Correlation between gene mutation status and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1DF6PD6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1DF6PD6
Overview
Introduction

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

Summary

Testing the association between mutation status of 114 genes and 10 molecular subtypes across 291 patients, 15 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 114 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, 15 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 Chi-square test Chi-square test
IDH1 15 (5%) 276 3.45e-07
(0.000303) 		1.17e-07
(0.000103) 		0.000619
(0.532) 		2.5e-06
(0.00219) 		2.61e-05
(0.0228) 		0.00121
(1.00) 		0.00327
(1.00) 		0.045
(1.00) 		0.00154
(1.00) 		0.00023
(0.199)
ATRX 17 (6%) 274 8.02e-05
(0.0698) 		5.04e-05
(0.0439) 		0.0103
(1.00) 		3.46e-05
(0.0303) 		0.000138
(0.119) 		0.155
(1.00) 		0.00538
(1.00) 		0.00217
(1.00) 		0.000527
(0.454) 		0.000194
(0.168)
EGFR 77 (26%) 214 0.0001
(0.0873) 		0.0296
(1.00) 		0.122
(1.00) 		0.159
(1.00) 		9.19e-08
(8.08e-05) 		0.0108
(1.00) 		0.00029
(0.25) 		3.99e-05
(0.0348) 		0.0647
(1.00) 		0.0249
(1.00)
TP53 83 (29%) 208 5.84e-05
(0.0509) 		0.000372
(0.321) 		0.00153
(1.00) 		0.0118
(1.00) 		0.000113
(0.0982) 		0.0083
(1.00) 		0.037
(1.00) 		0.00357
(1.00) 		0.00905
(1.00) 		0.0165
(1.00)
PIK3R1 33 (11%) 258 0.891
(1.00) 		0.644
(1.00) 		0.381
(1.00) 		0.36
(1.00) 		0.0851
(1.00) 		0.84
(1.00) 		0.988
(1.00) 		0.12
(1.00) 		0.546
(1.00) 		0.31
(1.00)
BRAF 6 (2%) 285 0.396
(1.00) 		0.466
(1.00) 		0.62
(1.00) 		0.175
(1.00) 		0.587
(1.00) 		1
(1.00) 		1
(1.00) 		0.438
(1.00) 		0.643
(1.00)
PTEN 90 (31%) 201 0.533
(1.00) 		0.417
(1.00) 		0.0728
(1.00) 		0.664
(1.00) 		0.749
(1.00) 		0.95
(1.00) 		0.386
(1.00) 		0.0244
(1.00) 		0.206
(1.00) 		0.559
(1.00)
PIK3CA 32 (11%) 259 0.827
(1.00) 		0.304
(1.00) 		0.584
(1.00) 		0.769
(1.00) 		0.576
(1.00) 		0.627
(1.00) 		0.835
(1.00) 		0.105
(1.00) 		0.422
(1.00) 		0.392
(1.00)
RB1 24 (8%) 267 0.00654
(1.00) 		0.0268
(1.00) 		0.0718
(1.00) 		0.357
(1.00) 		0.0878
(1.00) 		0.027
(1.00) 		0.48
(1.00) 		0.438
(1.00) 		0.0404
(1.00) 		0.239
(1.00)
NF1 32 (11%) 259 0.0179
(1.00) 		0.0118
(1.00) 		0.0243
(1.00) 		0.257
(1.00) 		0.000399
(0.344) 		0.00396
(1.00) 		0.249
(1.00) 		0.0551
(1.00) 		0.00328
(1.00) 		0.00488
(1.00)
SPTA1 27 (9%) 264 0.801
(1.00) 		0.0628
(1.00) 		0.42
(1.00) 		0.915
(1.00) 		0.338
(1.00) 		0.223
