.0578
(0.835) 		0.208
(1.00) 		0.355
(1.00) 		0.0685
(0.835) 		0.929
(1.00) 		0.0183
(0.597) 		0.132
(0.969)
NF1 24 (5%) 442 0.239
(1.00) 		0.539
(1.00) 		0.745
(1.00) 		0.73
(1.00) 		0.46
(1.00) 		0.0382
(0.748) 		0.0755
(0.835) 		0.00896
(0.576) 		0.229
(1.00) 		0.232
(1.00) 		0.932
(1.00) 		0.235
(1.00)
CDK12 15 (3%) 451 0.0767
(0.835) 		0.119
(0.969) 		0.031
(0.659) 		0.679
(1.00) 		0.392
(1.00) 		0.226
(1.00) 		0.722
(1.00) 		0.331
(1.00) 		0.473
(1.00) 		0.905
(1.00) 		0.928
(1.00) 		0.839
(1.00)
KRAS 5 (1%) 461 0.0211
(0.619) 		0.358
(1.00) 		0.0296
(0.659) 		0.395
(1.00) 		0.00557
(0.576) 		0.0817
(0.858) 		0.0651
(0.835) 		1
(1.00) 		0.358
(1.00) 		0.418
(1.00) 		0.286
(1.00) 		0.52
(1.00)
HNF1B 5 (1%) 461 0.821
(1.00) 		0.558
(1.00) 		1
(1.00) 		0.601
(1.00) 		0.173
(1.00) 		0.257
(1.00) 		0.0098
(0.576) 		0.588
(1.00) 		0.356
(1.00) 		0.417
(1.00) 		0.479
(1.00) 		0.587
(1.00)
PTEN 5 (1%) 461 0.653
(1.00) 		0.559
(1.00) 		0.307
(1.00) 		0.143
(0.969) 		0.549
(1.00) 		0.112
(0.969) 		1
(1.00) 		0.507
(1.00) 		0.787
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.83
(1.00)
LARP1 4 (1%) 462 0.844
(1.00) 		0.0297
(0.659) 		0.563
(1.00) 		0.176
(1.00) 		0.832
(1.00) 		0.647
(1.00) 		0.214
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.117
(0.969)
BRCA2 13 (3%) 453 0.962
(1.00) 		0.53
(1.00) 		1
(1.00) 		0.651
(1.00) 		0.82
(1.00) 		0.324
(1.00) 		0.656
(1.00) 		0.466
(1.00) 		0.557
(1.00) 		0.877
(1.00) 		0.7
(1.00) 		0.577
(1.00)
EFEMP1 7 (2%) 459 0.843
(1.00) 		1
(1.00) 		0.145
(0.969) 		0.747
(1.00) 		0.434
(1.00) 		0.532
(1.00) 		0.602
(1.00) 		0.859
(1.00) 		0.359
(1.00) 		0.477
(1.00)
NRAS 4 (1%) 462 0.783
(1.00) 		0.369
(1.00) 		0.453
(1.00) 		0.202
(1.00) 		0.125
(0.969) 		0.295
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.589
(1.00) 		0.231
(1.00)
MTA2 4 (1%) 462 0.315
(1.00) 		0.369
(1.00) 		0.69
(1.00) 		0.841
(1.00) 		0.797
(1.00) 		0.144
(0.969) 		0.534
(1.00) 		0.655
(1.00)
ERCC6 4 (1%) 462 1
(1.00) 		0.186
(1.00) 		0.0314
(0.659) 		0.276
(1.00) 		0.831
(1.00) 		0.239
(1.00) 		0.777
(1.00) 		1
(1.00) 		0.219
(1.00) 		0.273
(1.00)
IL21R 8 (2%) 458 0.0084
(0.576) 		0.148
(0.969) 		1
(1.00) 		0.0182
(0.597) 		0.0704
(0.835) 		0.0928
(0.91) 		0.805
(1.00) 		0.116
(0.969) 		0.265
(1.00) 		0.123
(0.969) 		0.166
(1.00) 		0.552
(1.00)
PKD1L1 6 (1%) 460 0.946
(1.00) 		0.865
(1.00) 		0.768
(1.00) 		0.476
(1.00) 		0.511
(1.00) 		0.141
(0.969) 		0.243
(1.00) 		0.189
(1.00) 		0.827
(1.00) 		0.39
(1.00) 		0.275
(1.00) 		0.356
(1.00)
SAMD9L 9 (2%) 457 0.794
(1.00) 		0.896
(1.00) 		0.389
(1.00) 		0.981
(1.00) 		0.692
(1.00) 		0.803
(1.00) 		0.0757
(0.835) 		0.402
(1.00) 		0.852
(1.00) 		0.585
(1.00) 		0.606
(1.00) 		1
(1.00)
AQP2 3 (1%) 463 0.241
(1.00) 		0.125
(0.969) 		0.611
(1.00) 		0.65
(1.00) 		0.45
(1.00) 		0.0573
(0.835) 		0.776
(1.00) 		1
(1.00)
CREBBP 11 (2%) 455 1
(1.00) 		0.632
(1.00) 		0.859
(1.00) 		0.494
(1.00) 		0.794
(1.00) 		0.0904
(0.91) 		0.449
(1.00) 		0.833
(1.00) 		0.452
(1.00) 		0.582
(1.00) 		1
(1.00) 		0.637
(1.00)
C9ORF171 5 (1%) 461 0.0148
(0.597) 		0.00424
(0.576) 		0.53
(1.00) 		0.255
(1.00) 		0.548
(1.00) 		0.223
(1.00) 		0.401
(1.00) 		0.166
(1.00) 		0.0574
(0.835) 		0.496
(1.00)
NCOA3 5 (1%) 461 0.367
(1.00) 		0.226
(1.00) 		1
(1.00) 		0.642
(1.00) 		0.458
(1.00) 		0.0737
(0.835) 		0.263
(1.00) 		0.229
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
TP53 MUTATED 116 82 89 97
TP53 WILD-TYPE 26 17 14 24
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
TP53 MUTATED 220 106 58
TP53 WILD-TYPE 39 30 12
'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
TP53 MUTATED 130 86 168
TP53 WILD-TYPE 25 23 33
'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
TP53 MUTATED 58 42 41 61 26 51 23 20 31 31
TP53 WILD-TYPE 15 3 8 9 4 13 4 9 8 8
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
TP53 MUTATED 156 78 143
TP53 WILD-TYPE 30 26 22

