Correlation between gene mutation status and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C16T0JKF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Glioblastoma Multiforme (Primary solid tumor cohort) - 21 April 2013: Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16T0JKF
Overview
Introduction

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

Summary

Testing the association between mutation status of 110 genes and 10 molecular subtypes across 284 patients, 14 significant findings detected with P value < 0.05 and Q value < 0.25.

  • EGFR mutation correlated to 'CN_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • IDH1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • TP53 mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • ATRX mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 110 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, 14 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
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
IDH1 14 (5%) 270 1.13e-06
(0.000969) 		4.41e-07
(0.00038) 		0.000227
(0.193) 		1.24e-05
(0.0106) 		1.68e-05
(0.0143) 		0.00121
(1.00) 		0.00352
(1.00) 		0.0203
(1.00) 		0.000712
(0.601) 		0.00263
(1.00)
ATRX 16 (6%) 268 0.000227
(0.192) 		0.000201
(0.171) 		0.00455
(1.00) 		0.000137
(0.117) 		6.23e-05
(0.0532) 		0.155
(1.00) 		0.00605
(1.00) 		0.0121
(1.00) 		0.00195
(1.00) 		0.0421
(1.00)
EGFR 74 (26%) 210 0.000485
(0.41) 		0.0656
(1.00) 		0.242
(1.00) 		0.217
(1.00) 		7.49e-07
(0.000643) 		0.0108
(1.00) 		6.37e-05
(0.0543) 		1.46e-06
(0.00125) 		0.0413
(1.00) 		0.357
(1.00)
TP53 79 (28%) 205 4.16e-05
(0.0356) 		0.000502
(0.424) 		0.000313
(0.265) 		0.0272
(1.00) 		0.000166
(0.141) 		0.0083
(1.00) 		0.0384
(1.00) 		0.00968
(1.00) 		0.00184
(1.00) 		0.0375
(1.00)
PIK3R1 32 (11%) 252 0.96
(1.00) 		0.779
(1.00) 		0.467
(1.00) 		0.205
(1.00) 		0.115
(1.00) 		0.84
(1.00) 		0.988
(1.00) 		0.273
(1.00) 		0.406
(1.00) 		0.649
(1.00)
BRAF 6 (2%) 278 0.395
(1.00) 		0.567
(1.00) 		0.616
(1.00) 		0.175
(1.00) 		0.586
(1.00) 		1
(1.00) 		0.0781
(1.00) 		0.791
(1.00) 		1
(1.00)
PTEN 87 (31%) 197 0.458
(1.00) 		0.366
(1.00) 		0.0452
(1.00) 		0.594
(1.00) 		0.584
(1.00) 		0.95
(1.00) 		0.378
(1.00) 		0.389
(1.00) 		0.27
(1.00) 		0.196
(1.00)
PIK3CA 30 (11%) 254 0.689
(1.00) 		0.195
(1.00) 		0.571
(1.00) 		0.785
(1.00) 		0.501
(1.00) 		0.627
(1.00) 		0.754
(1.00) 		0.281
(1.00) 		0.262
(1.00) 		0.838
(1.00)
RB1 24 (8%) 260 0.00652
(1.00) 		0.0265
(1.00) 		0.0653
(1.00) 		0.357
(1.00) 		0.0873
(1.00) 		0.027
(1.00) 		0.493
(1.00) 		0.691
(1.00) 		0.0818
(1.00) 		0.0754
(1.00)
NF1 29 (10%) 255 0.0435
(1.00) 		0.071
(1.00) 		0.0897
(1.00) 		0.501
