Correlation between gene mutation status and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M61JRK
Overview
Introduction

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

Summary

Testing the association between mutation status of 36 genes and 10 molecular subtypes across 492 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

  • BRAF mutation correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NRAS mutation correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • EIF1AX mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • LMTK2 mutation correlated to 'CN_CNMF'.

  • TG mutation correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • AKT1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • ZC3H11A mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 36 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 36 significant findings detected.

Clinical
Features
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
HRAS 16 (3%) 476 0.00032
(0.0048)
1e-05
(0.000157)
0.00509
(0.0611)
0.00767
(0.0891)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
BRAF 290 (59%) 202 0.944
(1.00)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
NRAS 40 (8%) 452 0.211
(0.987)
1e-05
(0.000157)
0.139
(0.807)
0.0104
(0.116)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
1e-05
(0.000157)
TG 20 (4%) 472 0.0965
(0.685)
0.0154
(0.154)
0.0135
(0.139)
0.826
(1.00)
0.0415
(0.355)
0.0337
(0.303)
0.0304
(0.28)
0.00043
(0.00619)
0.00129
(0.0172)
0.00121
(0.0168)
EIF1AX 7 (1%) 485 0.136
(0.807)
0.273
(0.987)
0.457
(1.00)
0.3
(1.00)
0.0345
(0.303)
0.0113
(0.12)
0.177
(0.939)
0.136
(0.807)
0.0549
(0.451)
0.029
(0.28)
LMTK2 4 (1%) 488 0.0107
(0.116)
1
(1.00)
0.902
(1.00)
0.72
(1.00)
0.824
(1.00)
0.835
(1.00)
0.506
(1.00)
0.62
(1.00)
AKT1 5 (1%) 487 0.0297
(0.28)
0.161
(0.892)
0.122
(0.771)
0.00241
(0.031)
0.223
(0.987)
0.452
(1.00)
0.538
(1.00)
0.455
(1.00)
ZC3H11A 3 (1%) 489 0.102
(0.695)
0.341
(1.00)
0.101
(0.695)
0.00371
(0.0461)
0.68
(1.00)
0.627
(1.00)
0.504
(1.00)
0.622
(1.00)
NUDT11 10 (2%) 482 0.713
(1.00)
0.826
(1.00)
0.934
(1.00)
0.703
(1.00)
0.438
(1.00)
0.977
(1.00)
0.863
(1.00)
1
(1.00)
1
(1.00)
0.913
(1.00)
RPTN 10 (2%) 482 0.925
(1.00)
0.599
(1.00)
0.486
(1.00)
1
(1.00)
0.549
(1.00)
0.679
(1.00)
0.152
(0.857)
1
(1.00)
0.681
(1.00)
0.849
(1.00)
EMG1 11 (2%) 481 0.308
(1.00)
0.181
(0.943)
0.0753
(0.59)
0.0551
(0.451)
0.282
(0.987)
0.212
(0.987)
0.107
(0.716)
1
(1.00)
1
(1.00)
0.924
(1.00)
FAM47C 14 (3%) 478 0.281
(0.987)
0.923
(1.00)
1
(1.00)
0.454
(1.00)
0.653
(1.00)
0.282
(0.987)
0.097
(0.685)
0.196
(0.982)
0.468
(1.00)
0.31
(1.00)
DLX6 7 (1%) 485 0.796
(1.00)
0.508
(1.00)
0.912
(1.00)
0.924
(1.00)
0.0926
(0.685)
1
(1.00)
0.28
(0.987)
0.0835
(0.64)
GPR44 4 (1%) 488 0.701
(1.00)
0.437
(1.00)
0.808
(1.00)
0.12
(0.771)
0.164
(0.896)
0.379
(1.00)
0.177
(0.939)
0.374
(1.00)
TMEM184A 5 (1%) 487 0.457
(1.00)
0.894
(1.00)
1
(1.00)
0.904
(1.00)
1
(1.00)
0.638
(1.00)
0.907
(1.00)
0.831
(1.00)
NUP93 4 (1%) 488 0.588
(1.00)
0.733
(1.00)
0.458
(1.00)
0.566
(1.00)
0.748
(1.00)
1
(1.00)
0.592
(1.00)
1
(1.00)
GAGE2A 4 (1%) 488 0.814
(1.00)
0.651
(1.00)
1
(1.00)
0.483
(1.00)
0.747
(1.00)
0.305
(1.00)
0.215
(0.987)
0.479
(1.00)
ABL1 5 (1%) 487 0.225
(0.987)
0.687
(1.00)
0.225
(0.987)
0.335
(1.00)
0.442
(1.00)
0.374
(1.00)
0.339
(1.00)
0.744
(1.00)
0.794
(1.00)
0.57
(1.00)
SRPX 4 (1%) 488 0.294
(1.00)
0.853
(1.00)
0.605
(1.00)
0.808
(1.00)
0.905
(1.00)
0.571
(1.00)
0.623
(1.00)
0.355
(1.00)
PPM1D 6 (1%) 486 0.385
(1.00)
0.394
(1.00)
0.272
(0.987)
0.64
(1.00)
0.482
(1.00)
0.251
(0.987)
0.582
(1.00)
0.251
(0.987)
0.489
(1.00)
1
(1.00)
PTCD1 3 (1%) 489 1
(1.00)
1
(1.00)
0.558
(1.00)
0.708
(1.00)
0.746
(1.00)
0.472
(1.00)
0.228
(0.987)
0.362
(1.00)
0.627
(1.00)
0.357
(1.00)
TSC22D1 4 (1%) 488 0.39
(1.00)
0.0961
(0.685)
1
(1.00)
0.664
(1.00)
0.905
(1.00)
0.564
(1.00)
1
(1.00)
1
(1.00)
ZNF878 3 (1%) 489 0.458
(1.00)
0.214
(0.987)
0.28
(0.987)
0.143
(0.819)
1
(1.00)
1
(1.00)
1
(1.00)
RBM10 4 (1%) 488 0.7
(1.00)
0.535
(1.00)
0.81
(1.00)
1
(1.00)
0.745
(1.00)
1
(1.00)
0.738
(1.00)
1
(1.00)
EP400 3 (1%) 489 1
(1.00)
0.071
(0.568)
0.137
(0.807)
0.234
(0.987)
0.676
(1.00)
0.624
(1.00)
0.261
(0.987)
0.626
(1.00)
ABCD1 4 (1%) 488 0.7
(1.00)
0.921
(1.00)
1
(1.00)
0.876
(1.00)
0.269
(0.987)
1
(1.00)
0.219
(0.987)
0.244
(0.987)
MYH10 4 (1%) 488 0.699
(1.00)
0.502
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.138
(0.807)
0.266
(0.987)
0.828
(1.00)
NLRP6 4 (1%) 488 0.7
(1.00)
0.793
(1.00)
0.739
(1.00)
0.481
(1.00)
0.367
(1.00)
0.303
(1.00)
0.541
(1.00)
0.31
(1.00)
IGSF3 4 (1%) 488 0.388
(1.00)
0.921
(1.00)
1
(1.00)
0.665
(1.00)
0.27
(0.987)
0.245
(0.987)
0.239
(0.987)
0.243
(0.987)
PRMT8 3 (1%) 489 0.255
(0.987)
0.885
(1.00)
0.425
(1.00)
0.876
(1.00)
0.859
(1.00)
0.362
(1.00)
0.626
(1.00)
0.357
(1.00)
ARMCX3 3 (1%) 489 0.622
(1.00)
0.885
(1.00)
0.648
(1.00)
0.875
(1.00)
0.111
(0.728)
0.479
(1.00)
RYR1 7 (1%) 485 0.213
(0.987)
0.419
(1.00)
0.953
(1.00)
1
(1.00)
0.834
(1.00)
0.898
(1.00)
0.782
(1.00)
0.801
(1.00)
TNRC18 4 (1%) 488 0.59
(1.00)
0.694
(1.00)
0.603
(1.00)
0.346
(1.00)
0.622
(1.00)
0.834
(1.00)
0.897
(1.00)
0.361
(1.00)
TMEM90B 3 (1%) 489 0.622
(1.00)
0.885
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.898
(1.00)
1
(1.00)
RANBP9 3 (1%) 489 0.623
(1.00)
0.684
(1.00)
0.494
(1.00)
0.259
(0.987)
0.677
(1.00)
0.626
(1.00)
0.259
(0.987)
0.623
(1.00)
DGCR8 3 (1%) 489 0.776
(1.00)
0.323
(1.00)
0.415
(1.00)
0.645
(1.00)
0.719
(1.00)
0.597
(1.00)
0.187
(0.95)
0.898
(1.00)
0.187
(0.95)
'BRAF MUTATION STATUS' versus 'CN_CNMF'