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
TP53 MUTATED 87 60 118 120
TP53 WILD-TYPE 15 19 31 15

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
TP53 MUTATED 99 128 48
TP53 WILD-TYPE 28 23 13
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
TP53 MUTATED 92 37 44 102
TP53 WILD-TYPE 30 6 10 18
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
TP53 MUTATED 53 74 85
TP53 WILD-TYPE 11 11 14
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
TP53 MUTATED 104 39 69
TP53 WILD-TYPE 18 4 14
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
TP53 MUTATED 44 98 108 74
TP53 WILD-TYPE 12 19 16 11
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.914 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
TP53 MUTATED 75 50 118 81
TP53 WILD-TYPE 15 10 19 14
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.97

Table S13.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
RB1 MUTATED 8 4 2 1
RB1 WILD-TYPE 134 95 101 120
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
RB1 MUTATED 6 5 4
RB1 WILD-TYPE 253 131 66
'RB1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S15.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
RB1 MUTATED 4 3 8
RB1 WILD-TYPE 151 106 193
'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S16.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
RB1 MUTATED 1 3 1 2 1 2 1 1 2 1
RB1 WILD-TYPE 72 42 48 68 29 62 26 28 37 38
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.97

Table S17.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
RB1 MUTATED 8 5 2
RB1 WILD-TYPE 178 99 163
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S18.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
RB1 MUTATED 3 2 4 6
RB1 WILD-TYPE 99 77 145 129
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S19.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
RB1 MUTATED 4 7 3
RB1 WILD-TYPE 123 144 58
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
RB1 MUTATED 4 3 4 3
RB1 WILD-TYPE 118 40 50 117
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S21.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
RB1 MUTATED 0 4 3
RB1 WILD-TYPE 64 81 96
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
RB1 MUTATED 3 2 2
RB1 WILD-TYPE 119 41 81
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S23.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
RB1 MUTATED 1 7 2 4
RB1 WILD-TYPE 55 110 122 81
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S24.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
RB1 MUTATED 3 0 8 3
RB1 WILD-TYPE 87 60 129 92
'BRCA1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S25.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
BRCA1 MUTATED 3 3 4 8
BRCA1 WILD-TYPE 139 96 99 113
'BRCA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
BRCA1 MUTATED 8 7 3
BRCA1 WILD-TYPE 251 129 67
'BRCA1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
BRCA1 MUTATED 5 7 6
BRCA1 WILD-TYPE 150 102 195
'BRCA1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.993 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
BRCA1 MUTATED 4 2 1 3 1 3 0 1 1 2
BRCA1 WILD-TYPE 69 43 48 67 29 61 27 28 38 37
'BRCA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.6

Table S29.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
BRCA1 MUTATED 2 6 10
BRCA1 WILD-TYPE 184 98 155

Figure S3.  Get High-res Image Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'BRCA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0578 (Fisher's exact test), Q value = 0.84

