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 19 genes and 14 molecular subtypes across 316 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.

  • C9ORF171 mutation correlated to 'MRNA_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 19 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, one 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
C9ORF171 5 (2%) 311 0.00097
(0.205) 		0.00483
(1.00) 		0.395
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.0128
(1.00) 		0.394
(1.00) 		0.691
(1.00) 		0.381
(1.00) 		0.498
(1.00)
TP53 273 (86%) 43 0.956
(1.00) 		0.0874
(1.00) 		0.536
(1.00) 		0.919
(1.00) 		0.396
(1.00) 		0.936
(1.00) 		0.206
(1.00) 		0.226
(1.00) 		0.869
(1.00) 		0.413
(1.00) 		0.392
(1.00) 		0.578
(1.00)
BRCA1 12 (4%) 304 0.201
(1.00) 		0.424
(1.00) 		0.258
(1.00) 		0.385
(1.00) 		0.574
(1.00) 		0.296
(1.00) 		0.487
(1.00) 		0.193
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.718
(1.00) 		0.263
(1.00)
FAM86B2 6 (2%) 310 0.452
(1.00) 		0.443
(1.00) 		0.221
(1.00) 		0.586
(1.00) 		0.876
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.0681
(1.00) 		0.384
(1.00) 		0.704
(1.00)
TBP 4 (1%) 312 1
(1.00) 		1
(1.00) 		0.694
(1.00) 		0.0845
(1.00) 		0.0353
(1.00) 		0.0182
(1.00) 		0.131
(1.00) 		0.866
(1.00) 		1
(1.00) 		1
(1.00) 		0.69
(1.00) 		1
(1.00)
NBPF10 4 (1%) 312 0.838
(1.00) 		0.806
(1.00) 		0.235
(1.00) 		0.783
(1.00) 		0.844
(1.00) 		0.199
(1.00) 		0.527
(1.00) 		0.337
(1.00) 		0.102
(1.00) 		1
(1.00) 		0.82
(1.00) 		0.455
(1.00)
NF1 14 (4%) 302 0.373
(1.00) 		0.305
(1.00) 		0.838
(1.00) 		0.164
(1.00) 		0.485
(1.00) 		0.175
(1.00) 		0.112
(1.00) 		0.221
(1.00) 		0.435
(1.00) 		0.0316
(1.00) 		0.734
(1.00) 		0.531
(1.00) 		0.385
(1.00)
C10ORF140 5 (2%) 311 0.308
(1.00) 		0.0621
(1.00) 		0.867
(1.00) 		0.908
(1.00) 		0.375
(1.00) 		0.741
(1.00) 		0.591
(1.00) 		0.596
(1.00) 		0.134
(1.00) 		0.495
(1.00)
BRCA2 11 (3%) 305 0.467
(1.00) 		0.918
(1.00) 		0.927
(1.00) 		0.628
(1.00) 		0.639
(1.00) 		0.431
(1.00) 		0.669
(1.00) 		0.521
(1.00) 		0.237
(1.00) 		0.486
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.385
(1.00)
CDK12 8 (3%) 308 0.0624
(1.00) 		0.267
(1.00) 		0.309
(1.00) 		0.793
(1.00) 		0.823
(1.00) 		0.145
(1.00) 		0.598
(1.00) 		0.0412
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.508
(1.00) 		1
(1.00)
OR4F21 3 (1%) 313 0.632
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.901
(1.00) 		0.213
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.785
(1.00) 		0.694
(1.00)
HYDIN 11 (3%) 305 0.583
(1.00) 		0.0363
(1.00) 		0.212
(1.00) 		0.429
(1.00) 		0.551
(1.00) 		0.289
(1.00) 		0.847
(1.00) 		0.281
(1.00) 		1
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.69
(1.00)
RB1 8 (3%) 308 0.899
(1.00) 		0.231
(1.00) 		0.447
(1.00) 		0.439
(1.00) 		0.608
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.906
(1.00) 		0.604
(1.00) 		0.695
(1.00)
GART 3 (1%) 313 1
(1.00) 		0.57
(1.00) 		0.633
(1.00) 		0.383
(1.00) 		0.0681
(1.00) 		0.0579
(1.00)
SRC 4 (1%) 312 0.837
(1.00) 		1
(1.00) 		0.562
(1.00) 		0.248
(1.00) 		0.126
(1.00) 		0.464
(1.00) 		0.485
(1.00) 		0.609
(1.00) 		1
(1.00)
ZNF236 7 (2%) 309 1
(1.00) 		1
(1.00) 		0.802
(1.00) 		0.311
(1.00) 		0.461
(1.00) 		0.269
(1.00) 		0.311
(1.00) 		0.752
(1.00) 		0.216
(1.00) 		0.0246
(1.00)
NBPF16 4 (1%) 312 0.57
(1.00) 		1
(1.00) 		0.232
(1.00) 		0.0883
(1.00) 		0.276
(1.00) 		0.832
(1.00) 		0.411
(1.00) 		0.332
(1.00) 		0.178
(1.00) 		1
(1.00) 		0.227
(1.00) 		0.311
(1.00) 		1
(1.00)
CYP11B1 7 (2%) 309 0.0245
(1.00) 		0.361
(1.00) 		0.572
(1.00) 		0.319
(1.00) 		0.898
(1.00) 		0.209
(1.00) 		0.588
(1.00) 		0.151
(1.00) 		0.721
(1.00) 		1
(1.00) 		0.38
(1.00) 		0.868
(1.00)
SON 8 (3%) 308 0.39
(1.00) 		0.432
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.116
(1.00) 		0.0389
(1.00) 		0.137
(1.00) 		0.195
(1.00) 		0.468
(1.00) 		0.774
(1.00) 		0.772
(1.00) 		0.658
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.956 (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 119 115 82
TP53 MUTATED 103 100 70
TP53 WILD-TYPE 16 15 12
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0874 (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 173 94 49
TP53 MUTATED 156 77 40
TP53 WILD-TYPE 17 17 9
'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.536 (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 92 96 128
TP53 MUTATED 82 80 111
TP53 WILD-TYPE 10 16 17
