Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 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 1
(1.00) 		0.218
(1.00) 		0.894
(1.00) 		0.312
(1.00) 		0.486
(1.00) 		0.214
(1.00) 		0.301
(1.00) 		0.238
(1.00) 		0.502
(1.00) 		0.568
(1.00) 		0.967
(1.00) 		0.913
(1.00) 		1
(1.00)
RB1 15 (3%) 451 0.0971
(1.00) 		0.285
(1.00) 		0.674
(1.00) 		0.932
(1.00) 		0.118
(1.00) 		0.0149
(0.624) 		0.817
(1.00) 		0.278
(1.00) 		0.232
(1.00) 		0.769
(1.00) 		0.513
(1.00) 		0.268
(1.00)
BRCA1 18 (4%) 448 0.0441
(0.77) 		0.533
(1.00) 		0.756
(1.00) 		0.993
(1.00) 		0.0463
(0.77) 		0.0471
(0.77) 		0.207
(1.00) 		0.361
(1.00) 		0.0673
(0.977) 		0.929
(1.00) 		0.0698
(0.977) 		0.13
(1.00)
NF1 24 (5%) 442 0.622
(1.00) 		0.54
(1.00) 		0.723
(1.00) 		0.729
(1.00) 		0.382
(1.00) 		0.0329
(0.77) 		0.0768
(0.982) 		0.00891
(0.624) 		0.247
(1.00) 		0.233
(1.00) 		0.59
(1.00) 		0.235
(1.00) 		0.357
(1.00)
CDK12 15 (3%) 451 0.0144
(0.624) 		0.117
(1.00) 		0.221
(1.00) 		0.678
(1.00) 		0.336
(1.00) 		0.0445
(0.77) 		0.722
(1.00) 		0.331
(1.00) 		0.47
(1.00) 		0.903
(1.00) 		0.697
(1.00) 		0.84
(1.00) 		1
(1.00)
KRAS 5 (1%) 461 0.26
(1.00) 		0.357
(1.00) 		0.089
(1.00) 		0.397
(1.00) 		0.0404
(0.77) 		0.74
(1.00) 		0.0659
(0.977) 		1
(1.00) 		0.186
(1.00) 		0.418
(1.00) 		0.348
(1.00) 		0.523
(1.00)
HNF1B 5 (1%) 461 0.549
(1.00) 		0.555
(1.00) 		0.868
(1.00) 		0.601
(1.00) 		0.136
(1.00) 		0.625
(1.00) 		0.00942
(0.624) 		0.585
(1.00) 		0.355
(1.00) 		0.418
(1.00) 		0.686
(1.00) 		0.589
(1.00)
PTEN 5 (1%) 461 0.65
(1.00) 		0.557
(1.00) 		0.191
(1.00) 		0.145
(1.00) 		0.281
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.786
(1.00) 		0.754
(1.00) 		0.687
(1.00) 		0.829
(1.00)
LARP1 4 (1%) 462 0.192
(1.00) 		0.0311
(0.77) 		0.312
(1.00) 		0.176
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.212
(1.00) 		0.24
(1.00) 		0.621
(1.00) 		0.12
(1.00) 		0.357
(1.00)
BRCA2 13 (3%) 453 0.935
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.649
(1.00) 		0.357
(1.00) 		0.307
(1.00) 		0.656
(1.00) 		0.466
(1.00) 		0.557
(1.00) 		0.878
(1.00) 		0.817
(1.00) 		0.575
(1.00) 		0.357
(1.00)
EFEMP1 7 (2%) 459 1
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.749
(1.00) 		0.207
(1.00) 		0.0327
(0.77) 		0.605
(1.00) 		0.86
(1.00) 		0.709
(1.00) 		0.477
(1.00)
NRAS 4 (1%) 462 0.838
(1.00) 		0.366
(1.00) 		0.566
(1.00) 		0.205
(1.00) 		0.465
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.619
(1.00) 		0.234
(1.00)
MTA2 4 (1%) 462 0.456
(1.00) 		0.367
(1.00) 		0.31
(1.00) 		0.843
(1.00) 		0.403
(1.00) 		0.475
(1.00) 		0.531
(1.00) 		0.656
(1.00) 		1
(1.00)
ERCC6 4 (1%) 462 0.839
(1.00) 		0.184
(1.00) 		0.104
(1.00) 		0.279
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.272
(1.00)
IL21R 8 (2%) 458 0.0451
(0.77) 		0.144
(1.00) 		0.247
(1.00) 		0.0191
(0.702) 		0.127
(1.00) 		0.15
(1.00) 		0.804
(1.00) 		0.117
(1.00) 		0.267
(1.00) 		0.121
(1.00) 		0.733
(1.00) 		0.555
(1.00)
PKD1L1 6 (1%) 460 1
(1.00) 		0.864
(1.00) 		0.512
(1.00) 		0.47
(1.00) 		0.17
(1.00) 		0.0362
(0.77) 		0.244
(1.00) 		0.189
(1.00) 		0.828
(1.00) 		0.391