Table S30.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
BRCA1 MUTATED 2 3 11 2
BRCA1 WILD-TYPE 100 76 138 133
'BRCA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S31.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
BRCA1 MUTATED 5 3 4
BRCA1 WILD-TYPE 122 148 57
'BRCA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S32.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
BRCA1 MUTATED 6 0 3 3
BRCA1 WILD-TYPE 116 43 51 117
'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0685 (Fisher's exact test), Q value = 0.84

Table S33.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
BRCA1 MUTATED 7 2 4
BRCA1 WILD-TYPE 57 83 95
'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S34.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
BRCA1 MUTATED 6 2 5
BRCA1 WILD-TYPE 116 41 78
'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.6

Table S35.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
BRCA1 MUTATED 5 1 7 1
BRCA1 WILD-TYPE 51 116 117 84

Figure S4.  Get High-res Image Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.97

Table S36.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
BRCA1 MUTATED 5 1 2 6
BRCA1 WILD-TYPE 85 59 135 89
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
NF1 MUTATED 4 7 8 5
NF1 WILD-TYPE 138 92 95 116
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
NF1 MUTATED 13 9 2
NF1 WILD-TYPE 246 127 68
'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
NF1 MUTATED 8 7 9
NF1 WILD-TYPE 147 102 192
'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S40.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
NF1 MUTATED 4 2 1 3 2 5 0 2 1 4
NF1 WILD-TYPE 69 43 48 67 28 59 27 27 38 35
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S41.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
NF1 MUTATED 7 7 10
NF1 WILD-TYPE 179 97 155
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.75

Table S42.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
NF1 MUTATED 6 3 13 2
NF1 WILD-TYPE 96 76 136 133

Figure S5.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 0.84

Table S43.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
NF1 MUTATED 9 3 4
NF1 WILD-TYPE 118 148 57
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00896 (Fisher's exact test), Q value = 0.58

Table S44.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
NF1 MUTATED 10 4 0 2
NF1 WILD-TYPE 112 39 54 118

Figure S6.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S45.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
NF1 MUTATED 3 1 6
NF1 WILD-TYPE 61 84 93
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
NF1 MUTATED 3 1 6
NF1 WILD-TYPE 119 42 77
'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S47.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
NF1 MUTATED 2 7 6 5
NF1 WILD-TYPE 54 110 118 80
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S48.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
NF1 MUTATED 7 1 5 7
NF1 WILD-TYPE 83 59 132 88
'CDK12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0767 (Fisher's exact test), Q value = 0.84

Table S49.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
CDK12 MUTATED 4 0 4 7
CDK12 WILD-TYPE 138 99 99 114
'CDK12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.97

Table S50.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
CDK12 MUTATED 12 3 0
CDK12 WILD-TYPE 247 133 70
'CDK12 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.66

Table S51.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
CDK12 MUTATED 10 2 3
CDK12 WILD-TYPE 145 107 198

Figure S7.  Get High-res Image Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'CDK12 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S52.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
CDK12 MUTATED 5 0 2 3 0 2 1 1 0 1
CDK12 WILD-TYPE 68 45 47 67 30 62 26 28 39 38
'CDK12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
CDK12 MUTATED 7 1 6
CDK12 WILD-TYPE 179 103 159
'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S54.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
CDK12 MUTATED 1 1 6 7
CDK12 WILD-TYPE 101 78 143 128
'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S55.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
CDK12 MUTATED 3 6 2
CDK12 WILD-TYPE 124 145 59
'CDK12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S56.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
CDK12 MUTATED 2 3 2 4
CDK12 WILD-TYPE 120 40 52 116
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S57.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
CDK12 MUTATED 4 2 3
CDK12 WILD-TYPE 60 83 96
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S58.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
CDK12 MUTATED 4 2 3
CDK12 WILD-TYPE 118 41 80
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S59.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
CDK12 MUTATED 2 5 5 2
CDK12 WILD-TYPE 54 112 119 83
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S60.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
CDK12 MUTATED 4 3 4 3
CDK12 WILD-TYPE 86 57 133 92
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
KRAS MUTATED 1 0 4 0
KRAS WILD-TYPE 141 99 99 121

Figure S8.  Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S62.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
KRAS MUTATED 4 0 1
KRAS WILD-TYPE 255 136 69
'KRAS MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.66

Table S63.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
KRAS MUTATED 2 3 0
KRAS WILD-TYPE 153 106 201

Figure S9.  Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'KRAS MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 1

Table S64.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
KRAS MUTATED 2 1 0 0 0 0 1 0 1 0
KRAS WILD-TYPE 71 44 49 70 30 64 26 29 38 39
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.58

Table S65.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
KRAS MUTATED 0 4 1
KRAS WILD-TYPE 186 100 164

Figure S10.  Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0817 (Fisher's exact test), Q value = 0.86