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

Table S1.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
BRAF MUTATED 79 80 129
BRAF WILD-TYPE 52 57 91
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S2.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
BRAF MUTATED 41 14 49 40 146
BRAF WILD-TYPE 5 130 35 0 32

Figure S1.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S3.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
BRAF MUTATED 20 43 9 46
BRAF WILD-TYPE 43 18 31 5

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

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S4.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
BRAF MUTATED 4 22 29 5 38 12 8
BRAF WILD-TYPE 42 5 2 21 11 15 1

Figure S3.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S5.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
BRAF MUTATED 143 21 34 92
BRAF WILD-TYPE 11 143 24 22

Figure S4.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S6.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
BRAF MUTATED 100 4 47 73 66
BRAF WILD-TYPE 3 127 38 22 10

Figure S5.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S7.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
BRAF MUTATED 123 13 100 53
BRAF WILD-TYPE 40 130 19 13

Figure S6.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S8.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
BRAF MUTATED 136 3 150
BRAF WILD-TYPE 40 122 40

Figure S7.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S9.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
BRAF MUTATED 95 10 88 84
BRAF WILD-TYPE 34 112 18 21

Figure S8.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S10.  Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
BRAF MUTATED 120 3 154
BRAF WILD-TYPE 40 115 30

Figure S9.  Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.99

Table S11.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
NRAS MUTATED 15 9 14
NRAS WILD-TYPE 116 128 206
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S12.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
NRAS MUTATED 0 40 0 0 0
NRAS WILD-TYPE 46 104 84 40 178

Figure S10.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.81

Table S13.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
NRAS MUTATED 5 5 3 0
NRAS WILD-TYPE 58 56 37 51
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
NRAS MUTATED 4 1 0 3 0 5 0
NRAS WILD-TYPE 42 26 31 23 49 22 9

Figure S11.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S15.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
NRAS MUTATED 0 40 0 0
NRAS WILD-TYPE 154 124 58 114

Figure S12.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S16.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
NRAS MUTATED 0 40 0 0 0
NRAS WILD-TYPE 103 91 85 95 76

Figure S13.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S17.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
NRAS MUTATED 1 38 0 1
NRAS WILD-TYPE 162 105 119 65

Figure S14.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S18.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
NRAS MUTATED 1 39 0
NRAS WILD-TYPE 175 86 190

Figure S15.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S19.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
NRAS MUTATED 2 36 0 0
NRAS WILD-TYPE 127 86 106 105

Figure S16.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S20.  Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
NRAS MUTATED 1 37 0
NRAS WILD-TYPE 159 81 184

Figure S17.  Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0048

Table S21.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
HRAS MUTATED 11 0 5
HRAS WILD-TYPE 120 137 215

Figure S18.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S22.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
HRAS MUTATED 0 16 0 0 0
HRAS WILD-TYPE 46 128 84 40 178

Figure S19.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.061

Table S23.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
HRAS MUTATED 8 1 1 0
HRAS WILD-TYPE 55 60 39 51

Figure S20.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.089

Table S24.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
HRAS MUTATED 7 0 0 2 0 1 0
HRAS WILD-TYPE 39 27 31 24 49 26 9

Figure S21.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S25.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
HRAS MUTATED 0 16 0 0
HRAS WILD-TYPE 154 148 58 114

Figure S22.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S26.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
HRAS MUTATED 0 16 0 0 0
HRAS WILD-TYPE 103 115 85 95 76

Figure S23.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S27.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
HRAS MUTATED 0 16 0 0
HRAS WILD-TYPE 163 127 119 66

Figure S24.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S28.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
HRAS MUTATED 0 16 0
HRAS WILD-TYPE 176 109 190

Figure S25.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S29.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
HRAS MUTATED 0 14 0 0
HRAS WILD-TYPE 129 108 106 105

Figure S26.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S30.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
HRAS MUTATED 0 14 0
HRAS WILD-TYPE 160 104 184