(1.00) 		0.387
(1.00) 		0.352
(1.00) 		1
(1.00)
SAMD9L 9 (2%) 457 0.832
(1.00) 		0.896
(1.00) 		0.691
(1.00) 		0.981
(1.00) 		0.84
(1.00) 		1
(1.00) 		0.075
(0.982) 		0.397
(1.00) 		0.853
(1.00) 		0.579
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
AQP2 3 (1%) 463 0.256
(1.00) 		0.125
(1.00) 		0.373
(1.00) 		0.648
(1.00) 		0.404
(1.00) 		0.384
(1.00) 		0.775
(1.00) 		1
(1.00)
CREBBP 11 (2%) 455 0.592
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.747
(1.00) 		0.692
(1.00) 		0.45
(1.00) 		0.833
(1.00) 		0.45
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.639
(1.00)
C9ORF171 5 (1%) 461 0.00093
(0.273) 		0.00445
(0.624) 		0.397
(1.00) 		0.255
(1.00) 		0.864
(1.00) 		0.0141
(0.624) 		0.402
(1.00) 		0.166
(1.00) 		0.3
(1.00) 		0.495
(1.00)
NCOA3 5 (1%) 461 0.0939
(1.00) 		0.227
(1.00) 		0.737
(1.00) 		0.645
(1.00) 		0.865
(1.00) 		0.526
(1.00) 		0.177
(1.00) 		0.23
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1 (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
ALL 176 175 114
TP53 MUTATED 145 145 94
TP53 WILD-TYPE 31 30 20
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.218 (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 = 0.894 (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 134 139 192
TP53 MUTATED 109 115 160
TP53 WILD-TYPE 25 24 32
'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.312 (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 = 0.486 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
TP53 MUTATED 109 139 129
TP53 WILD-TYPE 28 26 24
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
TP53 MUTATED 120 113 152
TP53 WILD-TYPE 18 30 32
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.301 (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 = 0.238 (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 = 0.502 (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 84 100
TP53 MUTATED 52 74 86
TP53 WILD-TYPE 12 10 14
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (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 = 0.967 (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
ALL 97 159 126
TP53 MUTATED 83 135 106
TP53 WILD-TYPE 14 24 20
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.913 (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
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S13.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
TP53 MUTATED 8 5
TP53 WILD-TYPE 1 0
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0971 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
RB1 MUTATED 9 2 4
RB1 WILD-TYPE 167 173 110
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S15.  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 = 0.674 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
RB1 MUTATED 3 4 8
RB1 WILD-TYPE 131 135 184
'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S17.  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 = 0.118 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
RB1 MUTATED 5 2 8
RB1 WILD-TYPE 132 163 145
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.62