'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.919 (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 51 28 33 53 20 44 20 16 21 30
TP53 MUTATED 43 25 28 47 19 37 18 14 16 26
TP53 WILD-TYPE 8 3 5 6 1 7 2 2 5 4
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.396 (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 108 102 101
TP53 MUTATED 92 92 85
TP53 WILD-TYPE 16 10 16
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.936 (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 90 105 121
TP53 MUTATED 79 90 104
TP53 WILD-TYPE 11 15 17
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.206 (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 76 96 38
TP53 MUTATED 63 88 33
TP53 WILD-TYPE 13 8 5
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.226 (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 67 48 64 31
TP53 MUTATED 54 44 57 29
TP53 WILD-TYPE 13 4 7 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.869 (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 70 40 51
TP53 MUTATED 60 36 45
TP53 WILD-TYPE 10 4 6
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.413 (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 66 76 19
TP53 MUTATED 58 68 15
TP53 WILD-TYPE 8 8 4
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.392 (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 79 119 89
TP53 MUTATED 65 106 78
TP53 WILD-TYPE 14 13 11
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.578 (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 74 46 99 68
TP53 MUTATED 64 38 85 62
TP53 WILD-TYPE 10 8 14 6
'BRCA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
BRCA1 MUTATED 4 7 1
BRCA1 WILD-TYPE 115 108 81
'BRCA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S14.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
BRCA1 MUTATED 7 2 3
BRCA1 WILD-TYPE 166 92 46
'BRCA1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
BRCA1 MUTATED 1 4 7
BRCA1 WILD-TYPE 91 92 121
'BRCA1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: '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 51 28 33 53 20 44 20 16 21 30
BRCA1 MUTATED 0 2 1 4 1 3 0 0 1 0
BRCA1 WILD-TYPE 51 26 32 49 19 41 20 16 20 30
'BRCA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
BRCA1 MUTATED 5 5 2
BRCA1 WILD-TYPE 103 97 99
'BRCA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
BRCA1 MUTATED 1 5 6
BRCA1 WILD-TYPE 89 100 115
'BRCA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.487 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
BRCA1 MUTATED 3 3 3
BRCA1 WILD-TYPE 73 93 35
'BRCA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S20.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
BRCA1 MUTATED 1 1 4 3
BRCA1 WILD-TYPE 66 47 60 28
'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S21.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
BRCA1 MUTATED 4 2 2
BRCA1 WILD-TYPE 66 38 49
'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
BRCA1 MUTATED 4 3 1
BRCA1 WILD-TYPE 62 73 18
'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S23.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
BRCA1 MUTATED 3 3 4
BRCA1 WILD-TYPE 76 116 85
'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S24.  Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
BRCA1 MUTATED 4 0 2 4
BRCA1 WILD-TYPE 70 46 97 64
'FAM86B2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S25.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
FAM86B2 MUTATED 2 1 3
FAM86B2 WILD-TYPE 117 114 79
'FAM86B2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
FAM86B2 MUTATED 2 3 1
FAM86B2 WILD-TYPE 171 91 48
'FAM86B2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
FAM86B2 MUTATED 3 0 3
FAM86B2 WILD-TYPE 89 96 125
'FAM86B2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'FAM86B2 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 51 28 33 53 20 44 20 16 21 30
FAM86B2 MUTATED 2 0 0 2 1 0 1 0 0 0
FAM86B2 WILD-TYPE 49 28 33 51 19 44 19 16 21 30
'FAM86B2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S29.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
FAM86B2 MUTATED 3 2 1
FAM86B2 WILD-TYPE 105 100 100
'FAM86B2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
FAM86B2 MUTATED 0 3 3
FAM86B2 WILD-TYPE 90 102 118
'FAM86B2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S31.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
FAM86B2 MUTATED 2 2 1
FAM86B2 WILD-TYPE 74 94 37
'FAM86B2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0681 (Fisher's exact test), Q value = 1