Figure S27.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
NUDT11 MUTATED 2 4 4
NUDT11 WILD-TYPE 129 133 216
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
NUDT11 MUTATED 1 2 1 1 5
NUDT11 WILD-TYPE 45 142 83 39 173
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
NUDT11 MUTATED 1 2 1 1
NUDT11 WILD-TYPE 62 59 39 50
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
NUDT11 MUTATED 1 0 1 0 1 2 0
NUDT11 WILD-TYPE 45 27 30 26 48 25 9
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
NUDT11 MUTATED 4 2 0 4
NUDT11 WILD-TYPE 150 162 58 110
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.977 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
NUDT11 MUTATED 2 2 2 2 2
NUDT11 WILD-TYPE 101 129 83 93 74
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
NUDT11 MUTATED 4 2 2 2
NUDT11 WILD-TYPE 159 141 117 64
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S38.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
NUDT11 MUTATED 4 2 4
NUDT11 WILD-TYPE 172 123 186
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
NUDT11 MUTATED 3 2 2 2
NUDT11 WILD-TYPE 126 120 104 103
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
NUDT11 MUTATED 4 2 3
NUDT11 WILD-TYPE 156 116 181
'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.925 (Fisher's exact test), Q value = 1

Table S41.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
RPTN MUTATED 3 3 4
RPTN WILD-TYPE 128 134 216
'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
RPTN MUTATED 1 3 1 2 3
RPTN WILD-TYPE 45 141 83 38 175
'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S43.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
RPTN MUTATED 2 0 0 1
RPTN WILD-TYPE 61 61 40 50
'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S44.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
RPTN MUTATED 1 0 1 0 1 0 0
RPTN WILD-TYPE 45 27 30 26 48 27 9
'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S45.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
RPTN MUTATED 3 2 1 4
RPTN WILD-TYPE 151 162 57 110
'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S46.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
RPTN MUTATED 2 2 1 4 1
RPTN WILD-TYPE 101 129 84 91 75
'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.86

Table S47.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
RPTN MUTATED 2 1 4 3
RPTN WILD-TYPE 161 142 115 63
'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S48.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
RPTN MUTATED 4 2 4
RPTN WILD-TYPE 172 123 186
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S49.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
RPTN MUTATED 2 2 2 4
RPTN WILD-TYPE 127 120 104 101
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'RPTN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
RPTN MUTATED 3 2 5
RPTN WILD-TYPE 157 116 179
'EMG1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S51.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
EMG1 MUTATED 3 1 7
EMG1 WILD-TYPE 128 136 213
'EMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.94

Table S52.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
EMG1 MUTATED 3 3 0 1 4
EMG1 WILD-TYPE 43 141 84 39 174
'EMG1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0753 (Fisher's exact test), Q value = 0.59

Table S53.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
EMG1 MUTATED 0 3 0 3
EMG1 WILD-TYPE 63 58 40 48
'EMG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0551 (Fisher's exact test), Q value = 0.45

Table S54.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
EMG1 MUTATED 0 0 3 0 2 0 1
EMG1 WILD-TYPE 46 27 28 26 47 27 8
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.99

Table S55.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
EMG1 MUTATED 6 3 0 1
EMG1 WILD-TYPE 148 161 58 113
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.99

Table S56.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
EMG1 MUTATED 5 3 0 1 1
EMG1 WILD-TYPE 98 128 85 94 75
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.72

Table S57.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
EMG1 MUTATED 2 4 1 4
EMG1 WILD-TYPE 161 139 118 62
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
EMG1 MUTATED 4 3 4
EMG1 WILD-TYPE 172 122 186
'EMG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S59.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
EMG1 MUTATED 3 3 2 2
EMG1 WILD-TYPE 126 119 104 103
'EMG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
EMG1 MUTATED 3 3 4
EMG1 WILD-TYPE 157 115 180
'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.99

Table S61.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
FAM47C MUTATED 6 4 4
FAM47C WILD-TYPE 125 133 216
'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
FAM47C MUTATED 1 5 1 1 6
FAM47C WILD-TYPE 45 139 83 39 172
'FAM47C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
FAM47C MUTATED 2 1 1 1
FAM47C WILD-TYPE 61 60 39 50
'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S64.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
FAM47C MUTATED 1 1 0 1 1 0 1
FAM47C WILD-TYPE 45 26 31 25 48 27 8
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S65.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
FAM47C MUTATED 5 5 0 4
FAM47C WILD-TYPE 149 159 58 110
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.99

Table S66.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
FAM47C MUTATED 4 5 0 4 1
FAM47C WILD-TYPE 99 126 85 91 75
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.097 (Fisher's exact test), Q value = 0.68

Table S67.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
FAM47C MUTATED 1 5 6 2
FAM47C WILD-TYPE 162 138 113 64
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.98

Table S68.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
FAM47C MUTATED 2 5 7
FAM47C WILD-TYPE 174 120 183
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S69.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
FAM47C MUTATED 2 4 2 5
FAM47C WILD-TYPE 127 118 104 100
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S70.  Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
FAM47C MUTATED 2 4 7
FAM47C WILD-TYPE 158 114 177
'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.81

Table S71.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
EIF1AX MUTATED 0 4 3
EIF1AX WILD-TYPE 131 133 217
'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.99

Table S72.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
EIF1AX MUTATED 0 5 1 0 1
EIF1AX WILD-TYPE 46 139 83 40 177
'EIF1AX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S73.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
EIF1AX MUTATED 2 1 2 0
EIF1AX WILD-TYPE 61 60 38 51
'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
EIF1AX MUTATED 3 0 0 1 0 1 0
EIF1AX WILD-TYPE 43 27 31 25 49 26 9
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.3

Table S75.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
EIF1AX MUTATED 0 6 0 1
EIF1AX WILD-TYPE 154 158 58 113

Figure S28.  Get High-res Image Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.12

Table S76.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
EIF1AX MUTATED 0 6 1 0 0
EIF1AX WILD-TYPE 103 125 84 95 76

Figure S29.  Get High-res Image Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.94

Table S77.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
EIF1AX MUTATED 1 5 1 0
EIF1AX WILD-TYPE 162 138 118 66
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.81

Table S78.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
EIF1AX MUTATED 2 4 1
EIF1AX WILD-TYPE 174 121 189
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0549 (Fisher's exact test), Q value = 0.45

Table S79.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
EIF1AX MUTATED 1 5 0 1
EIF1AX WILD-TYPE 128 117 106 104
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.28