Table S19.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
RB1 MUTATED 8 6 1
RB1 WILD-TYPE 130 137 183

Figure S1.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S20.  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 = 0.278 (Fisher's exact test), Q value = 1

Table S21.  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 = 0.232 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
RB1 MUTATED 0 4 3
RB1 WILD-TYPE 64 80 97
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S23.  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 = 0.513 (Fisher's exact test), Q value = 1

Table S24.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
RB1 MUTATED 3 8 3
RB1 WILD-TYPE 94 151 123
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S25.  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 = 0.0441 (Fisher's exact test), Q value = 0.77

Table S26.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
BRCA1 MUTATED 3 12 3
BRCA1 WILD-TYPE 173 163 111

Figure S2.  Get High-res Image Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BRCA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S27.  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 = 0.756 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
BRCA1 MUTATED 6 6 6
BRCA1 WILD-TYPE 128 133 186
'BRCA1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S29.  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 = 0.0463 (Fisher's exact test), Q value = 0.77

Table S30.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
BRCA1 MUTATED 5 11 2
BRCA1 WILD-TYPE 132 154 151

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 = 0.0471 (Fisher's exact test), Q value = 0.77

Table S31.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
BRCA1 MUTATED 1 7 10
BRCA1 WILD-TYPE 137 136 174

Figure S4.  Get High-res Image Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'BRCA1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S32.  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 = 0.361 (Fisher's exact test), Q value = 1

Table S33.  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 = 0.0673 (Fisher's exact test), Q value = 0.98

Table S34.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
BRCA1 MUTATED 7 2 4
BRCA1 WILD-TYPE 57 82 96
'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S35.  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 = 0.0698 (Fisher's exact test), Q value = 0.98

Table S36.  Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
BRCA1 MUTATED 6 2 6
BRCA1 WILD-TYPE 91 157 120
'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S37.  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 = 0.622 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
NF1 MUTATED 7 11 6
NF1 WILD-TYPE 169 164 108
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S39.  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 = 0.723 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
NF1 MUTATED 8 8 8
NF1 WILD-TYPE 126 131 184
'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S41.  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 = 0.382 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
NF1 MUTATED 9 10 5
NF1 WILD-TYPE 128 155 148
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.77

Table S43.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
NF1 MUTATED 2 8 14
NF1 WILD-TYPE 136 135 170

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 = 0.0768 (Fisher's exact test), Q value = 0.98

Table S44.  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 = 0.00891 (Fisher's exact test), Q value = 0.62

Table S45.  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 = 0.247 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
NF1 MUTATED 3 1 6
NF1 WILD-TYPE 61 83 94
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S47.  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 = 0.59 (Fisher's exact test), Q value = 1

Table S48.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
NF1 MUTATED 3 10 7
NF1 WILD-TYPE 94 149 119
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S49.  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
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S50.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
NF1 MUTATED 0 1
NF1 WILD-TYPE 9 4
'CDK12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.62

Table S51.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
CDK12 MUTATED 5 10 0
CDK12 WILD-TYPE 171 165 114

Figure S7.  Get High-res Image Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDK12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S52.  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 = 0.221 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
CDK12 MUTATED 7 2 6
CDK12 WILD-TYPE 127 137 186
'CDK12 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 1

Table S54.  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 = 0.336 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
CDK12 MUTATED 2 5 7
CDK12 WILD-TYPE 135 160 146
'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.77

Table S56.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
CDK12 MUTATED 4 1 10
CDK12 WILD-TYPE 134 142 174

Figure S8.  Get High-res Image Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S57.  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 S58.  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 = 0.47 (Fisher's exact test), Q value = 1

Table S59.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
CDK12 MUTATED 4 2 3
CDK12 WILD-TYPE 60 82 97
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S60.  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 = 0.697 (Fisher's exact test), Q value = 1

Table S61.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
CDK12 MUTATED 2 7 5
CDK12 WILD-TYPE 95 152 121
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S62.  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
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63.  Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
CDK12 MUTATED 1 0
CDK12 WILD-TYPE 8 5
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S64.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
KRAS MUTATED 4 1 0
KRAS WILD-TYPE 172 174 114
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S65.  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 = 0.089 (Fisher's exact test), Q value = 1

Table S66.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
KRAS MUTATED 3 2 0
KRAS WILD-TYPE 131 137 192
'KRAS MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S67.  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 = 0.0404 (Fisher's exact test), Q value = 0.77

Table S68.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
KRAS MUTATED 4 1 0
KRAS WILD-TYPE 133 164 153