Table S66.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
KRAS MUTATED 0 1 4 0
KRAS WILD-TYPE 102 78 145 135
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0651 (Fisher's exact test), Q value = 0.84

Table S67.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
KRAS MUTATED 2 0 2
KRAS WILD-TYPE 125 151 59
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S68.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
KRAS MUTATED 2 0 0 2
KRAS WILD-TYPE 120 43 54 118
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S69.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
KRAS MUTATED 1 2 0
KRAS WILD-TYPE 63 83 99
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 1

Table S70.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
KRAS MUTATED 2 1 0
KRAS WILD-TYPE 120 42 83
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S71.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
KRAS MUTATED 1 0 2 0
KRAS WILD-TYPE 55 117 122 85
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S72.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
KRAS MUTATED 0 0 1 2
KRAS WILD-TYPE 90 60 136 93
'HNF1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S73.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
HNF1B MUTATED 1 2 1 1
HNF1B WILD-TYPE 141 97 102 120
'HNF1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S74.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
HNF1B MUTATED 2 2 1
HNF1B WILD-TYPE 257 134 69
'HNF1B MUTATION STATUS' versus 'MIR_CNMF'

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

Table S75.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
HNF1B MUTATED 2 1 2
HNF1B WILD-TYPE 153 108 199
'HNF1B MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
HNF1B MUTATED 1 1 0 1 1 0 1 0 0 0
HNF1B WILD-TYPE 72 44 49 69 29 64 26 29 39 39
'HNF1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S77.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
HNF1B MUTATED 1 0 4
HNF1B WILD-TYPE 185 104 161
'HNF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
HNF1B MUTATED 1 1 0 3
HNF1B WILD-TYPE 101 78 149 132
'HNF1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0098 (Fisher's exact test), Q value = 0.58

Table S79.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
HNF1B MUTATED 1 0 3
HNF1B WILD-TYPE 126 151 58

Figure S11.  Get High-res Image Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'HNF1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
HNF1B MUTATED 3 0 0 1
HNF1B WILD-TYPE 119 43 54 119
'HNF1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S81.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
HNF1B MUTATED 1 2 0
HNF1B WILD-TYPE 63 83 99
'HNF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.417 (Fisher's exact test), Q value = 1

Table S82.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
HNF1B MUTATED 2 1 0
HNF1B WILD-TYPE 120 42 83
'HNF1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S83.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
HNF1B MUTATED 0 1 3 0
HNF1B WILD-TYPE 56 116 121 85
'HNF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S84.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
HNF1B MUTATED 0 0 2 2
HNF1B WILD-TYPE 90 60 135 93
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
PTEN MUTATED 2 2 0 1
PTEN WILD-TYPE 140 97 103 120
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 1

Table S86.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
PTEN MUTATED 2 2 1
PTEN WILD-TYPE 257 134 69
'PTEN MUTATION STATUS' versus 'MIR_CNMF'

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

Table S87.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
PTEN MUTATED 1 0 4
PTEN WILD-TYPE 154 109 197
'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.97

Table S88.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
PTEN MUTATED 0 0 0 3 0 0 1 0 1 0
PTEN WILD-TYPE 73 45 49 67 30 64 26 29 38 39
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S89.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
PTEN MUTATED 1 1 3
PTEN WILD-TYPE 185 103 162
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.97

Table S90.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
PTEN MUTATED 3 1 0 1
PTEN WILD-TYPE 99 78 149 134
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S91.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
PTEN MUTATED 1 2 0
PTEN WILD-TYPE 126 149 61
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S92.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
PTEN MUTATED 2 0 1 0
PTEN WILD-TYPE 120 43 53 120
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S93.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
PTEN MUTATED 0 1 2
PTEN WILD-TYPE 64 84 97
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S94.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
PTEN MUTATED 1 1 1
PTEN WILD-TYPE 121 42 82
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S95.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
PTEN MUTATED 0 1 2 1
PTEN WILD-TYPE 56 116 122 84
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S96.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
PTEN MUTATED 1 0 1 2
PTEN WILD-TYPE 89 60 136 93
'LARP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S97.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
LARP1 MUTATED 2 1 0 1
LARP1 WILD-TYPE 140 98 103 120
'LARP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.66

Table S98.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
LARP1 MUTATED 0 2 2
LARP1 WILD-TYPE 259 134 68

Figure S12.  Get High-res Image Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'LARP1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S99.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
LARP1 MUTATED 1 0 3
LARP1 WILD-TYPE 154 109 198
'LARP1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S100.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
LARP1 MUTATED 0 0 0 0 1 1 1 0 1 0
LARP1 WILD-TYPE 73 45 49 70 29 63 26 29 38 39
'LARP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S101.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
LARP1 MUTATED 1 1 2
LARP1 WILD-TYPE 185 103 163
'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S102.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
LARP1 MUTATED 2 0 1 1
LARP1 WILD-TYPE 100 79 148 134
'LARP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S103.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
LARP1 MUTATED 2 0 1
LARP1 WILD-TYPE 125 151 60
'LARP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S104.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
LARP1 MUTATED 1 1 1 0
LARP1 WILD-TYPE 121 42 53 120
'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S105.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
LARP1 MUTATED 0 1 1 1
LARP1 WILD-TYPE 56 116 123 84
'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.97