(1.00) 		0.00154
(1.00) 		0.00396
(1.00) 		0.23
(1.00) 		0.12
(1.00) 		0.566
(1.00) 		0.915
(1.00)
SPTA1 26 (9%) 258 0.705
(1.00) 		0.0354
(1.00) 		0.543
(1.00) 		0.913
(1.00) 		0.335
(1.00) 		0.223
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.018
(1.00) 		0.573
(1.00)
KRTAP4-11 9 (3%) 275 0.113
(1.00) 		0.0873
(1.00) 		1
(1.00) 		0.658
(1.00) 		0.693
(1.00) 		0.343
(1.00) 		0.116
(1.00) 		0.474
(1.00) 		0.209
(1.00) 		0.0823
(1.00)
GABRA6 11 (4%) 273 0.126
(1.00) 		0.426
(1.00) 		0.506
(1.00) 		0.486
(1.00) 		0.365
(1.00) 		0.943
(1.00) 		0.318
(1.00) 		0.474
(1.00) 		0.124
(1.00) 		1
(1.00)
KEL 15 (5%) 269 0.162
(1.00) 		0.49
(1.00) 		1
(1.00) 		1
(1.00) 		0.394
(1.00) 		0.179
(1.00) 		0.376
(1.00) 		0.911
(1.00) 		0.408
(1.00) 		0.908
(1.00)
CDH18 11 (4%) 273 0.0384
(1.00) 		0.0166
(1.00) 		0.104
(1.00) 		0.253
(1.00) 		0.853
(1.00) 		0.258
(1.00) 		0.791
(1.00) 		0.776
(1.00) 		0.318
(1.00) 		0.049
(1.00)
PRB2 6 (2%) 278 0.284
(1.00) 		1
(1.00) 		0.441
(1.00) 		0.634
(1.00) 		0.772
(1.00)
RPL5 7 (2%) 277 0.528
(1.00) 		0.174
(1.00) 		0.388
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.843
(1.00) 		0.532
(1.00) 		0.465
(1.00) 		1
(1.00)
SEMA3C 11 (4%) 273 0.0448
(1.00) 		0.296
(1.00) 		0.147
(1.00) 		0.383
(1.00) 		0.293
(1.00) 		0.339
(1.00) 		0.532
(1.00) 		0.103
(1.00) 		0.649
(1.00)
TPTE2 8 (3%) 276 0.908
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.289
(1.00) 		0.271
(1.00) 		0.506
(1.00) 		0.624
(1.00) 		0.409
(1.00) 		0.376
(1.00) 		0.741
(1.00)
ZNF844 6 (2%) 278 0.693
(1.00) 		0.874
(1.00) 		0.143
(1.00) 		0.767
(1.00) 		0.192
(1.00)
OR8K3 7 (2%) 277 0.625
(1.00) 		0.376
(1.00) 		0.762
(1.00) 		0.462
(1.00) 		0.0783
(1.00) 		0.765
(1.00) 		0.905
(1.00) 		0.821
(1.00) 		1
(1.00) 		0.764
(1.00)
OR5AR1 7 (2%) 277 0.241
(1.00) 		0.312
(1.00) 		0.388
(1.00) 		0.679
(1.00) 		0.433
(1.00) 		0.882
(1.00) 		0.514
(1.00) 		0.858
(1.00)
STAG2 12 (4%) 272 0.85
(1.00) 		0.204
(1.00) 		0.21
(1.00) 		0.132
(1.00) 		0.756
(1.00) 		0.676
(1.00) 		0.00694
(1.00) 		0.184
(1.00) 		0.479
(1.00) 		0.771
(1.00)
SEMG1 8 (3%) 276 0.493
(1.00) 		0.117
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.764
(1.00)
CDC27 6 (2%) 278 0.241
(1.00) 		0.376
(1.00) 		0.261
(1.00) 		0.29
(1.00) 		0.449
(1.00) 		0.138
(1.00) 		0.278
(1.00) 		0.325
(1.00)
PDGFRA 11 (4%) 273 0.333
(1.00) 		0.223
(1.00) 		0.729
(1.00) 		0.846
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.851
(1.00) 		0.0265
(1.00) 		0.129
(1.00)
ADAM29 9 (3%) 275 0.82
(1.00) 		0.73
(1.00) 		0.701
(1.00) 		0.794
(1.00) 		0.835
(1.00) 		0.489
(1.00) 		0.673
(1.00) 		0.0559
(1.00) 		0.384
(1.00)
SULT1B1 6 (2%) 278 0.0442
(1.00) 		0.617