Figure S9.  Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
KRAS MUTATED 1 1 3
KRAS WILD-TYPE 137 142 181
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0659 (Fisher's exact test), Q value = 0.98

Table S70.  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 S71.  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 = 0.186 (Fisher's exact test), Q value = 1

Table S72.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
KRAS MUTATED 2 1 0
KRAS WILD-TYPE 62 83 100
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S73.  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 = 0.348 (Fisher's exact test), Q value = 1

Table S74.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
KRAS MUTATED 1 0 2
KRAS WILD-TYPE 96 159 124
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S75.  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 = 0.549 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
HNF1B MUTATED 1 2 2
HNF1B WILD-TYPE 175 173 112
'HNF1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S77.  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 = 0.868 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
HNF1B MUTATED 2 1 2
HNF1B WILD-TYPE 132 138 190
'HNF1B MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S79.  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 = 0.136 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
HNF1B MUTATED 0 4 1
HNF1B WILD-TYPE 137 161 152
'HNF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S81.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
HNF1B MUTATED 2 2 1
HNF1B WILD-TYPE 136 141 183
'HNF1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.62

Table S82.  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 S10.  Get High-res Image Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'HNF1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S83.  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 = 0.355 (Fisher's exact test), Q value = 1

Table S84.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
HNF1B MUTATED 1 2 0
HNF1B WILD-TYPE 63 82 100
'HNF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S85.  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 = 0.686 (Fisher's exact test), Q value = 1

Table S86.  Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
HNF1B MUTATED 0 2 2
HNF1B WILD-TYPE 97 157 124
'HNF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S87.  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 = 0.65 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
PTEN MUTATED 2 1 2
PTEN WILD-TYPE 174 174 112
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S89.  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 = 0.191 (Fisher's exact test), Q value = 1

Table S90.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
PTEN MUTATED 1 0 4
PTEN WILD-TYPE 133 139 188
'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S91.  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 = 0.281 (Fisher's exact test), Q value = 1

Table S92.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
PTEN MUTATED 2 3 0
PTEN WILD-TYPE 135 162 153
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S93.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
PTEN MUTATED 1 1 3
PTEN WILD-TYPE 137 142 181
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S94.  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 = 0.506 (Fisher's exact test), Q value = 1

Table S95.  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 = 0.786 (Fisher's exact test), Q value = 1

Table S96.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
PTEN MUTATED 0 1 2
PTEN WILD-TYPE 64 83 98
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S97.  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 = 0.687 (Fisher's exact test), Q value = 1

Table S98.  Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
PTEN MUTATED 0 2 2
PTEN WILD-TYPE 97 157 124
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S99.  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 = 0.192 (Fisher's exact test), Q value = 1

Table S100.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
LARP1 MUTATED 2 0 2
LARP1 WILD-TYPE 174 175 112
'LARP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.77

Table S101.  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 S11.  Get High-res Image Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'LARP1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S102.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
LARP1 MUTATED 1 0 3
LARP1 WILD-TYPE 133 139 189
'LARP1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S103.  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 = 1 (Fisher's exact test), Q value = 1

Table S104.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
LARP1 MUTATED 1 2 1
LARP1 WILD-TYPE 136 163 152
'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S105.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
LARP1 MUTATED 1 2 1
LARP1 WILD-TYPE 137 141 183
'LARP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S106.  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 = 0.24 (Fisher's exact test), Q value = 1

Table S107.  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 = 0.621 (Fisher's exact test), Q value = 1

Table S108.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
LARP1 MUTATED 0 1 2
LARP1 WILD-TYPE 97 158 124
'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S109.  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
'LARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S110.  Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
LARP1 MUTATED 0 1
LARP1 WILD-TYPE 9 4
'BRCA2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S111.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
BRCA2 MUTATED 6 4 3
BRCA2 WILD-TYPE 170 171 111
'BRCA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S112.  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 S113.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
BRCA2 MUTATED 4 4 5
BRCA2 WILD-TYPE 130 135 187
'BRCA2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.649 (Fisher's exact test), Q value = 1

Table S114.  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 = 0.357 (Fisher's exact test), Q value = 1