Table S80.  Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
EIF1AX MUTATED 1 5 1
EIF1AX WILD-TYPE 159 113 183

Figure S30.  Get High-res Image Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'DLX6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
DLX6 MUTATED 2 1 4
DLX6 WILD-TYPE 129 136 216
'DLX6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
DLX6 MUTATED 0 2 0 0 5
DLX6 WILD-TYPE 46 142 84 40 173
'DLX6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
DLX6 MUTATED 2 3 0 2
DLX6 WILD-TYPE 152 161 58 112
'DLX6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
DLX6 MUTATED 1 2 1 1 2
DLX6 WILD-TYPE 102 129 84 94 74
'DLX6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0926 (Fisher's exact test), Q value = 0.68

Table S85.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
DLX6 MUTATED 0 2 3 2
DLX6 WILD-TYPE 163 141 116 64
'DLX6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S86.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
DLX6 MUTATED 2 2 3
DLX6 WILD-TYPE 174 123 187
'DLX6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.99

Table S87.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
DLX6 MUTATED 0 2 2 3
DLX6 WILD-TYPE 129 120 104 102
'DLX6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0835 (Fisher's exact test), Q value = 0.64

Table S88.  Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
DLX6 MUTATED 0 2 5
DLX6 WILD-TYPE 160 116 179
'GPR44 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S89.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
GPR44 MUTATED 2 1 1
GPR44 WILD-TYPE 129 136 219
'GPR44 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S90.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
GPR44 MUTATED 0 2 0 1 1
GPR44 WILD-TYPE 46 142 84 39 177
'GPR44 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
GPR44 MUTATED 1 1 1 1
GPR44 WILD-TYPE 153 163 57 113
'GPR44 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.77

Table S92.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
GPR44 MUTATED 0 0 1 1 2
GPR44 WILD-TYPE 103 131 84 94 74
'GPR44 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.9

Table S93.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
GPR44 MUTATED 3 0 0 1
GPR44 WILD-TYPE 160 143 119 65
'GPR44 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S94.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
GPR44 MUTATED 3 0 1
GPR44 WILD-TYPE 173 125 189
'GPR44 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.94

Table S95.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
GPR44 MUTATED 3 0 1 0
GPR44 WILD-TYPE 126 122 105 105
'GPR44 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
GPR44 MUTATED 3 0 1
GPR44 WILD-TYPE 157 118 183
'TMEM184A MUTATION STATUS' versus 'CN_CNMF'

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

Table S97.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
TMEM184A MUTATED 2 0 3
TMEM184A WILD-TYPE 129 137 217
'TMEM184A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S98.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
TMEM184A MUTATED 0 2 0 0 3
TMEM184A WILD-TYPE 46 142 84 40 175
'TMEM184A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S99.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
TMEM184A MUTATED 2 2 0 1
TMEM184A WILD-TYPE 152 162 58 113
'TMEM184A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S100.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
TMEM184A MUTATED 1 2 1 0 1
TMEM184A WILD-TYPE 102 129 84 95 75
'TMEM184A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S101.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
TMEM184A MUTATED 2 2 1 0
TMEM184A WILD-TYPE 161 141 118 66
'TMEM184A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
TMEM184A MUTATED 2 2 1
TMEM184A WILD-TYPE 174 123 189
'TMEM184A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S103.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
TMEM184A MUTATED 2 1 1 0
TMEM184A WILD-TYPE 127 121 105 105
'TMEM184A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S104.  Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
TMEM184A MUTATED 2 1 1
TMEM184A WILD-TYPE 158 117 183
'NUP93 MUTATION STATUS' versus 'CN_CNMF'

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

Table S105.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
NUP93 MUTATED 0 1 3
NUP93 WILD-TYPE 131 136 217
'NUP93 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S106.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
NUP93 MUTATED 1 1 0 0 2
NUP93 WILD-TYPE 45 143 84 40 176
'NUP93 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S107.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
NUP93 MUTATED 3 1 0 0
NUP93 WILD-TYPE 151 163 58 114
'NUP93 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S108.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
NUP93 MUTATED 2 1 0 0 1
NUP93 WILD-TYPE 101 130 85 95 75
'NUP93 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

Table S109.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
NUP93 MUTATED 1 1 2 0
NUP93 WILD-TYPE 162 142 117 66
'NUP93 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S110.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
NUP93 MUTATED 1 1 2
NUP93 WILD-TYPE 175 124 188
'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
NUP93 MUTATED 1 1 0 2
NUP93 WILD-TYPE 128 121 106 103
'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S112.  Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
NUP93 MUTATED 1 1 2
NUP93 WILD-TYPE 159 117 182
'GAGE2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 1

Table S113.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
GAGE2A MUTATED 1 2 1
GAGE2A WILD-TYPE 130 135 219
'GAGE2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S114.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
GAGE2A MUTATED 0 1 0 1 2
GAGE2A WILD-TYPE 46 143 84 39 176
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
GAGE2A MUTATED 1 2 0 1
GAGE2A WILD-TYPE 153 162 58 113
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S116.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
GAGE2A MUTATED 0 1 0 2 1
GAGE2A WILD-TYPE 103 130 85 93 75
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
GAGE2A MUTATED 1 1 2 0
GAGE2A WILD-TYPE 162 142 117 66
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
GAGE2A MUTATED 0 1 3
GAGE2A WILD-TYPE 176 124 187
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.99

Table S119.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
GAGE2A MUTATED 0 1 2 0
GAGE2A WILD-TYPE 129 121 104 105
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S120.  Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
GAGE2A MUTATED 0 1 2
GAGE2A WILD-TYPE 160 117 182
'ABL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.99

Table S121.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
ABL1 MUTATED 3 1 1
ABL1 WILD-TYPE 128 136 219
'ABL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S122.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
ABL1 MUTATED 0 3 1 0 1
ABL1 WILD-TYPE 46 141 83 40 177
'ABL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.99