(1.00) 		0.27
(1.00) 		0.37
(1.00) 		0.289
(1.00) 		0.496
(1.00) 		0.588
(1.00) 		0.466
(1.00) 		0.802
(1.00)
ABCC9 11 (4%) 273 0.12
(1.00) 		0.316
(1.00) 		0.246
(1.00) 		0.735
(1.00) 		0.503
(1.00) 		0.0162
(1.00) 		0.453
(1.00) 		0.661
(1.00) 		0.336
(1.00) 		0.37
(1.00)
NLRP5 12 (4%) 272 0.861
(1.00) 		1
(1.00) 		0.929
(1.00) 		0.377
(1.00) 		0.548
(1.00) 		0.477
(1.00) 		0.913
(1.00) 		0.221
(1.00) 		0.72
(1.00) 		0.568
(1.00)
LZTR1 10 (4%) 274 0.706
(1.00) 		0.795
(1.00) 		0.754
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.138
(1.00) 		0.839
(1.00) 		1
(1.00) 		0.173
(1.00) 		0.536
(1.00)
CALCR 8 (3%) 276 0.253
(1.00) 		0.874
(1.00) 		0.93
(1.00) 		0.736
(1.00) 		0.208
(1.00) 		1
(1.00) 		0.262
(1.00) 		0.506
(1.00)
QKI 5 (2%) 279 0.0442
(1.00) 		0.312
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.738
(1.00) 		0.173
(1.00) 		0.496
(1.00) 		0.776
(1.00)
ZPBP 5 (2%) 279 0.166
(1.00) 		0.287
(1.00) 		0.0929
(1.00) 		0.454
(1.00) 		0.23
(1.00) 		0.609
(1.00) 		1
(1.00)
PSPH 5 (2%) 279 0.329
(1.00) 		0.533
(1.00) 		0.869
(1.00) 		0.462
(1.00) 		0.0138
(1.00) 		0.106
(1.00) 		0.093
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.536
(1.00)
UGT2A3 6 (2%) 278 1
(1.00) 		0.533
(1.00) 		0.762
(1.00) 		0.462
(1.00) 		0.673
(1.00) 		0.788
(1.00) 		0.575
(1.00) 		0.532
(1.00)
WNT2 5 (2%) 279 0.0209
(1.00) 		0.00332
(1.00) 		1
(1.00) 		0.789
(1.00) 		1
(1.00) 		0.0416
(1.00) 		0.423
(1.00)
OR5D18 6 (2%) 278 0.217
(1.00) 		1
(1.00) 		0.475
(1.00) 		0.555
(1.00) 		0.515
(1.00) 		0.531
(1.00) 		0.728
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.764
(1.00)
OR5W2 5 (2%) 279 0.312
(1.00) 		0.184
(1.00) 		0.328
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.439
(1.00) 		0.195
(1.00)
ABCB1 10 (4%) 274 0.64
(1.00) 		0.0873
(1.00) 		0.309
(1.00) 		0.23
(1.00) 		0.435
(1.00) 		0.613
(1.00) 		0.931
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.0828
(1.00)
COL1A2 11 (4%) 273 0.666
(1.00) 		0.333
(1.00) 		0.447
(1.00) 		0.817
(1.00) 		0.859
(1.00) 		0.829
(1.00) 		0.489
(1.00) 		1
(1.00) 		0.855
(1.00) 		0.0126
(1.00)
C1ORF150 3 (1%) 281 0.379
(1.00) 		0.613
(1.00) 		0.892
(1.00) 		0.776
(1.00)
LRRC55 6 (2%) 278 0.329
(1.00) 		0.449
(1.00) 		0.539
(1.00) 		0.143
(1.00) 		0.328
(1.00)
DCAF12L2 8 (3%) 276 0.868
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.679
(1.00) 		0.311
(1.00) 		0.697
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.466
(1.00) 		1
(1.00)
LRFN5 7 (2%) 277 0.896
(1.00) 		0.619
(1.00) 		0.426
(1.00) 		1
(1.00) 		1
(1.00) 		0.817
(1.00) 		0.292
(1.00) 		0.434
(1.00) 		1
(1.00) 		0.848
(1.00)
LUM 5 (2%) 279 0.312
(1.00) 		0.474
(1.00) 		0.507
(1.00) 		1
(1.00) 		0.33