Table S115.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
BRCA2 MUTATED 5 6 2
BRCA2 WILD-TYPE 132 159 151
'BRCA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S116.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
BRCA2 MUTATED 6 2 5
BRCA2 WILD-TYPE 132 141 179
'BRCA2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S117.  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 S118.  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 S119.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
BRCA2 MUTATED 2 1 4
BRCA2 WILD-TYPE 62 83 96
'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S120.  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 = 0.817 (Fisher's exact test), Q value = 1

Table S121.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
BRCA2 MUTATED 3 4 5
BRCA2 WILD-TYPE 94 155 121
'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S122.  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
'BRCA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S123.  Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
BRCA2 MUTATED 0 1
BRCA2 WILD-TYPE 9 4
'EFEMP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S124.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
EFEMP1 MUTATED 3 3 1
EFEMP1 WILD-TYPE 173 172 113
'EFEMP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S125.  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 = 0.121 (Fisher's exact test), Q value = 1

Table S126.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
EFEMP1 MUTATED 0 4 3
EFEMP1 WILD-TYPE 134 135 189
'EFEMP1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 1

Table S127.  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 = 0.207 (Fisher's exact test), Q value = 1

Table S128.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
EFEMP1 MUTATED 0 4 3
EFEMP1 WILD-TYPE 137 161 150
'EFEMP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.77

Table S129.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
EFEMP1 MUTATED 1 0 6
EFEMP1 WILD-TYPE 137 143 178

Figure S12.  Get High-res Image Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EFEMP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 1

Table S130.  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 = 0.86 (Fisher's exact test), Q value = 1

Table S131.  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 = 0.709 (Fisher's exact test), Q value = 1

Table S132.  Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
EFEMP1 MUTATED 2 2 3
EFEMP1 WILD-TYPE 95 157 123
'EFEMP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S133.  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 = 0.838 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
NRAS MUTATED 1 2 1
NRAS WILD-TYPE 175 173 113
'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 1

Table S135.  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 = 0.566 (Fisher's exact test), Q value = 1

Table S136.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
NRAS MUTATED 0 2 2
NRAS WILD-TYPE 134 137 190
'NRAS MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S137.  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 = 0.465 (Fisher's exact test), Q value = 1

Table S138.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
NRAS MUTATED 2 2 0
NRAS WILD-TYPE 135 163 153
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S139.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
NRAS MUTATED 0 2 2
NRAS WILD-TYPE 138 141 182
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S140.  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 S141.  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 = 0.619 (Fisher's exact test), Q value = 1

Table S142.  Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
NRAS MUTATED 0 1 2
NRAS WILD-TYPE 97 158 124
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S143.  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 = 0.456 (Fisher's exact test), Q value = 1

Table S144.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
MTA2 MUTATED 3 1 0
MTA2 WILD-TYPE 173 174 114
'MTA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S145.  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 = 0.31 (Fisher's exact test), Q value = 1

Table S146.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
MTA2 MUTATED 1 0 3
MTA2 WILD-TYPE 133 139 189
'MTA2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S147.  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 = 0.403 (Fisher's exact test), Q value = 1

Table S148.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
MTA2 MUTATED 1 0 2
MTA2 WILD-TYPE 136 165 151
'MTA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S149.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
MTA2 MUTATED 2 0 2
MTA2 WILD-TYPE 136 143 182
'MTA2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S150.  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 = 0.656 (Fisher's exact test), Q value = 1

Table S151.  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
'MTA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S152.  Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
MTA2 MUTATED 1 0
MTA2 WILD-TYPE 8 5
'ERCC6 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S153.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
ERCC6 MUTATED 1 2 1
ERCC6 WILD-TYPE 175 173 113
'ERCC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S154.  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 = 0.104 (Fisher's exact test), Q value = 1

Table S155.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
ERCC6 MUTATED 1 3 0
ERCC6 WILD-TYPE 133 136 192
'ERCC6 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S156.  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 = 1 (Fisher's exact test), Q value = 1