Table S123.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
ABL1 MUTATED 0 2 1 0
ABL1 WILD-TYPE 63 59 39 51
'ABL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
ABL1 MUTATED 0 0 1 1 0 1 0
ABL1 WILD-TYPE 46 27 30 25 49 26 9
'ABL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S125.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
ABL1 MUTATED 1 3 1 0
ABL1 WILD-TYPE 153 161 57 114
'ABL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S126.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
ABL1 MUTATED 0 3 1 0 1
ABL1 WILD-TYPE 103 128 84 95 75
'ABL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S127.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
ABL1 MUTATED 1 3 0 1
ABL1 WILD-TYPE 162 140 119 65
'ABL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S128.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
ABL1 MUTATED 1 2 2
ABL1 WILD-TYPE 175 123 188
'ABL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S129.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
ABL1 MUTATED 1 2 1 0
ABL1 WILD-TYPE 128 120 105 105
'ABL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S130.  Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
ABL1 MUTATED 1 2 1
ABL1 WILD-TYPE 159 116 183
'LMTK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.12

Table S131.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
LMTK2 MUTATED 0 4 0
LMTK2 WILD-TYPE 131 133 220

Figure S31.  Get High-res Image Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'LMTK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S132.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
LMTK2 MUTATED 0 1 1 0 2
LMTK2 WILD-TYPE 46 143 83 40 176
'LMTK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S133.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
LMTK2 MUTATED 2 1 0 1
LMTK2 WILD-TYPE 152 163 58 113
'LMTK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S134.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
LMTK2 MUTATED 2 1 0 1 0
LMTK2 WILD-TYPE 101 130 85 94 76
'LMTK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S135.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
LMTK2 MUTATED 1 1 1 1
LMTK2 WILD-TYPE 162 142 118 65
'LMTK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S136.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
LMTK2 MUTATED 2 1 1
LMTK2 WILD-TYPE 174 124 189
'LMTK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S137.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
LMTK2 MUTATED 2 0 1 0
LMTK2 WILD-TYPE 127 122 105 105
'LMTK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S138.  Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
LMTK2 MUTATED 2 0 1
LMTK2 WILD-TYPE 158 118 183
'SRPX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 1

Table S139.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
SRPX MUTATED 2 0 2
SRPX WILD-TYPE 129 137 218
'SRPX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S140.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
SRPX MUTATED 0 2 1 0 1
SRPX WILD-TYPE 46 142 83 40 177
'SRPX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S141.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
SRPX MUTATED 1 2 1 0
SRPX WILD-TYPE 153 162 57 114
'SRPX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S142.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
SRPX MUTATED 1 2 1 0 0
SRPX WILD-TYPE 102 129 84 95 76
'SRPX MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S143.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
SRPX MUTATED 1 2 1 0
SRPX WILD-TYPE 162 141 118 66
'SRPX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S144.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
SRPX MUTATED 1 2 1
SRPX WILD-TYPE 175 123 189
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S145.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
SRPX MUTATED 2 1 0 0
SRPX WILD-TYPE 127 121 106 105
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S146.  Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
SRPX MUTATED 2 1 0
SRPX WILD-TYPE 158 117 184
'PPM1D MUTATION STATUS' versus 'CN_CNMF'

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

Table S147.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
PPM1D MUTATED 2 0 4
PPM1D WILD-TYPE 129 137 216
'PPM1D MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S148.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
PPM1D MUTATED 0 1 0 1 4
PPM1D WILD-TYPE 46 143 84 39 174
'PPM1D MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.99

Table S149.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
PPM1D MUTATED 0 1 0 2
PPM1D WILD-TYPE 63 60 40 49
'PPM1D MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S150.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
PPM1D MUTATED 0 0 1 0 2 0 0
PPM1D WILD-TYPE 46 27 30 26 47 27 9
'PPM1D MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S151.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
PPM1D MUTATED 2 1 0 3
PPM1D WILD-TYPE 152 163 58 111
'PPM1D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.99

Table S152.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
PPM1D MUTATED 1 0 1 3 1
PPM1D WILD-TYPE 102 131 84 92 75
'PPM1D MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S153.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
PPM1D MUTATED 2 1 3 0
PPM1D WILD-TYPE 161 142 116 66
'PPM1D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.99

Table S154.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
PPM1D MUTATED 2 0 4
PPM1D WILD-TYPE 174 125 186
'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S155.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
PPM1D MUTATED 2 0 2 2
PPM1D WILD-TYPE 127 122 104 103
'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S156.  Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
PPM1D MUTATED 2 1 3
PPM1D WILD-TYPE 158 117 181
'TG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0965 (Fisher's exact test), Q value = 0.68

Table S157.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
TG MUTATED 4 10 6
TG WILD-TYPE 127 127 214
'TG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.15

Table S158.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
TG MUTATED 1 12 0 0 7
TG WILD-TYPE 45 132 84 40 171

Figure S32.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.14

Table S159.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
TG MUTATED 1 4 5 0
TG WILD-TYPE 62 57 35 51

Figure S33.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S160.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
TG MUTATED 2 0 2 2 2 2 0
TG WILD-TYPE 44 27 29 24 47 25 9
'TG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.36

Table S161.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
TG MUTATED 4 13 1 2
TG WILD-TYPE 150 151 57 112

Figure S34.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.3

Table S162.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
TG MUTATED 3 12 1 2 2
TG WILD-TYPE 100 119 84 93 74

Figure S35.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.28

Table S163.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
TG MUTATED 2 11 4 3
TG WILD-TYPE 161 132 115 63

Figure S36.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0062

Table S164.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
TG MUTATED 1 12 7
TG WILD-TYPE 175 113 183

Figure S37.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.017

Table S165.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
TG MUTATED 0 11 4 3
TG WILD-TYPE 129 111 102 102

Figure S38.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.017

Table S166.  Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
TG MUTATED 1 11 6
TG WILD-TYPE 159 107 178

Figure S39.  Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTCD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S167.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
PTCD1 MUTATED 1 1 1
PTCD1 WILD-TYPE 130 136 219
'PTCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S168.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
PTCD1 MUTATED 0 1 0 0 2
PTCD1 WILD-TYPE 46 143 84 40 176
'PTCD1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S169.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
PTCD1 MUTATED 1 2 0 0
PTCD1 WILD-TYPE 62 59 40 51
'PTCD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S170.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
PTCD1 MUTATED 1 0 1 0 0 1 0
PTCD1 WILD-TYPE 45 27 30 26 49 26 9
'PTCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S171.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
PTCD1 MUTATED 2 1 0 0
PTCD1 WILD-TYPE 152 163 58 114
'PTCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S172.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
PTCD1 MUTATED 2 1 0 0 0
PTCD1 WILD-TYPE 101 130 85 95 76
'PTCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.99