(1.00)
MMP13 6 (2%) 278 0.743
(1.00) 		0.726
(1.00) 		0.504
(1.00) 		0.452
(1.00) 		0.88
(1.00) 		0.204
(1.00) 		0.195
(1.00) 		0.336
(1.00) 		0.37
(1.00)
HEATR7B2 11 (4%) 273 0.135
(1.00) 		0.712
(1.00) 		0.344
(1.00) 		0.342
(1.00) 		0.594
(1.00) 		0.355
(1.00) 		0.346
(1.00) 		0.851
(1.00) 		0.72
(1.00) 		1
(1.00)
UGT2B28 6 (2%) 278 1
(1.00) 		0.67
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.515
(1.00)
OR5D13 5 (2%) 279 0.0767
(1.00) 		1
(1.00) 		0.291
(1.00) 		0.831
(1.00) 		0.33
(1.00) 		0.439
(1.00) 		0.0781
(1.00)
ZNF99 6 (2%) 278 1
(1.00) 		0.821
(1.00) 		0.382
(1.00) 		0.617
(1.00) 		0.385
(1.00) 		0.402
(1.00) 		0.246
(1.00) 		0.3
(1.00)
SLC5A7 7 (2%) 277 0.102
(1.00) 		0.204
(1.00) 		0.352
(1.00) 		0.831
(1.00) 		0.385
(1.00) 		0.765
(1.00) 		0.682
(1.00) 		0.277
(1.00)
SEMA3E 8 (3%) 276 0.166
(1.00) 		0.171
(1.00) 		0.504
(1.00) 		0.37
(1.00) 		0.819
(1.00) 		0.0529
(1.00) 		0.00942
(1.00) 		0.0408
(1.00) 		0.336
(1.00) 		0.058
(1.00)
TCHH 16 (6%) 268 0.274
(1.00) 		0.131
(1.00) 		0.43
(1.00) 		0.137
(1.00) 		0.446
(1.00) 		0.354
(1.00) 		0.525
(1.00) 		0.593
(1.00) 		0.322
(1.00) 		0.135
(1.00)
SLC26A3 7 (2%) 277 0.45
(1.00) 		0.874
(1.00) 		0.554
(1.00) 		0.878
(1.00) 		0.801
(1.00) 		0.167
(1.00) 		0.0104
(1.00) 		0.156
(1.00) 		0.163
(1.00)
GABRB2 6 (2%) 278 0.693
(1.00) 		0.0944
(1.00) 		0.111
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.153
(1.00) 		0.0209
(1.00) 		0.3
(1.00) 		0.572
(1.00) 		0.12
(1.00)
CFHR4 5 (2%) 279 0.743
(1.00) 		0.853
(1.00) 		0.828
(1.00) 		0.679
(1.00) 		0.524
(1.00) 		0.411
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00)
IL18RAP 6 (2%) 278 0.329
(1.00) 		0.0595
(1.00) 		0.227
(1.00) 		0.121
(1.00) 		0.88
(1.00) 		0.138
(1.00) 		0.532
(1.00) 		0.673
(1.00) 		0.465
(1.00) 		0.764
(1.00)
OGDH 3 (1%) 281 1
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.791
(1.00) 		0.286
(1.00)
PCDH11X 9 (3%) 275 0.544
(1.00) 		0.533
(1.00) 		0.172
(1.00) 		0.0354
(1.00) 		0.116
(1.00) 		0.0251
(1.00) 		0.0203
(1.00) 		0.663
(1.00) 		0.312
(1.00)
SPRYD5 6 (2%) 278 0.874
(1.00) 		1
(1.00) 		0.214
(1.00) 		0.511
(1.00) 		0.586
(1.00) 		1
(1.00) 		0.434
(1.00) 		0.523
(1.00) 		0.705
(1.00)
TGFA 4 (1%) 280 0.688
(1.00) 		1
(1.00) 		0.434
(1.00)
OR5P2 4 (1%) 280 0.652
(1.00) 		0.792
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.193
(1.00)
UGT2B4 5 (2%) 279 0.0305
(1.00) 		0.26
(1.00) 		0.328
(1.00) 		0.789
(1.00) 		0.524
(1.00)
FOXR2 5 (2%) 279 1
(1.00) 		0.685
(1.00) 		0.754
(1.00) 		0.0385
(1.00) 		0.39
(1.00)
PSG8 6 (2%) 278 1
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.364
(1.00) 		0.673
(1.00) 		0.788
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.72