Table S32.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
FAM86B2 MUTATED 4 0 0 1
FAM86B2 WILD-TYPE 63 48 64 30
'FAM86B2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S33.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
FAM86B2 MUTATED 1 3 0
FAM86B2 WILD-TYPE 78 116 89
'FAM86B2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S34.  Gene #3: 'FAM86B2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
FAM86B2 MUTATED 1 1 2 0
FAM86B2 WILD-TYPE 73 45 97 68
'TBP MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
TBP MUTATED 2 1 1
TBP WILD-TYPE 117 114 81
'TBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S36.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
TBP MUTATED 3 1 0
TBP WILD-TYPE 170 93 49
'TBP MUTATION STATUS' versus 'MIR_CNMF'

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

Table S37.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
TBP MUTATED 2 1 1
TBP WILD-TYPE 90 95 127
'TBP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0845 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'TBP 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 51 28 33 53 20 44 20 16 21 30
TBP MUTATED 1 0 0 0 0 1 0 2 0 0
TBP WILD-TYPE 50 28 33 53 20 43 20 14 21 30
'TBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
TBP MUTATED 4 0 0
TBP WILD-TYPE 104 102 101

Figure S1.  Get High-res Image Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'TBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
TBP MUTATED 0 4 0
TBP WILD-TYPE 90 101 121

Figure S2.  Get High-res Image Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'TBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 1

Table S41.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
TBP MUTATED 3 0 0
TBP WILD-TYPE 73 96 38
'TBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
TBP MUTATED 2 0 1 0
TBP WILD-TYPE 65 48 63 31
'TBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
TBP MUTATED 1 1 1
TBP WILD-TYPE 69 39 50
'TBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S44.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
TBP MUTATED 1 2 0
TBP WILD-TYPE 65 74 19
'TBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
TBP MUTATED 2 1 1
TBP WILD-TYPE 77 118 88
'TBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46.  Gene #4: 'TBP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
TBP MUTATED 1 0 2 1
TBP WILD-TYPE 73 46 97 67
'NBPF10 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S47.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
NBPF10 MUTATED 1 2 1
NBPF10 WILD-TYPE 118 113 81
'NBPF10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.806 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
NBPF10 MUTATED 2 1 1
NBPF10 WILD-TYPE 171 93 48
'NBPF10 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S49.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
NBPF10 MUTATED 2 2 0
NBPF10 WILD-TYPE 90 94 128
'NBPF10 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S50.  Gene #5: 'NBPF10 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 51 28 33 53 20 44 20 16 21 30
NBPF10 MUTATED 2 1 0 0 0 1 0 0 0 0
NBPF10 WILD-TYPE 49 27 33 53 20 43 20 16 21 30
'NBPF10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S51.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
NBPF10 MUTATED 1 2 1
NBPF10 WILD-TYPE 107 100 100
'NBPF10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S52.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
NBPF10 MUTATED 2 2 0
NBPF10 WILD-TYPE 88 103 121
'NBPF10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
NBPF10 MUTATED 2 1 1
NBPF10 WILD-TYPE 74 95 37
'NBPF10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S54.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
NBPF10 MUTATED 1 2 0 1
NBPF10 WILD-TYPE 66 46 64 30
'NBPF10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S55.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
NBPF10 MUTATED 0 2 1
NBPF10 WILD-TYPE 70 38 50
'NBPF10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S56.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
NBPF10 MUTATED 1 2 0
NBPF10 WILD-TYPE 65 74 19
'NBPF10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S57.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
NBPF10 MUTATED 1 1 2
NBPF10 WILD-TYPE 78 118 87
'NBPF10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #5: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
NBPF10 MUTATED 0 0 2 2
NBPF10 WILD-TYPE 74 46 97 66
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S59.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
NF1 MUTATED 4 4 6
NF1 WILD-TYPE 115 111 76
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
NF1 MUTATED 6 7 1
NF1 WILD-TYPE 167 87 48
'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S61.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
NF1 MUTATED 3 5 6
NF1 WILD-TYPE 89 91 122
'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S62.  Gene #6: '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 51 28 33 53 20 44 20 16 21 30
NF1 MUTATED 3 0 0 1 0 4 0 2 1 3
NF1 WILD-TYPE 48 28 33 52 20 40 20 14 20 27
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 1