Table S157.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
ERCC6 MUTATED 1 2 1
ERCC6 WILD-TYPE 136 163 152
'ERCC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S158.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
ERCC6 MUTATED 1 3 0
ERCC6 WILD-TYPE 137 140 184
'ERCC6 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S159.  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 S160.  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 = 0.573 (Fisher's exact test), Q value = 1

Table S161.  Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
ERCC6 MUTATED 2 1 1
ERCC6 WILD-TYPE 95 158 125
'ERCC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S162.  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 = 0.0451 (Fisher's exact test), Q value = 0.77

Table S163.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
IL21R MUTATED 0 5 3
IL21R WILD-TYPE 176 170 111

Figure S13.  Get High-res Image Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'IL21R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S164.  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 = 0.247 (Fisher's exact test), Q value = 1

Table S165.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
IL21R MUTATED 3 4 1
IL21R WILD-TYPE 131 135 191
'IL21R MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.7

Table S166.  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 S14.  Get High-res Image Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'IL21R MUTATION STATUS' versus 'CN_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S167.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
IL21R MUTATED 0 5 3
IL21R WILD-TYPE 137 160 150
'IL21R MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S168.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
IL21R MUTATED 0 3 5
IL21R WILD-TYPE 138 140 179
'IL21R MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S169.  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 = 0.117 (Fisher's exact test), Q value = 1

Table S170.  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 = 0.267 (Fisher's exact test), Q value = 1

Table S171.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
IL21R MUTATED 0 1 4
IL21R WILD-TYPE 64 83 96
'IL21R MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 1

Table S172.  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 = 0.733 (Fisher's exact test), Q value = 1

Table S173.  Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
IL21R MUTATED 2 2 1
IL21R WILD-TYPE 95 157 125
'IL21R MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174.  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 = 1 (Fisher's exact test), Q value = 1

Table S175.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
PKD1L1 MUTATED 3 2 1
PKD1L1 WILD-TYPE 173 173 113
'PKD1L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S176.  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 = 0.512 (Fisher's exact test), Q value = 1

Table S177.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
PKD1L1 MUTATED 3 1 2
PKD1L1 WILD-TYPE 131 138 190
'PKD1L1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S178.  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 = 0.17 (Fisher's exact test), Q value = 1

Table S179.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
PKD1L1 MUTATED 0 2 4
PKD1L1 WILD-TYPE 137 163 149
'PKD1L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.77

Table S180.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
PKD1L1 MUTATED 4 2 0
PKD1L1 WILD-TYPE 134 141 184

Figure S15.  Get High-res Image Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'PKD1L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S181.  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 S182.  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 = 0.828 (Fisher's exact test), Q value = 1

Table S183.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
PKD1L1 MUTATED 1 2 1
PKD1L1 WILD-TYPE 63 82 99
'PKD1L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S184.  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 = 0.387 (Fisher's exact test), Q value = 1

Table S185.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
PKD1L1 MUTATED 0 3 3
PKD1L1 WILD-TYPE 97 156 123
'PKD1L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S186.  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
'PKD1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S187.  Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
PKD1L1 MUTATED 1 0
PKD1L1 WILD-TYPE 8 5
'SAMD9L MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S188.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
SAMD9L MUTATED 3 3 3
SAMD9L WILD-TYPE 173 172 111
'SAMD9L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S189.  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 = 0.691 (Fisher's exact test), Q value = 1

Table S190.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
SAMD9L MUTATED 2 4 3
SAMD9L WILD-TYPE 132 135 189
'SAMD9L MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S191.  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 = 0.84 (Fisher's exact test), Q value = 1

Table S192.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
SAMD9L MUTATED 2 3 4
SAMD9L WILD-TYPE 135 162 149
'SAMD9L MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S193.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
SAMD9L MUTATED 3 3 3
SAMD9L WILD-TYPE 135 140 181
'SAMD9L MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.075 (Fisher's exact test), Q value = 0.98

Table S194.  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 = 0.397 (Fisher's exact test), Q value = 1

Table S195.  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 = 0.853 (Fisher's exact test), Q value = 1

Table S196.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
SAMD9L MUTATED 1 1 3
SAMD9L WILD-TYPE 63 83 97
'SAMD9L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S197.  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 = 1 (Fisher's exact test), Q value = 1