(1.00) 		0.848
(1.00)
CNTNAP2 13 (5%) 271 0.815
(1.00) 		0.553
(1.00) 		0.17
(1.00) 		0.514
(1.00) 		0.756
(1.00) 		0.676
(1.00) 		0.861
(1.00) 		0.713
(1.00) 		0.685
(1.00) 		1
(1.00)
PIK3C2G 9 (3%) 275 0.226
(1.00) 		0.0355
(1.00) 		0.891
(1.00) 		0.577
(1.00) 		0.266
(1.00) 		0.703
(1.00) 		0.761
(1.00) 		0.709
(1.00)
SCN9A 11 (4%) 273 0.686
(1.00) 		0.498
(1.00) 		0.963
(1.00) 		0.31
(1.00) 		0.687
(1.00) 		0.761
(1.00) 		0.851
(1.00) 		0.523
(1.00) 		0.705
(1.00)
GABRA1 6 (2%) 278 0.202
(1.00) 		0.726
(1.00) 		0.703
(1.00) 		0.37
(1.00) 		0.88
(1.00) 		0.439
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.802
(1.00)
DYNC1I1 7 (2%) 277 0.377
(1.00) 		0.0441
(1.00) 		0.47
(1.00) 		0.212
(1.00) 		1
(1.00) 		0.147
(1.00) 		0.821
(1.00)
PODXL 3 (1%) 281 1
(1.00) 		1
(1.00) 		0.507
(1.00) 		0.789
(1.00)
HCN1 11 (4%) 273 0.922
(1.00) 		0.921
(1.00) 		0.134
(1.00) 		0.0435
(1.00) 		0.687
(1.00) 		0.953
(1.00) 		1
(1.00) 		0.536
(1.00)
POTEF 5 (2%) 279 0.0305
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.789
(1.00) 		0.0709
(1.00)
CXORF22 8 (3%) 276 0.307
(1.00) 		0.795
(1.00) 		0.111
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.506
(1.00) 		0.581
(1.00) 		0.574
(1.00) 		0.572
(1.00) 		0.802
(1.00)
AFM 6 (2%) 278 1
(1.00) 		0.533
(1.00) 		0.809
(1.00) 		0.452
(1.00) 		0.515
(1.00) 		0.791
(1.00) 		0.588
(1.00)
KRTAP20-2 3 (1%) 281 0.312
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.617
(1.00) 		0.281
(1.00) 		0.439
(1.00) 		0.0781
(1.00)
OTC 3 (1%) 281 0.417
(1.00) 		0.792
(1.00) 		0.194
(1.00)
TRAT1 4 (1%) 280 0.469
(1.00) 		0.685
(1.00) 		0.762
(1.00) 		0.789
(1.00) 		0.827
(1.00) 		0.254
(1.00) 		0.764
(1.00)
KLK6 4 (1%) 280 0.00654
(1.00) 		1
(1.00) 		0.434
(1.00)
OR4D5 4 (1%) 280 0.272
(1.00) 		0.465
(1.00) 		0.352
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.466
(1.00) 		0.163
(1.00)
GPX5 3 (1%) 281 0.776
(1.00) 		0.339
(1.00) 		0.498
(1.00) 		0.093
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.536
(1.00)
KRTAP4-7 3 (1%) 281 0.208
(1.00) 		0.26
(1.00) 		0.379
(1.00) 		0.292
(1.00) 		0.434
(1.00)
CDH9 8 (3%) 276 0.402
(1.00) 		0.129
(1.00) 		0.616
(1.00) 		0.577
(1.00) 		0.801
(1.00) 		0.335
(1.00) 		0.247
(1.00) 		0.261
(1.00) 		0.233
(1.00)
CDHR3 3 (1%) 281 0.417
(1.00) 		1
(1.00) 		0.194
(1.00)
OR4P4 4 (1%) 280 0.193
(1.00)
OR52M1 4 (1%) 280 0.469
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.0587
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.764
(1.00)
KLF17 5 (2%) 279 0.625
(1.00) 		0.449
(1.00) 		0.631
(1.00) 		0.831
(1.00) 		0.738
(1.00) 		0.785
(1.00) 		0.673
(1.00)
OR8J3 4 (1%) 280 0.693
(1.00) 		0.821
(1.00) 		0.291