Table S106.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
LARP1 MUTATED 0 2 1 0
LARP1 WILD-TYPE 90 58 136 95
'BRCA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S107.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
BRCA2 MUTATED 4 3 2 4
BRCA2 WILD-TYPE 138 96 101 117
'BRCA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S108.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
BRCA2 MUTATED 9 2 2
BRCA2 WILD-TYPE 250 134 68
'BRCA2 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S109.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
BRCA2 MUTATED 4 3 6
BRCA2 WILD-TYPE 151 106 195
'BRCA2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
BRCA2 MUTATED 2 1 0 1 1 2 2 2 1 1
BRCA2 WILD-TYPE 71 44 49 69 29 62 25 27 38 38
'BRCA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S111.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
BRCA2 MUTATED 5 2 6
BRCA2 WILD-TYPE 181 102 159
'BRCA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S112.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
BRCA2 MUTATED 4 0 4 5
BRCA2 WILD-TYPE 98 79 145 130
'BRCA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S113.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
BRCA2 MUTATED 2 4 0
BRCA2 WILD-TYPE 125 147 61
'BRCA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S114.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
BRCA2 MUTATED 1 0 1 4
BRCA2 WILD-TYPE 121 43 53 116
'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S115.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
BRCA2 MUTATED 2 1 4
BRCA2 WILD-TYPE 62 84 95
'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S116.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
BRCA2 MUTATED 3 1 3
BRCA2 WILD-TYPE 119 42 80
'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S117.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
BRCA2 MUTATED 3 3 3 3
BRCA2 WILD-TYPE 53 114 121 82
'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.577 (Fisher's exact test), Q value = 1

Table S118.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
BRCA2 MUTATED 4 3 3 2
BRCA2 WILD-TYPE 86 57 134 93
'EFEMP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S119.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
EFEMP1 MUTATED 2 1 1 3
EFEMP1 WILD-TYPE 140 98 102 118
'EFEMP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S120.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
EFEMP1 MUTATED 4 2 1
EFEMP1 WILD-TYPE 255 134 69
'EFEMP1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.97

Table S121.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
EFEMP1 MUTATED 0 2 5
EFEMP1 WILD-TYPE 155 107 196
'EFEMP1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S122.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
EFEMP1 MUTATED 0 1 2 2 0 1 0 0 1 0
EFEMP1 WILD-TYPE 73 44 47 68 30 63 27 29 38 39
'EFEMP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S123.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
EFEMP1 MUTATED 4 0 3
EFEMP1 WILD-TYPE 182 104 162
'EFEMP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S124.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
EFEMP1 MUTATED 1 0 4 2
EFEMP1 WILD-TYPE 101 79 145 133
'EFEMP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S125.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
EFEMP1 MUTATED 3 2 0
EFEMP1 WILD-TYPE 124 149 61
'EFEMP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S126.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
EFEMP1 MUTATED 3 0 0 2
EFEMP1 WILD-TYPE 119 43 54 118
'EFEMP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S127.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
EFEMP1 MUTATED 2 2 3 0
EFEMP1 WILD-TYPE 54 115 121 85
'EFEMP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 1

Table S128.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
EFEMP1 MUTATED 3 1 1 2
EFEMP1 WILD-TYPE 87 59 136 93
'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S129.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
NRAS MUTATED 1 0 1 2
NRAS WILD-TYPE 141 99 102 119
'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 1

Table S130.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
NRAS MUTATED 4 0 0
NRAS WILD-TYPE 255 136 70
'NRAS MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S131.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
NRAS MUTATED 1 2 1
NRAS WILD-TYPE 154 107 200
'NRAS MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 1

Table S132.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
NRAS MUTATED 0 0 1 0 0 0 0 1 1 1
NRAS WILD-TYPE 73 45 48 70 30 64 27 28 38 38
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.97

Table S133.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
NRAS MUTATED 0 2 2
NRAS WILD-TYPE 186 102 163
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S134.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
NRAS MUTATED 1 0 3 0
NRAS WILD-TYPE 101 79 146 135
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S135.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
NRAS MUTATED 1 2 0
NRAS WILD-TYPE 126 149 61
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S136.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
NRAS MUTATED 1 0 0 2
NRAS WILD-TYPE 121 43 54 118
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S137.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
NRAS MUTATED 0 0 2 1
NRAS WILD-TYPE 56 117 122 84
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S138.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
NRAS MUTATED 1 0 0 2
NRAS WILD-TYPE 89 60 137 93
'MTA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S139.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
MTA2 MUTATED 3 0 0 1
MTA2 WILD-TYPE 139 99 103 120
'MTA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 1