Table S63.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
NF1 MUTATED 7 4 3
NF1 WILD-TYPE 101 98 98
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S64.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
NF1 MUTATED 1 6 7
NF1 WILD-TYPE 89 99 114
'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S65.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
NF1 MUTATED 4 1 3
NF1 WILD-TYPE 72 95 35
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S66.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
NF1 MUTATED 5 0 2 1
NF1 WILD-TYPE 62 48 62 30
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S67.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
NF1 MUTATED 4 0 2
NF1 WILD-TYPE 66 40 49
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 1

Table S68.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
NF1 MUTATED 5 0 1
NF1 WILD-TYPE 61 76 18

Figure S3.  Get High-res Image Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 1

Table S69.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
NF1 MUTATED 4 7 3
NF1 WILD-TYPE 75 112 86
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S70.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
NF1 MUTATED 6 1 4 3
NF1 WILD-TYPE 68 45 95 65
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S71.  Gene #6: 'NF1 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 8 5
NF1 MUTATED 0 1
NF1 WILD-TYPE 8 4
'C10ORF140 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S72.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
C10ORF140 MUTATED 1 1 3
C10ORF140 WILD-TYPE 118 114 79
'C10ORF140 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0621 (Fisher's exact test), Q value = 1

Table S73.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
C10ORF140 MUTATED 1 4 0
C10ORF140 WILD-TYPE 172 90 49
'C10ORF140 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S74.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
C10ORF140 MUTATED 2 1 2
C10ORF140 WILD-TYPE 90 95 126
'C10ORF140 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S75.  Gene #7: 'C10ORF140 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 51 28 33 53 20 44 20 16 21 30
C10ORF140 MUTATED 2 0 0 1 0 2 0 0 0 0
C10ORF140 WILD-TYPE 49 28 33 52 20 42 20 16 21 30
'C10ORF140 MUTATION STATUS' versus 'CN_CNMF'

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

Table S76.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
C10ORF140 MUTATED 3 2 0
C10ORF140 WILD-TYPE 105 100 101
'C10ORF140 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S77.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
C10ORF140 MUTATED 1 1 3
C10ORF140 WILD-TYPE 89 104 118
'C10ORF140 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
C10ORF140 MUTATED 2 1 0
C10ORF140 WILD-TYPE 74 95 38
'C10ORF140 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S79.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
C10ORF140 MUTATED 2 1 0 0
C10ORF140 WILD-TYPE 65 47 64 31
'C10ORF140 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
C10ORF140 MUTATED 3 1 0
C10ORF140 WILD-TYPE 76 118 89
'C10ORF140 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S81.  Gene #7: 'C10ORF140 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
C10ORF140 MUTATED 1 0 3 0
C10ORF140 WILD-TYPE 73 46 96 68
'BRCA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S82.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
BRCA2 MUTATED 5 2 4
BRCA2 WILD-TYPE 114 113 78
'BRCA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S83.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
BRCA2 MUTATED 7 3 1
BRCA2 WILD-TYPE 166 91 48
'BRCA2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S84.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
BRCA2 MUTATED 3 4 4
BRCA2 WILD-TYPE 89 92 124
'BRCA2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S85.  Gene #8: '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 51 28 33 53 20 44 20 16 21 30
BRCA2 MUTATED 3 1 0 1 0 2 2 1 0 1
BRCA2 WILD-TYPE 48 27 33 52 20 42 18 15 21 29
'BRCA2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S86.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
BRCA2 MUTATED 5 4 2
BRCA2 WILD-TYPE 103 98 99
'BRCA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S87.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
BRCA2 MUTATED 5 2 4
BRCA2 WILD-TYPE 85 103 117
'BRCA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.669 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
BRCA2 MUTATED 1 3 0
BRCA2 WILD-TYPE 75 93 38
'BRCA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S89.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
BRCA2 MUTATED 2 1 0 1
BRCA2 WILD-TYPE 65 47 64 30
'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S90.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
BRCA2 MUTATED 4 2 0
BRCA2 WILD-TYPE 66 38 51
'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S91.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
BRCA2 MUTATED 4 2 0
BRCA2 WILD-TYPE 62 74 19
'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S92.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
BRCA2 MUTATED 3 4 3
BRCA2 WILD-TYPE 76 115 86
'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S93.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
BRCA2 MUTATED 4 2 3 1
BRCA2 WILD-TYPE 70 44 96 67
'BRCA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S94.  Gene #8: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 8 5
BRCA2 MUTATED 0 1
BRCA2 WILD-TYPE 8 4
'CDK12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0624 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
CDK12 MUTATED 2 6 0
CDK12 WILD-TYPE 117 109 82
'CDK12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
CDK12 MUTATED 7 1 0
CDK12 WILD-TYPE 166 93 49
'CDK12 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S97.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
CDK12 MUTATED 4 1 3
CDK12 WILD-TYPE 88 95 125
'CDK12 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S98.  Gene #9: '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 51 28 33 53 20 44 20 16 21 30
CDK12 MUTATED 3 0 0 2 0 1 0 1 0 1
CDK12 WILD-TYPE 48 28 33 51 20 43 20 15 21 29
'CDK12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S99.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
CDK12 MUTATED 2 3 3
CDK12 WILD-TYPE 106 99 98
'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S100.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
CDK12 MUTATED 1 1 6
CDK12 WILD-TYPE 89 104 115
'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S101.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
CDK12 MUTATED 3 2 0
CDK12 WILD-TYPE 73 94 38
'CDK12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 1