Table S173.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
PTCD1 MUTATED 2 0 0 1
PTCD1 WILD-TYPE 161 143 119 65
'PTCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
PTCD1 MUTATED 2 1 0
PTCD1 WILD-TYPE 174 124 190
'PTCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S175.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
PTCD1 MUTATED 2 1 0 0
PTCD1 WILD-TYPE 127 121 106 105
'PTCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S176.  Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
PTCD1 MUTATED 2 1 0
PTCD1 WILD-TYPE 158 117 184
'TSC22D1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S177.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
TSC22D1 MUTATED 0 2 2
TSC22D1 WILD-TYPE 131 135 218
'TSC22D1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0961 (Fisher's exact test), Q value = 0.68

Table S178.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
TSC22D1 MUTATED 1 2 0 1 0
TSC22D1 WILD-TYPE 45 142 84 39 178
'TSC22D1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S179.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
TSC22D1 MUTATED 1 2 0 1
TSC22D1 WILD-TYPE 153 162 58 113
'TSC22D1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 1

Table S180.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
TSC22D1 MUTATED 0 2 0 1 1
TSC22D1 WILD-TYPE 103 129 85 94 75
'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S181.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
TSC22D1 MUTATED 1 2 1 0
TSC22D1 WILD-TYPE 162 141 118 66
'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S182.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
TSC22D1 MUTATED 1 2 1
TSC22D1 WILD-TYPE 175 123 189
'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S183.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
TSC22D1 MUTATED 1 1 1 0
TSC22D1 WILD-TYPE 128 121 105 105
'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S184.  Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
TSC22D1 MUTATED 1 1 1
TSC22D1 WILD-TYPE 159 117 183
'AKT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.28

Table S185.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
AKT1 MUTATED 4 0 1
AKT1 WILD-TYPE 127 137 219

Figure S40.  Get High-res Image Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'AKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 0.89

Table S186.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
AKT1 MUTATED 0 0 0 1 4
AKT1 WILD-TYPE 46 144 84 39 174
'AKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.77

Table S187.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
AKT1 MUTATED 4 0 0 1
AKT1 WILD-TYPE 150 164 58 113
'AKT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.031

Table S188.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
AKT1 MUTATED 1 0 0 0 4
AKT1 WILD-TYPE 102 131 85 95 72

Figure S41.  Get High-res Image Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AKT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.99

Table S189.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
AKT1 MUTATED 2 0 3 0
AKT1 WILD-TYPE 161 143 116 66
'AKT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S190.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
AKT1 MUTATED 2 0 3
AKT1 WILD-TYPE 174 125 187
'AKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S191.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
AKT1 MUTATED 2 0 1 2
AKT1 WILD-TYPE 127 122 105 103
'AKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S192.  Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
AKT1 MUTATED 2 0 3
AKT1 WILD-TYPE 158 118 181
'ZNF878 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S193.  Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
ZNF878 MUTATED 0 2 1 0 0
ZNF878 WILD-TYPE 46 142 83 40 178
'ZNF878 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.99

Table S194.  Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
ZNF878 MUTATED 0 2 1 0
ZNF878 WILD-TYPE 154 162 57 114
'ZNF878 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.99

Table S195.  Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
ZNF878 MUTATED 0 1 2 0 0
ZNF878 WILD-TYPE 103 130 83 95 76
'ZNF878 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.82

Table S196.  Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
ZNF878 MUTATED 0 2 0 1
ZNF878 WILD-TYPE 163 141 119 65
'ZNF878 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S197.  Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
ZNF878 MUTATED 1 1 1
ZNF878 WILD-TYPE 175 124 189
'ZNF878 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S198.  Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
ZNF878 MUTATED 1 1 1 0
ZNF878 WILD-TYPE 128 121 105 105
'ZNF878 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S199.  Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
ZNF878 MUTATED 1 1 1
ZNF878 WILD-TYPE 159 117 183
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S200.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
RBM10 MUTATED 2 1 1
RBM10 WILD-TYPE 129 136 219
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S201.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
RBM10 MUTATED 0 1 1 1 1
RBM10 WILD-TYPE 46 143 83 39 177
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S202.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
RBM10 MUTATED 1 1 1 1
RBM10 WILD-TYPE 153 163 57 113
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S203.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
RBM10 MUTATED 1 1 1 1 0
RBM10 WILD-TYPE 102 130 84 94 76
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S204.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
RBM10 MUTATED 1 1 2 0
RBM10 WILD-TYPE 162 142 117 66
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S205.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
RBM10 MUTATED 1 1 2
RBM10 WILD-TYPE 175 124 188
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S206.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
RBM10 MUTATED 1 2 0 1
RBM10 WILD-TYPE 128 120 106 104
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S207.  Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
RBM10 MUTATED 1 1 2
RBM10 WILD-TYPE 159 117 182
'EP400 MUTATION STATUS' versus 'CN_CNMF'

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

Table S208.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
EP400 MUTATED 1 1 1
EP400 WILD-TYPE 130 136 219
'EP400 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.071 (Fisher's exact test), Q value = 0.57

Table S209.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
EP400 MUTATED 2 0 0 0 1
EP400 WILD-TYPE 44 144 84 40 177
'EP400 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.81

Table S210.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
EP400 MUTATED 2 0 1 0
EP400 WILD-TYPE 152 164 57 114
'EP400 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 0.99

Table S211.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
EP400 MUTATED 2 0 1 0 0
EP400 WILD-TYPE 101 131 84 95 76
'EP400 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S212.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
EP400 MUTATED 2 0 1 0
EP400 WILD-TYPE 161 143 118 66
'EP400 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S213.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
EP400 MUTATED 2 0 1
EP400 WILD-TYPE 174 125 189
'EP400 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.99

Table S214.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
EP400 MUTATED 1 0 0 2
EP400 WILD-TYPE 128 122 106 103
'EP400 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S215.  Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
EP400 MUTATED 2 0 1
EP400 WILD-TYPE 158 118 183
'ABCD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S216.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
ABCD1 MUTATED 2 1 1
ABCD1 WILD-TYPE 129 136 219
'ABCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S217.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
ABCD1 MUTATED 0 2 0 0 2
ABCD1 WILD-TYPE 46 142 84 40 176
'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S218.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
ABCD1 MUTATED 1 2 0 1
ABCD1 WILD-TYPE 153 162 58 113
'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S219.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
ABCD1 MUTATED 1 2 0 1 0
ABCD1 WILD-TYPE 102 129 85 94 76
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.99