(1.00) 		0.174
(1.00) 		0.194
(1.00) 		0.496
(1.00) 		0.434
(1.00)
AP3S1 3 (1%) 281 0.534
(1.00) 		1
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.633
(1.00)
ST6GAL2 6 (2%) 278 1
(1.00) 		0.874
(1.00) 		0.374
(1.00) 		0.878
(1.00) 		0.862
(1.00) 		0.208
(1.00) 		0.163
(1.00)
CD3EAP 3 (1%) 281 1
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00)
F9 4 (1%) 280 0.776
(1.00) 		1
(1.00) 		0.144
(1.00) 		0.183
(1.00) 		1
(1.00)
DPP10 7 (2%) 277 0.706
(1.00) 		0.129
(1.00) 		0.267
(1.00) 		0.658
(1.00) 		0.88
(1.00) 		0.647
(1.00) 		0.168
(1.00) 		0.609
(1.00) 		1
(1.00)
TCN1 4 (1%) 280 0.693
(1.00) 		0.567
(1.00) 		0.673
(1.00) 		0.121
(1.00) 		0.391
(1.00) 		0.0529
(1.00) 		0.336
(1.00) 		0.37
(1.00)
TRPV6 7 (2%) 277 0.874
(1.00) 		0.766
(1.00) 		0.238
(1.00) 		0.338
(1.00) 		0.673
(1.00) 		0.164
(1.00) 		0.588
(1.00) 		0.0941
(1.00) 		0.465
(1.00)
PAN3 6 (2%) 278 0.868
(1.00) 		0.617
(1.00) 		0.539
(1.00) 		0.634
(1.00) 		0.772
(1.00)
CDKN2C 3 (1%) 281 0.652
(1.00) 		0.792
(1.00) 		0.673
(1.00) 		0.617
(1.00) 		0.781
(1.00) 		0.465
(1.00) 		0.286
(1.00)
AZGP1 5 (2%) 279 0.868
(1.00) 		0.617
(1.00) 		0.109
(1.00) 		0.174
(1.00) 		1
(1.00)
DRD5 7 (2%) 277 0.896
(1.00) 		0.619
(1.00) 		0.595
(1.00) 		0.385
(1.00) 		0.433
(1.00) 		0.374
(1.00) 		0.532
(1.00) 		0.791
(1.00) 		1
(1.00)
FGA 6 (2%) 278 0.241
(1.00) 		0.617
(1.00) 		0.0809
(1.00) 		0.0647
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.764
(1.00)
FGG 5 (2%) 279 0.217
(1.00) 		0.287
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.209
(1.00) 		0.325
(1.00)
OR10G8 4 (1%) 280 0.842
(1.00) 		1
(1.00) 		0.869
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.703
(1.00) 		1
(1.00)
PCMTD1 3 (1%) 281 1
(1.00) 		0.792
(1.00) 		0.781
(1.00) 		0.791
(1.00) 		0.588
(1.00)
PROKR2 6 (2%) 278 0.533
(1.00) 		0.211
(1.00) 		0.864
(1.00) 		0.847
(1.00) 		0.112
(1.00) 		0.209
(1.00) 		0.233
(1.00)
SHB 3 (1%) 281 0.312
(1.00) 		0.474
(1.00) 		1
(1.00)
CYP3A5 5 (2%) 279 1
(1.00) 		0.474
(1.00) 		0.862
(1.00) 		0.765
(1.00) 		0.622
(1.00) 		0.132
(1.00) 		0.609
(1.00) 		1
(1.00)
FRMD7 6 (2%) 278 0.693
(1.00) 		1
(1.00) 		0.673
(1.00) 		0.789
(1.00) 		0.449
(1.00) 		0.402
(1.00) 		0.411
(1.00) 		0.673
(1.00) 		0.791
(1.00) 		0.536
(1.00)
KCNB2 6 (2%) 278 0.451
(1.00) 		0.312
(1.00) 		0.144
(1.00) 		0.679
(1.00) 		0.189
(1.00) 		0.788
(1.00) 		0.439
(1.00) 		0.0781
(1.00) 		0.609
(1.00) 		1
(1.00)
KDR 8 (3%) 276 0.256
(1.00) 		0.304
(1.00) 		0.134
(1.00) 		0.0017
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.144
(1.00) 		0.851
(1.00)
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 7.49e-07 (Fisher's exact test), Q value = 0.00064