Table S102.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
CDK12 MUTATED 1 0 1 3
CDK12 WILD-TYPE 66 48 63 28

Figure S4.  Get High-res Image Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S103.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
CDK12 MUTATED 3 1 0
CDK12 WILD-TYPE 67 39 51
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S104.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
CDK12 MUTATED 2 2 0
CDK12 WILD-TYPE 64 74 19
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S105.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
CDK12 MUTATED 1 4 3
CDK12 WILD-TYPE 78 115 86
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S106.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
CDK12 MUTATED 3 2 1 2
CDK12 WILD-TYPE 71 44 98 66
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S107.  Gene #9: 'CDK12 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 8 5
CDK12 MUTATED 1 0
CDK12 WILD-TYPE 7 5
'OR4F21 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S108.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
OR4F21 MUTATED 1 2 0
OR4F21 WILD-TYPE 118 113 82
'OR4F21 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S109.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
OR4F21 MUTATED 2 1 0
OR4F21 WILD-TYPE 171 93 49
'OR4F21 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
OR4F21 MUTATED 1 0 2
OR4F21 WILD-TYPE 91 96 126
'OR4F21 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S111.  Gene #10: 'OR4F21 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 51 28 33 53 20 44 20 16 21 30
OR4F21 MUTATED 1 0 0 2 0 0 0 0 0 0
OR4F21 WILD-TYPE 50 28 33 51 20 44 20 16 21 30
'OR4F21 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S112.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
OR4F21 MUTATED 0 1 2
OR4F21 WILD-TYPE 108 101 99
'OR4F21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 1

Table S113.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
OR4F21 MUTATED 1 0 2
OR4F21 WILD-TYPE 89 105 119
'OR4F21 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S114.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
OR4F21 MUTATED 1 2 0
OR4F21 WILD-TYPE 75 94 38
'OR4F21 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S115.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
OR4F21 MUTATED 0 0 2 1
OR4F21 WILD-TYPE 67 48 62 30
'OR4F21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S116.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
OR4F21 MUTATED 0 2 1
OR4F21 WILD-TYPE 79 117 88
'OR4F21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S117.  Gene #10: 'OR4F21 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
OR4F21 MUTATED 0 0 2 1
OR4F21 WILD-TYPE 74 46 97 67
'C9ORF171 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.2

Table S118.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
C9ORF171 MUTATED 0 0 5
C9ORF171 WILD-TYPE 119 115 77

Figure S5.  Get High-res Image Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'C9ORF171 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 1

Table S119.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
C9ORF171 MUTATED 0 5 0
C9ORF171 WILD-TYPE 173 89 49

Figure S6.  Get High-res Image Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'C9ORF171 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S120.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
C9ORF171 MUTATED 3 1 1
C9ORF171 WILD-TYPE 89 95 127
'C9ORF171 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S121.  Gene #11: '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 51 28 33 53 20 44 20 16 21 30
C9ORF171 MUTATED 1 0 0 1 2 0 0 0 0 1
C9ORF171 WILD-TYPE 50 28 33 52 18 44 20 16 21 29
'C9ORF171 MUTATION STATUS' versus 'CN_CNMF'