Table S140.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
MTA2 MUTATED 4 0 0
MTA2 WILD-TYPE 255 136 70
'MTA2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S141.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
MTA2 MUTATED 2 0 2
MTA2 WILD-TYPE 153 109 199
'MTA2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S142.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
MTA2 MUTATED 0 0 1 2 0 1 0 0 0 0
MTA2 WILD-TYPE 73 45 48 68 30 63 27 29 39 39
'MTA2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S143.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
MTA2 MUTATED 2 0 1
MTA2 WILD-TYPE 184 104 164
'MTA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.97

Table S144.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
MTA2 MUTATED 1 0 0 3
MTA2 WILD-TYPE 101 79 149 132
'MTA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 1

Table S145.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
MTA2 MUTATED 1 3 0
MTA2 WILD-TYPE 126 148 61
'MTA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S146.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
MTA2 MUTATED 1 1 0 2
MTA2 WILD-TYPE 121 42 54 118
'ERCC6 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S147.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
ERCC6 MUTATED 1 1 1 1
ERCC6 WILD-TYPE 141 98 102 120
'ERCC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S148.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
ERCC6 MUTATED 1 3 0
ERCC6 WILD-TYPE 258 133 70
'ERCC6 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.66

Table S149.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
ERCC6 MUTATED 1 3 0
ERCC6 WILD-TYPE 154 106 201

Figure S13.  Get High-res Image Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'ERCC6 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S150.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
ERCC6 MUTATED 0 1 1 0 1 0 0 0 0 1
ERCC6 WILD-TYPE 73 44 48 70 29 64 27 29 39 38
'ERCC6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S151.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
ERCC6 MUTATED 1 1 2
ERCC6 WILD-TYPE 185 103 163
'ERCC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S152.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
ERCC6 MUTATED 1 2 1 0
ERCC6 WILD-TYPE 101 77 148 135
'ERCC6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S153.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
ERCC6 MUTATED 2 1 0
ERCC6 WILD-TYPE 125 150 61
'ERCC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S154.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
ERCC6 MUTATED 2 0 0 1
ERCC6 WILD-TYPE 120 43 54 119
'ERCC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S155.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
ERCC6 MUTATED 2 1 1 0
ERCC6 WILD-TYPE 54 116 123 85
'ERCC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S156.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
ERCC6 MUTATED 0 2 1 1
ERCC6 WILD-TYPE 90 58 136 94
'IL21R MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0084 (Fisher's exact test), Q value = 0.58

Table S157.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
IL21R MUTATED 0 3 0 5
IL21R WILD-TYPE 142 96 103 116

Figure S14.  Get High-res Image Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'IL21R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.97

Table S158.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
IL21R MUTATED 3 5 0
IL21R WILD-TYPE 256 131 70
'IL21R MUTATION STATUS' versus 'MIR_CNMF'

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

Table S159.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
IL21R MUTATED 3 2 3
IL21R WILD-TYPE 152 107 198
'IL21R MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.6

Table S160.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
IL21R MUTATED 0 1 1 0 0 3 0 3 0 0
IL21R WILD-TYPE 73 44 48 70 30 61 27 26 39 39

Figure S15.  Get High-res Image Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'IL21R MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0704 (Fisher's exact test), Q value = 0.84

Table S161.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
IL21R MUTATED 2 0 6
IL21R WILD-TYPE 184 104 159
'IL21R MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0928 (Fisher's exact test), Q value = 0.91

Table S162.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
IL21R MUTATED 1 3 4 0
IL21R WILD-TYPE 101 76 145 135
'IL21R MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S163.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
IL21R MUTATED 3 3 2
IL21R WILD-TYPE 124 148 59
'IL21R MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.97

Table S164.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
IL21R MUTATED 2 2 3 1
IL21R WILD-TYPE 120 41 51 119
'IL21R MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S165.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
IL21R MUTATED 0 1 4
IL21R WILD-TYPE 64 84 95
'IL21R MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.97

Table S166.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
IL21R MUTATED 1 0 4
IL21R WILD-TYPE 121 43 79
'IL21R MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 1