Table S198.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
SAMD9L MUTATED 2 3 2
SAMD9L WILD-TYPE 95 156 124
'SAMD9L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S199.  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
'SAMD9L MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S200.  Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 9 5
SAMD9L MUTATED 1 0
SAMD9L WILD-TYPE 8 5
'AQP2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S201.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
AQP2 MUTATED 1 0 2
AQP2 WILD-TYPE 175 175 112
'AQP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S202.  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 = 0.373 (Fisher's exact test), Q value = 1

Table S203.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
AQP2 MUTATED 2 0 1
AQP2 WILD-TYPE 132 139 191
'AQP2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S204.  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 = 0.404 (Fisher's exact test), Q value = 1

Table S205.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
AQP2 MUTATED 1 0 2
AQP2 WILD-TYPE 136 165 151
'AQP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S206.  Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
AQP2 MUTATED 2 0 1
AQP2 WILD-TYPE 136 143 183
'AQP2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S207.  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 S208.  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 = 0.592 (Fisher's exact test), Q value = 1

Table S209.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
CREBBP MUTATED 6 3 2
CREBBP WILD-TYPE 170 172 112
'CREBBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S210.  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 = 1 (Fisher's exact test), Q value = 1

Table S211.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
CREBBP MUTATED 3 3 5
CREBBP WILD-TYPE 131 136 187
'CREBBP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S212.  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 = 0.747 (Fisher's exact test), Q value = 1

Table S213.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
CREBBP MUTATED 3 3 5
CREBBP WILD-TYPE 134 162 148
'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S214.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
CREBBP MUTATED 4 2 5
CREBBP WILD-TYPE 134 141 179
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S215.  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 S216.  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 = 0.45 (Fisher's exact test), Q value = 1

Table S217.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 84 100
CREBBP MUTATED 0 2 3
CREBBP WILD-TYPE 64 82 97
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S218.  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 S219.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
CREBBP MUTATED 2 4 3
CREBBP WILD-TYPE 95 155 123
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S220.  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 = 0.00093 (Fisher's exact test), Q value = 0.27

Table S221.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
C9ORF171 MUTATED 0 0 5
C9ORF171 WILD-TYPE 176 175 109

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 = 0.00445 (Fisher's exact test), Q value = 0.62

Table S222.  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 = 0.397 (Fisher's exact test), Q value = 1

Table S223.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
C9ORF171 MUTATED 3 1 1
C9ORF171 WILD-TYPE 131 138 191
'C9ORF171 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S224.  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 = 0.864 (Fisher's exact test), Q value = 1

Table S225.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
C9ORF171 MUTATED 2 2 1
C9ORF171 WILD-TYPE 135 163 152
'C9ORF171 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.62

Table S226.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
C9ORF171 MUTATED 0 0 5
C9ORF171 WILD-TYPE 138 143 179

Figure S18.  Get High-res Image Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'C9ORF171 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S227.  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 S228.  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 = 0.3 (Fisher's exact test), Q value = 1

Table S229.  Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
C9ORF171 MUTATED 2 2 0
C9ORF171 WILD-TYPE 95 157 126
'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S230.  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 = 0.0939 (Fisher's exact test), Q value = 1

Table S231.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 175 114
NCOA3 MUTATED 0 4 1
NCOA3 WILD-TYPE 176 171 113
'NCOA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S232.  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 = 0.737 (Fisher's exact test), Q value = 1

Table S233.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 134 139 192
NCOA3 MUTATED 1 1 3
NCOA3 WILD-TYPE 133 138 189
'NCOA3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S234.  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 = 0.865 (Fisher's exact test), Q value = 1

Table S235.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 165 153
NCOA3 MUTATED 2 2 1
NCOA3 WILD-TYPE 135 163 152
'NCOA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S236.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 143 184
NCOA3 MUTATED 1 3 1
NCOA3 WILD-TYPE 137 140 183
'NCOA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237.  Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 159 126
NCOA3 MUTATED 1 4 0
NCOA3 WILD-TYPE 96 155 126
'NCOA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S238.  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/20020407/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/20141012/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.

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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