Table S220.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
ABCD1 MUTATED 0 2 2 0
ABCD1 WILD-TYPE 163 141 117 66
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S221.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
ABCD1 MUTATED 1 1 2
ABCD1 WILD-TYPE 175 124 188
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.99

Table S222.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
ABCD1 MUTATED 0 2 0 2
ABCD1 WILD-TYPE 129 120 106 103
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 0.99

Table S223.  Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
ABCD1 MUTATED 0 2 2
ABCD1 WILD-TYPE 160 116 182
'MYH10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S224.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
MYH10 MUTATED 2 1 1
MYH10 WILD-TYPE 129 136 219
'MYH10 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S225.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
MYH10 MUTATED 1 2 0 0 1
MYH10 WILD-TYPE 45 142 84 40 177
'MYH10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S226.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
MYH10 MUTATED 1 2 0 1
MYH10 WILD-TYPE 153 162 58 113
'MYH10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S227.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
MYH10 MUTATED 1 1 1 1 0
MYH10 WILD-TYPE 102 130 84 94 76
'MYH10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S228.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
MYH10 MUTATED 2 1 1 0
MYH10 WILD-TYPE 161 142 118 66
'MYH10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.81

Table S229.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
MYH10 MUTATED 3 1 0
MYH10 WILD-TYPE 173 124 190
'MYH10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.99

Table S230.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
MYH10 MUTATED 3 1 0 0
MYH10 WILD-TYPE 126 121 106 105
'MYH10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S231.  Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
MYH10 MUTATED 2 1 1
MYH10 WILD-TYPE 158 117 183
'NLRP6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S232.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
NLRP6 MUTATED 2 1 1
NLRP6 WILD-TYPE 129 136 219
'NLRP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S233.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
NLRP6 MUTATED 0 1 0 0 3
NLRP6 WILD-TYPE 46 143 84 40 175
'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S234.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
NLRP6 MUTATED 1 1 0 2
NLRP6 WILD-TYPE 153 163 58 112
'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S235.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
NLRP6 MUTATED 0 1 0 2 1
NLRP6 WILD-TYPE 103 130 85 93 75
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S236.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
NLRP6 MUTATED 0 2 1 1
NLRP6 WILD-TYPE 163 141 118 65
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S237.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
NLRP6 MUTATED 0 1 3
NLRP6 WILD-TYPE 176 124 187
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S238.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
NLRP6 MUTATED 0 2 1 1
NLRP6 WILD-TYPE 129 120 105 104
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S239.  Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
NLRP6 MUTATED 0 1 3
NLRP6 WILD-TYPE 160 117 181
'IGSF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S240.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
IGSF3 MUTATED 0 2 2
IGSF3 WILD-TYPE 131 135 218
'IGSF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S241.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
IGSF3 MUTATED 0 2 0 0 2
IGSF3 WILD-TYPE 46 142 84 40 176
'IGSF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S242.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
IGSF3 MUTATED 1 2 0 1
IGSF3 WILD-TYPE 153 162 58 113
'IGSF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S243.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
IGSF3 MUTATED 0 2 0 1 1
IGSF3 WILD-TYPE 103 129 85 94 75
'IGSF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.99

Table S244.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
IGSF3 MUTATED 0 2 2 0
IGSF3 WILD-TYPE 163 141 117 66
'IGSF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 0.99

Table S245.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
IGSF3 MUTATED 0 2 2
IGSF3 WILD-TYPE 176 123 188
'IGSF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.99

Table S246.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
IGSF3 MUTATED 0 2 2 0
IGSF3 WILD-TYPE 129 120 104 105
'IGSF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 0.99

Table S247.  Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
IGSF3 MUTATED 0 2 2
IGSF3 WILD-TYPE 160 116 182
'PRMT8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.99

Table S248.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
PRMT8 MUTATED 0 0 3
PRMT8 WILD-TYPE 131 137 217
'PRMT8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S249.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
PRMT8 MUTATED 0 1 1 0 1
PRMT8 WILD-TYPE 46 143 83 40 177
'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S250.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
PRMT8 MUTATED 0 1 1 1
PRMT8 WILD-TYPE 154 163 57 113
'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S251.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
PRMT8 MUTATED 0 1 1 1 0
PRMT8 WILD-TYPE 103 130 84 94 76
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S252.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
PRMT8 MUTATED 2 1 0 0
PRMT8 WILD-TYPE 161 142 119 66
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S253.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
PRMT8 MUTATED 2 1 0
PRMT8 WILD-TYPE 174 124 190
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S254.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
PRMT8 MUTATED 2 1 0 0
PRMT8 WILD-TYPE 127 121 106 105
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S255.  Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
PRMT8 MUTATED 2 1 0
PRMT8 WILD-TYPE 158 117 184
'ARMCX3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S256.  Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
ARMCX3 MUTATED 1 0 2
ARMCX3 WILD-TYPE 130 137 218
'ARMCX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S257.  Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
ARMCX3 MUTATED 0 1 1 0 1
ARMCX3 WILD-TYPE 46 143 83 40 177
'ARMCX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S258.  Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
ARMCX3 MUTATED 0 2 0 1
ARMCX3 WILD-TYPE 154 162 58 113
'ARMCX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S259.  Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
ARMCX3 MUTATED 0 1 1 1 0
ARMCX3 WILD-TYPE 103 130 84 94 76
'ARMCX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.73

Table S260.  Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
ARMCX3 MUTATED 0 3 0 0
ARMCX3 WILD-TYPE 163 140 119 66
'ARMCX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S261.  Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
ARMCX3 MUTATED 0 1 2
ARMCX3 WILD-TYPE 176 124 188
'RYR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.99

Table S262.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
RYR1 MUTATED 3 0 4
RYR1 WILD-TYPE 128 137 216
'RYR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S263.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
RYR1 MUTATED 1 2 2 1 1
RYR1 WILD-TYPE 45 142 82 39 177
'RYR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.953 (Fisher's exact test), Q value = 1