Table S1.  Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 108 79
EGFR MUTATED 16 47 9
EGFR WILD-TYPE 71 61 70

Figure S1.  Get High-res Image Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 6.37e-05 (Fisher's exact test), Q value = 0.054

Table S2.  Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
EGFR MUTATED 13 5 16 2
EGFR WILD-TYPE 28 33 15 31

Figure S2.  Get High-res Image Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #7: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.0013

Table S3.  Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
EGFR MUTATED 24 6 6
EGFR WILD-TYPE 23 22 62

Figure S3.  Get High-res Image Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00097

Table S4.  Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 85 80
IDH1 MUTATED 0 13 0
IDH1 WILD-TYPE 76 72 80

Figure S4.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4.41e-07 (Fisher's exact test), Q value = 0.00038

Table S5.  Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 59 79
IDH1 MUTATED 0 0 13
IDH1 WILD-TYPE 103 59 66

Figure S5.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.19

Table S6.  Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 72 30 44
IDH1 MUTATED 0 10 0 0
IDH1 WILD-TYPE 57 62 30 44

Figure S6.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'MIR_CNMF'

'IDH1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.011

Table S7.  Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 81 49
IDH1 MUTATED 0 1 9
IDH1 WILD-TYPE 73 80 40

Figure S7.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.014

Table S8.  Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 108 79
IDH1 MUTATED 2 0 11
IDH1 WILD-TYPE 85 108 68

Figure S8.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.16e-05 (Fisher's exact test), Q value = 0.036

Table S9.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 85 80
TP53 MUTATED 19 38 11
TP53 WILD-TYPE 57 47 69

Figure S9.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.14

Table S10.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 108 79
TP53 MUTATED 34 16 28
TP53 WILD-TYPE 53 92 51

Figure S10.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.19

Table S11.  Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 85 80
ATRX MUTATED 2 11 0
ATRX WILD-TYPE 74 74 80

Figure S11.  Get High-res Image Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000201 (Fisher's exact test), Q value = 0.17

Table S12.  Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 59 79
ATRX MUTATED 2 0 11
ATRX WILD-TYPE 101 59 68

Figure S12.  Get High-res Image Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.12

Table S13.  Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 81 49
ATRX MUTATED 0 2 8
ATRX WILD-TYPE 73 79 41

Figure S13.  Get High-res Image Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 6.23e-05 (Fisher's exact test), Q value = 0.053

Table S14.  Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 87 108 79
ATRX MUTATED 2 1 12
ATRX WILD-TYPE 85 107 67

Figure S14.  Get High-res Image Gene #41: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

Methods & Data
Input

  • Mutation data file = GBM-TP.mutsig.cluster.txt

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

  • Number of patients = 284

  • Number of significantly mutated genes = 110

  • 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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