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

Table S122.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
C9ORF171 MUTATED 2 2 1
C9ORF171 WILD-TYPE 106 100 100
'C9ORF171 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S123.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
C9ORF171 MUTATED 0 0 5
C9ORF171 WILD-TYPE 90 105 116

Figure S7.  Get High-res Image Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'C9ORF171 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S124.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
C9ORF171 MUTATED 3 1 0
C9ORF171 WILD-TYPE 73 95 38
'C9ORF171 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S125.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
C9ORF171 MUTATED 2 0 2 0
C9ORF171 WILD-TYPE 65 48 62 31
'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S126.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
C9ORF171 MUTATED 2 2 0
C9ORF171 WILD-TYPE 77 117 89
'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S127.  Gene #11: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
C9ORF171 MUTATED 1 0 3 0
C9ORF171 WILD-TYPE 73 46 96 68
'HYDIN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S128.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
HYDIN MUTATED 6 3 2
HYDIN WILD-TYPE 113 112 80
'HYDIN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 1

Table S129.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
HYDIN MUTATED 4 2 5
HYDIN WILD-TYPE 169 92 44

Figure S8.  Get High-res Image Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'HYDIN MUTATION STATUS' versus 'MIR_CNMF'

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

Table S130.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
HYDIN MUTATED 1 3 7
HYDIN WILD-TYPE 91 93 121
'HYDIN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 1

Table S131.  Gene #12: 'HYDIN 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 51 28 33 53 20 44 20 16 21 30
HYDIN MUTATED 0 0 2 3 0 2 2 0 1 1
HYDIN WILD-TYPE 51 28 31 50 20 42 18 16 20 29
'HYDIN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S132.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
HYDIN MUTATED 4 5 2
HYDIN WILD-TYPE 104 97 99
'HYDIN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S133.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
HYDIN MUTATED 5 4 2
HYDIN WILD-TYPE 85 101 119
'HYDIN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S134.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
HYDIN MUTATED 1 3 1
HYDIN WILD-TYPE 75 93 37
'HYDIN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S135.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
HYDIN MUTATED 1 0 2 2
HYDIN WILD-TYPE 66 48 62 29
'HYDIN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S136.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
HYDIN MUTATED 1 1 1
HYDIN WILD-TYPE 69 39 50
'HYDIN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S137.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
HYDIN MUTATED 1 2 0
HYDIN WILD-TYPE 65 74 19
'HYDIN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S138.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
HYDIN MUTATED 3 5 2
HYDIN WILD-TYPE 76 114 87
'HYDIN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S139.  Gene #12: 'HYDIN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
HYDIN MUTATED 2 2 5 1
HYDIN WILD-TYPE 72 44 94 67
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.899 (Fisher's exact test), Q value = 1

Table S140.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
RB1 MUTATED 4 2 2
RB1 WILD-TYPE 115 113 80
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S141.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
RB1 MUTATED 3 2 3
RB1 WILD-TYPE 170 92 46
'RB1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S142.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
RB1 MUTATED 2 1 5
RB1 WILD-TYPE 90 95 123
'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S143.  Gene #13: '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 51 28 33 53 20 44 20 16 21 30
RB1 MUTATED 0 1 0 2 1 1 1 1 1 0
RB1 WILD-TYPE 51 27 33 51 19 43 19 15 20 30
'RB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S144.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
RB1 MUTATED 2 2 4
RB1 WILD-TYPE 106 100 97
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S145.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
RB1 MUTATED 4 3 1
RB1 WILD-TYPE 86 102 120
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S146.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
RB1 MUTATED 3 3 1
RB1 WILD-TYPE 73 93 37
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S147.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
RB1 MUTATED 2 1 3 1
RB1 WILD-TYPE 65 47 61 30
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 1

Table S148.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
RB1 MUTATED 1 5 2
RB1 WILD-TYPE 78 114 87
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S149.  Gene #13: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
RB1 MUTATED 3 0 3 2
RB1 WILD-TYPE 71 46 96 66
'GART MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S150.  Gene #14: 'GART MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
GART MUTATED 1 1 1
GART WILD-TYPE 118 114 81
'GART MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S151.  Gene #14: 'GART MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
GART MUTATED 1 1 1
GART WILD-TYPE 172 93 48
'GART MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S152.  Gene #14: 'GART MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
GART MUTATED 1 0 2
GART WILD-TYPE 91 96 126
'GART MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 1