Table S167.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
IL21R MUTATED 2 2 0 1
IL21R WILD-TYPE 54 115 124 84
'IL21R MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S168.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
IL21R MUTATED 1 1 3 0
IL21R WILD-TYPE 89 59 134 95
'PKD1L1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S169.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
PKD1L1 MUTATED 2 1 2 1
PKD1L1 WILD-TYPE 140 98 101 120
'PKD1L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S170.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
PKD1L1 MUTATED 4 1 1
PKD1L1 WILD-TYPE 255 135 69
'PKD1L1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S171.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
PKD1L1 MUTATED 3 1 2
PKD1L1 WILD-TYPE 152 108 199
'PKD1L1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 1

Table S172.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
PKD1L1 MUTATED 3 0 2 1 0 0 0 0 0 0
PKD1L1 WILD-TYPE 70 45 47 69 30 64 27 29 39 39
'PKD1L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S173.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
PKD1L1 MUTATED 3 0 3
PKD1L1 WILD-TYPE 183 104 162
'PKD1L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.97

Table S174.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
PKD1L1 MUTATED 1 1 0 4
PKD1L1 WILD-TYPE 101 78 149 131
'PKD1L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S175.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
PKD1L1 MUTATED 0 3 1
PKD1L1 WILD-TYPE 127 148 60
'PKD1L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 1

Table S176.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
PKD1L1 MUTATED 0 1 0 3
PKD1L1 WILD-TYPE 122 42 54 117
'PKD1L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S177.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
PKD1L1 MUTATED 1 2 1
PKD1L1 WILD-TYPE 63 83 98
'PKD1L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S178.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
PKD1L1 MUTATED 3 1 0
PKD1L1 WILD-TYPE 119 42 83
'PKD1L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S179.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
PKD1L1 MUTATED 0 4 2 0
PKD1L1 WILD-TYPE 56 113 122 85
'PKD1L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S180.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
PKD1L1 MUTATED 0 2 2 2
PKD1L1 WILD-TYPE 90 58 135 93
'SAMD9L MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S181.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
SAMD9L MUTATED 4 2 1 2
SAMD9L WILD-TYPE 138 97 102 119
'SAMD9L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S182.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
SAMD9L MUTATED 6 2 1
SAMD9L WILD-TYPE 253 134 69
'SAMD9L MUTATION STATUS' versus 'MIR_CNMF'

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

Table S183.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
SAMD9L MUTATED 2 4 3
SAMD9L WILD-TYPE 153 105 198
'SAMD9L MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.981 (Fisher's exact test), Q value = 1

Table S184.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
SAMD9L MUTATED 1 1 2 1 0 2 0 0 1 1
SAMD9L WILD-TYPE 72 44 47 69 30 62 27 29 38 38
'SAMD9L MUTATION STATUS' versus 'CN_CNMF'

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

Table S185.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
SAMD9L MUTATED 5 1 3
SAMD9L WILD-TYPE 181 103 162
'SAMD9L MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S186.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
SAMD9L MUTATED 3 1 2 3
SAMD9L WILD-TYPE 99 78 147 132
'SAMD9L MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0757 (Fisher's exact test), Q value = 0.84

Table S187.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
SAMD9L MUTATED 2 2 4
SAMD9L WILD-TYPE 125 149 57
'SAMD9L MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S188.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
SAMD9L MUTATED 5 1 1 1
SAMD9L WILD-TYPE 117 42 53 119
'SAMD9L MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S189.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
SAMD9L MUTATED 1 1 3
SAMD9L WILD-TYPE 63 84 96
'SAMD9L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S190.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
SAMD9L MUTATED 4 0 1
SAMD9L WILD-TYPE 118 43 82
'SAMD9L MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S191.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
SAMD9L MUTATED 1 1 2 3
SAMD9L WILD-TYPE 55 116 122 82
'SAMD9L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S192.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
SAMD9L MUTATED 1 1 3 2
SAMD9L WILD-TYPE 89 59 134 93
'AQP2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S193.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
AQP2 MUTATED 1 2 0 0
AQP2 WILD-TYPE 141 97 103 121
'AQP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.97

Table S194.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
AQP2 MUTATED 0 2 1
AQP2 WILD-TYPE 259 134 69
'AQP2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S195.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
AQP2 MUTATED 2 0 1
AQP2 WILD-TYPE 153 109 200
'AQP2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S196.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
AQP2 MUTATED 1 1 0 0 0 0 0 0 1 0
AQP2 WILD-TYPE 72 44 49 70 30 64 27 29 38 39
'AQP2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S197.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
AQP2 MUTATED 2 1 0
AQP2 WILD-TYPE 184 103 165
'AQP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.84