Table S264.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
RYR1 MUTATED 2 3 1 1
RYR1 WILD-TYPE 152 161 57 113
'RYR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S265.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
RYR1 MUTATED 2 2 1 1 1
RYR1 WILD-TYPE 101 129 84 94 75
'RYR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S266.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
RYR1 MUTATED 3 1 2 1
RYR1 WILD-TYPE 160 142 117 65
'RYR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S267.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
RYR1 MUTATED 3 1 3
RYR1 WILD-TYPE 173 124 187
'RYR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S268.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
RYR1 MUTATED 3 1 2 1
RYR1 WILD-TYPE 126 121 104 104
'RYR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S269.  Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
RYR1 MUTATED 3 2 2
RYR1 WILD-TYPE 157 116 182
'TNRC18 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S270.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
TNRC18 MUTATED 0 1 3
TNRC18 WILD-TYPE 131 136 217
'TNRC18 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S271.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
TNRC18 MUTATED 1 1 1 0 1
TNRC18 WILD-TYPE 45 143 83 40 177
'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S272.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
TNRC18 MUTATED 1 2 1 0
TNRC18 WILD-TYPE 153 162 57 114
'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S273.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
TNRC18 MUTATED 0 1 2 0 1
TNRC18 WILD-TYPE 103 130 83 95 75
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S274.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
TNRC18 MUTATED 2 1 0 1
TNRC18 WILD-TYPE 161 142 119 65
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S275.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
TNRC18 MUTATED 2 1 1
TNRC18 WILD-TYPE 174 124 189
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S276.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
TNRC18 MUTATED 1 1 0 1
TNRC18 WILD-TYPE 128 121 106 104
'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S277.  Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
TNRC18 MUTATED 2 1 0
TNRC18 WILD-TYPE 158 117 184
'TMEM90B MUTATION STATUS' versus 'CN_CNMF'

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

Table S278.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
TMEM90B MUTATED 1 0 2
TMEM90B WILD-TYPE 130 137 218
'TMEM90B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S279.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
TMEM90B MUTATED 0 1 1 0 1
TMEM90B WILD-TYPE 46 143 83 40 177
'TMEM90B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S280.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
TMEM90B MUTATED 1 1 0 1
TMEM90B WILD-TYPE 153 163 58 113
'TMEM90B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S281.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
TMEM90B MUTATED 1 1 0 1 0
TMEM90B WILD-TYPE 102 130 85 94 76
'TMEM90B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S282.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
TMEM90B MUTATED 1 1 1 0
TMEM90B WILD-TYPE 162 142 118 66
'TMEM90B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S283.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
TMEM90B MUTATED 1 1 1
TMEM90B WILD-TYPE 175 124 189
'TMEM90B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S284.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
TMEM90B MUTATED 1 1 0 1
TMEM90B WILD-TYPE 128 121 106 104
'TMEM90B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S285.  Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
TMEM90B MUTATED 1 1 1
TMEM90B WILD-TYPE 159 117 183
'ZC3H11A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.69

Table S286.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
ZC3H11A MUTATED 2 1 0
ZC3H11A WILD-TYPE 129 136 220
'ZC3H11A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S287.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
ZC3H11A MUTATED 0 0 0 1 2
ZC3H11A WILD-TYPE 46 144 84 39 176
'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.69

Table S288.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
ZC3H11A MUTATED 3 0 0 0
ZC3H11A WILD-TYPE 151 164 58 114
'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.046

Table S289.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
ZC3H11A MUTATED 0 0 0 0 3
ZC3H11A WILD-TYPE 103 131 85 95 73

Figure S42.  Get High-res Image Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S290.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
ZC3H11A MUTATED 2 0 1 0
ZC3H11A WILD-TYPE 161 143 118 66
'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S291.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
ZC3H11A MUTATED 2 0 1
ZC3H11A WILD-TYPE 174 125 189
'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S292.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
ZC3H11A MUTATED 2 0 1 0
ZC3H11A WILD-TYPE 127 122 105 105
'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S293.  Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
ZC3H11A MUTATED 2 0 1
ZC3H11A WILD-TYPE 158 118 183
'RANBP9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S294.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 137 220
RANBP9 MUTATED 1 0 2
RANBP9 WILD-TYPE 130 137 218
'RANBP9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S295.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
RANBP9 MUTATED 0 0 1 0 2
RANBP9 WILD-TYPE 46 144 83 40 176
'RANBP9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S296.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
RANBP9 MUTATED 2 0 0 1
RANBP9 WILD-TYPE 152 164 58 113
'RANBP9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.99

Table S297.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
RANBP9 MUTATED 1 0 0 2 0
RANBP9 WILD-TYPE 102 131 85 93 76
'RANBP9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S298.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
RANBP9 MUTATED 2 0 1 0
RANBP9 WILD-TYPE 161 143 118 66
'RANBP9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S299.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
RANBP9 MUTATED 2 0 1
RANBP9 WILD-TYPE 174 125 189
'RANBP9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.99

Table S300.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
RANBP9 MUTATED 1 0 0 2
RANBP9 WILD-TYPE 128 122 106 103
'RANBP9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S301.  Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
RANBP9 MUTATED 2 0 1
RANBP9 WILD-TYPE 158 118 183
'DGCR8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S302.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 144 84 40 178
DGCR8 MUTATED 0 2 0 0 1
DGCR8 WILD-TYPE 46 142 84 40 177
'DGCR8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S303.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 51
DGCR8 MUTATED 2 0 1 0
DGCR8 WILD-TYPE 61 61 39 51
'DGCR8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S304.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 27 31 26 49 27 9
DGCR8 MUTATED 2 1 0 0 0 0 0
DGCR8 WILD-TYPE 44 26 31 26 49 27 9
'DGCR8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S305.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 154 164 58 114
DGCR8 MUTATED 0 2 0 1
DGCR8 WILD-TYPE 154 162 58 113
'DGCR8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S306.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 131 85 95 76
DGCR8 MUTATED 1 2 0 0 0
DGCR8 WILD-TYPE 102 129 85 95 76
'DGCR8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S307.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 143 119 66
DGCR8 MUTATED 1 1 0 1
DGCR8 WILD-TYPE 162 142 119 65
'DGCR8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.95

Table S308.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 176 125 190
DGCR8 MUTATED 1 2 0
DGCR8 WILD-TYPE 175 123 190
'DGCR8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S309.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 129 122 106 105
DGCR8 MUTATED 1 1 0 1
DGCR8 WILD-TYPE 128 121 106 104
'DGCR8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.95

Table S310.  Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 118 184
DGCR8 MUTATED 1 2 0
DGCR8 WILD-TYPE 159 116 184
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/THCA-TP/22815543/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/22542946/THCA-TP.transferedmergedcluster.txt

  • Number of patients = 492

  • Number of significantly mutated genes = 36

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)