Table S153.  Gene #14: 'GART 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 51 28 33 53 20 44 20 16 21 30
GART MUTATED 0 0 0 2 1 0 0 0 0 0
GART WILD-TYPE 51 28 33 51 19 44 20 16 21 30
'GART MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0681 (Fisher's exact test), Q value = 1

Table S154.  Gene #14: 'GART MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
GART MUTATED 0 3 0
GART WILD-TYPE 108 99 101
'GART MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0579 (Fisher's exact test), Q value = 1

Table S155.  Gene #14: 'GART MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
GART MUTATED 0 3 0
GART WILD-TYPE 90 102 121
'SRC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S156.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
SRC MUTATED 1 2 1
SRC WILD-TYPE 118 113 81
'SRC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S157.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
SRC MUTATED 3 1 0
SRC WILD-TYPE 170 93 49
'SRC MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S158.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
SRC MUTATED 0 2 2
SRC WILD-TYPE 92 94 126
'SRC MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S159.  Gene #15: 'SRC 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 51 28 33 53 20 44 20 16 21 30
SRC MUTATED 0 1 0 0 0 1 0 0 0 2
SRC WILD-TYPE 51 27 33 53 20 43 20 16 21 28
'SRC MUTATION STATUS' versus 'CN_CNMF'

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

Table S160.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
SRC MUTATED 0 3 1
SRC WILD-TYPE 108 99 100
'SRC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S161.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
SRC MUTATED 0 1 3
SRC WILD-TYPE 90 104 118
'SRC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 1

Table S162.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
SRC MUTATED 0 1 2
SRC WILD-TYPE 79 118 87
'SRC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S163.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
SRC MUTATED 0 1 1 1
SRC WILD-TYPE 74 45 98 67
'SRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S164.  Gene #15: 'SRC MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 8 5
SRC MUTATED 1 0
SRC WILD-TYPE 7 5
'ZNF236 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S165.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
ZNF236 MUTATED 3 2 2
ZNF236 WILD-TYPE 116 113 80
'ZNF236 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S166.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
ZNF236 MUTATED 4 2 1
ZNF236 WILD-TYPE 169 92 48
'ZNF236 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S167.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
ZNF236 MUTATED 3 2 2
ZNF236 WILD-TYPE 89 94 126
'ZNF236 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S168.  Gene #16: 'ZNF236 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 51 28 33 53 20 44 20 16 21 30
ZNF236 MUTATED 0 2 0 1 1 2 1 0 0 0
ZNF236 WILD-TYPE 51 26 33 52 19 42 19 16 21 30
'ZNF236 MUTATION STATUS' versus 'CN_CNMF'

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

Table S169.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
ZNF236 MUTATED 4 1 2
ZNF236 WILD-TYPE 104 101 99
'ZNF236 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
ZNF236 MUTATED 1 1 5
ZNF236 WILD-TYPE 89 104 116
'ZNF236 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S171.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
ZNF236 MUTATED 0 3 1
ZNF236 WILD-TYPE 76 93 37
'ZNF236 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S172.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
ZNF236 MUTATED 1 2 1 0
ZNF236 WILD-TYPE 66 46 63 31
'ZNF236 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S173.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
ZNF236 MUTATED 1 1 4
ZNF236 WILD-TYPE 78 118 85
'ZNF236 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S174.  Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
ZNF236 MUTATED 2 0 0 4
ZNF236 WILD-TYPE 72 46 99 64

Figure S9.  Get High-res Image Gene #16: 'ZNF236 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'NBPF16 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S175.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
NBPF16 MUTATED 1 1 2
NBPF16 WILD-TYPE 118 114 80
'NBPF16 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S176.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
NBPF16 MUTATED 3 1 0
NBPF16 WILD-TYPE 170 93 49
'NBPF16 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S177.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
NBPF16 MUTATED 2 2 0
NBPF16 WILD-TYPE 90 94 128
'NBPF16 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0883 (Fisher's exact test), Q value = 1

Table S178.  Gene #17: 'NBPF16 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 51 28 33 53 20 44 20 16 21 30
NBPF16 MUTATED 0 0 1 0 2 1 0 0 0 0
NBPF16 WILD-TYPE 51 28 32 53 18 43 20 16 21 30
'NBPF16 MUTATION STATUS' versus 'CN_CNMF'