Table S198.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
AQP2 MUTATED 0 0 0 3
AQP2 WILD-TYPE 102 79 149 132
'AQP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S199.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
AQP2 MUTATED 2 1 0
AQP2 WILD-TYPE 125 150 61
'AQP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S200.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
AQP2 MUTATED 2 0 0 1
AQP2 WILD-TYPE 120 43 54 119
'CREBBP MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S201.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
CREBBP MUTATED 4 2 2 3
CREBBP WILD-TYPE 138 97 101 118
'CREBBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S202.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
CREBBP MUTATED 8 2 1
CREBBP WILD-TYPE 251 134 69
'CREBBP MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S203.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
CREBBP MUTATED 4 3 4
CREBBP WILD-TYPE 151 106 197
'CREBBP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S204.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
CREBBP MUTATED 1 3 1 2 1 0 1 1 0 1
CREBBP WILD-TYPE 72 42 48 68 29 64 26 28 39 38
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S205.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
CREBBP MUTATED 5 3 3
CREBBP WILD-TYPE 181 101 162
'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0904 (Fisher's exact test), Q value = 0.91

Table S206.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
CREBBP MUTATED 2 0 2 7
CREBBP WILD-TYPE 100 79 147 128
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S207.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
CREBBP MUTATED 4 5 0
CREBBP WILD-TYPE 123 146 61
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S208.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
CREBBP MUTATED 4 1 2 2
CREBBP WILD-TYPE 118 42 52 118
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S209.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 85 99
CREBBP MUTATED 0 2 3
CREBBP WILD-TYPE 64 83 96
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S210.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 43 83
CREBBP MUTATED 4 0 1
CREBBP WILD-TYPE 118 43 82
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S211.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
CREBBP MUTATED 1 3 3 2
CREBBP WILD-TYPE 55 114 121 83
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S212.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
CREBBP MUTATED 2 0 4 3
CREBBP WILD-TYPE 88 60 133 92
'C9ORF171 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.6

Table S213.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
C9ORF171 MUTATED 1 4 0 0
C9ORF171 WILD-TYPE 141 95 103 121

Figure S16.  Get High-res Image Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'C9ORF171 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.58

Table S214.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
C9ORF171 MUTATED 0 5 0
C9ORF171 WILD-TYPE 259 131 70

Figure S17.  Get High-res Image Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'C9ORF171 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S215.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
C9ORF171 MUTATED 2 2 1
C9ORF171 WILD-TYPE 153 107 200
'C9ORF171 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S216.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
C9ORF171 MUTATED 1 0 0 1 2 0 0 0 0 1
C9ORF171 WILD-TYPE 72 45 49 69 28 64 27 29 39 38
'C9ORF171 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S217.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
C9ORF171 MUTATED 1 1 3
C9ORF171 WILD-TYPE 185 103 162
'C9ORF171 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S218.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
C9ORF171 MUTATED 2 0 3 0
C9ORF171 WILD-TYPE 100 79 146 135
'C9ORF171 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S219.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 151 61
C9ORF171 MUTATED 3 1 0
C9ORF171 WILD-TYPE 124 150 61
'C9ORF171 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 1

Table S220.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 43 54 120
C9ORF171 MUTATED 2 0 2 0
C9ORF171 WILD-TYPE 120 43 52 120
'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0574 (Fisher's exact test), Q value = 0.84

Table S221.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
C9ORF171 MUTATED 2 2 0 0
C9ORF171 WILD-TYPE 54 115 124 85
'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S222.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
C9ORF171 MUTATED 1 0 3 0
C9ORF171 WILD-TYPE 89 60 134 95
'NCOA3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S223.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 99 103 121
NCOA3 MUTATED 0 1 2 2
NCOA3 WILD-TYPE 142 98 101 119
'NCOA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S224.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 259 136 70
NCOA3 MUTATED 5 0 0
NCOA3 WILD-TYPE 254 136 70
'NCOA3 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S225.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 109 201
NCOA3 MUTATED 2 1 2
NCOA3 WILD-TYPE 153 108 199
'NCOA3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S226.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 73 45 49 70 30 64 27 29 39 39
NCOA3 MUTATED 0 0 1 2 0 1 1 0 0 0
NCOA3 WILD-TYPE 73 45 48 68 30 63 26 29 39 39
'NCOA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S227.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 104 165
NCOA3 MUTATED 1 2 2
NCOA3 WILD-TYPE 185 102 163
'NCOA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0737 (Fisher's exact test), Q value = 0.84

Table S228.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 79 149 135
NCOA3 MUTATED 3 0 0 2
NCOA3 WILD-TYPE 99 79 149 133
'NCOA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 1

Table S229.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 117 124 85
NCOA3 MUTATED 1 3 0 1
NCOA3 WILD-TYPE 55 114 124 84
'NCOA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S230.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 60 137 95
NCOA3 MUTATED 3 0 2 0
NCOA3 WILD-TYPE 87 60 135 95
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/OV-TP/22572517/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/22555032/OV-TP.transferedmergedcluster.txt

  • Number of patients = 466

  • Number of significantly mutated genes = 21

  • Number of Molecular subtypes = 14

  • 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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