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

Table S179.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
NBPF16 MUTATED 3 0 1
NBPF16 WILD-TYPE 105 102 100
'NBPF16 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S180.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
NBPF16 MUTATED 1 2 1
NBPF16 WILD-TYPE 89 103 120
'NBPF16 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S181.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
NBPF16 MUTATED 0 2 1
NBPF16 WILD-TYPE 76 94 37
'NBPF16 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S182.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
NBPF16 MUTATED 1 2 0 0
NBPF16 WILD-TYPE 66 46 64 31
'NBPF16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S183.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
NBPF16 MUTATED 0 1 2
NBPF16 WILD-TYPE 70 39 49
'NBPF16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S184.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
NBPF16 MUTATED 1 2 0
NBPF16 WILD-TYPE 65 74 19
'NBPF16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S185.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
NBPF16 MUTATED 0 1 3
NBPF16 WILD-TYPE 79 118 86
'NBPF16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S186.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
NBPF16 MUTATED 1 1 0 2
NBPF16 WILD-TYPE 73 45 99 66
'NBPF16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S187.  Gene #17: 'NBPF16 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 8 5
NBPF16 MUTATED 1 0
NBPF16 WILD-TYPE 7 5
'CYP11B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 1

Table S188.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
CYP11B1 MUTATED 1 6 0
CYP11B1 WILD-TYPE 118 109 82

Figure S10.  Get High-res Image Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CYP11B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 1

Table S189.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
CYP11B1 MUTATED 6 1 0
CYP11B1 WILD-TYPE 167 93 49
'CYP11B1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S190.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
CYP11B1 MUTATED 2 1 4
CYP11B1 WILD-TYPE 90 95 124
'CYP11B1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S191.  Gene #18: 'CYP11B1 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 51 28 33 53 20 44 20 16 21 30
CYP11B1 MUTATED 1 0 0 1 0 1 0 1 0 3
CYP11B1 WILD-TYPE 50 28 33 52 20 43 20 15 21 27
'CYP11B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S192.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
CYP11B1 MUTATED 2 3 2
CYP11B1 WILD-TYPE 106 99 99
'CYP11B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 1

Table S193.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
CYP11B1 MUTATED 0 3 4
CYP11B1 WILD-TYPE 90 102 117
'CYP11B1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S194.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
CYP11B1 MUTATED 2 1 0
CYP11B1 WILD-TYPE 74 95 38
'CYP11B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S195.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
CYP11B1 MUTATED 3 0 0 0
CYP11B1 WILD-TYPE 64 48 64 31
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S196.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
CYP11B1 MUTATED 2 2 1
CYP11B1 WILD-TYPE 68 38 50
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S197.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
CYP11B1 MUTATED 2 3 0
CYP11B1 WILD-TYPE 64 73 19
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S198.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
CYP11B1 MUTATED 1 5 1
CYP11B1 WILD-TYPE 78 114 88
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S199.  Gene #18: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
CYP11B1 MUTATED 3 1 2 1
CYP11B1 WILD-TYPE 71 45 97 67
'SON MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S200.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
SON MUTATED 4 1 3
SON WILD-TYPE 115 114 79
'SON MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S201.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 94 49
SON MUTATED 3 3 2
SON WILD-TYPE 170 91 47
'SON MUTATION STATUS' versus 'MIR_CNMF'

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

Table S202.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
SON MUTATED 2 3 3
SON WILD-TYPE 90 93 125
'SON MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S203.  Gene #19: 'SON 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 51 28 33 53 20 44 20 16 21 30
SON MUTATED 2 0 1 1 0 2 2 0 0 0
SON WILD-TYPE 49 28 32 52 20 42 18 16 21 30
'SON MUTATION STATUS' versus 'CN_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S204.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 102 101
SON MUTATED 6 1 1
SON WILD-TYPE 102 101 100
'SON MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 1

Table S205.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
SON MUTATED 4 4 0
SON WILD-TYPE 86 101 121

Figure S11.  Get High-res Image Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'SON MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S206.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
SON MUTATED 0 2 2
SON WILD-TYPE 76 94 36
'SON MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S207.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 48 64 31
SON MUTATED 1 0 1 2
SON WILD-TYPE 66 48 63 29
'SON MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S208.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
SON MUTATED 1 2 1
SON WILD-TYPE 69 38 50
'SON MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S209.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 76 19
SON MUTATED 1 3 0
SON WILD-TYPE 65 73 19
'SON MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S210.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
SON MUTATED 2 3 1
SON WILD-TYPE 77 116 88
'SON MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S211.  Gene #19: 'SON MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 46 99 68
SON MUTATED 3 0 2 1
SON WILD-TYPE 71 46 97 67
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = OV-TP.transferedmergedcluster.txt

  • Number of patients = 316

  • Number of significantly mutated genes = 19

  • 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)
Made with Nozzle