(1.00) 		0.546
(1.00) 		0.769
(1.00) 		0.144
(1.00) 		0.00964
(1.00)
KRTAP4-11 9 (3%) 282 0.114
(1.00) 		0.0988
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.693
(1.00) 		0.343
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.527
(1.00)
GABRA6 11 (4%) 280 0.127
(1.00) 		0.427
(1.00) 		0.553
(1.00) 		0.486
(1.00) 		0.341
(1.00) 		0.943
(1.00) 		0.249
(1.00) 		0.375
(1.00) 		0.39
(1.00) 		0.473
(1.00)
KEL 15 (5%) 276 0.174
(1.00) 		0.491
(1.00) 		0.978
(1.00) 		1
(1.00) 		0.395
(1.00) 		0.179
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.969
(1.00)
RPL5 8 (3%) 283 0.353
(1.00) 		0.112
(1.00) 		0.756
(1.00) 		0.454
(1.00) 		0.906
(1.00) 		0.882
(1.00) 		0.841
(1.00) 		0.832
(1.00) 		0.662
(1.00) 		0.825
(1.00)
CDH18 11 (4%) 280 0.0423
(1.00) 		0.0168
(1.00) 		0.113
(1.00) 		0.254
(1.00) 		0.853
(1.00) 		0.258
(1.00) 		0.79
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.484
(1.00)
PRB2 6 (2%) 285 0.284
(1.00) 		1
(1.00) 		0.475
(1.00) 		0.544
(1.00) 		0.772
(1.00)
SEMA3C 11 (4%) 280 0.0416
(1.00) 		0.297
(1.00) 		0.131
(1.00) 		0.351
(1.00) 		0.293
(1.00) 		0.41
(1.00) 		0.832
(1.00) 		0.00731
(1.00) 		0.591
(1.00)
TPTE2 8 (3%) 283 0.908
(1.00) 		1
(1.00) 		0.358
(1.00) 		0.336
(1.00) 		0.271
(1.00) 		0.506
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.00243
(1.00) 		0.462
(1.00)
ZNF844 6 (2%) 285 0.782
(1.00) 		0.875
(1.00) 		0.138
(1.00) 		0.877
(1.00) 		0.192
(1.00)
OR8K3 7 (2%) 284 0.625
(1.00) 		0.376
(1.00) 		0.767
(1.00) 		0.459
(1.00) 		0.078
(1.00) 		0.765
(1.00) 		0.905
(1.00) 		0.682
(1.00) 		0.818
(1.00) 		0.934
(1.00)
OR5AR1 7 (2%) 284 0.241
(1.00) 		0.313
(1.00) 		0.394
(1.00) 		0.68
(1.00) 		0.432
(1.00) 		0.882
(1.00) 		0.535
(1.00) 		0.504
(1.00) 		0.765
(1.00) 		0.00214
(1.00)
STAG2 12 (4%) 279 0.849
(1.00) 		0.205
(1.00) 		0.187
(1.00) 		0.132
(1.00) 		0.756
(1.00) 		0.676
(1.00) 		0.00518
(1.00) 		0.328
(1.00) 		0.117
(1.00) 		0.752
(1.00)
SEMG1 8 (3%) 283 0.494
(1.00) 		0.133
(1.00) 		0.733
(1.00) 		0.896
(1.00) 		0.146
(1.00) 		0.792
(1.00) 		0.758
(1.00)
CDC27 6 (2%) 285 0.241
(1.00) 		0.376
(1.00) 		0.24
(1.00) 		0.287
(1.00) 		0.448
(1.00) 		0.138
(1.00) 		0.278
(1.00) 		0.434
(1.00)
PDGFRA 11 (4%) 280 0.333
(1.00) 		0.224
(1.00) 		0.732
(1.00) 		0.918
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.0252
(1.00) 		0.00796
(1.00)
SULT1B1 6 (2%) 285 0.0439
(1.00) 		0.533
(1.00) 		0.275
(1.00) 		0.37
(1.00) 		0.289
(1.00) 		0.494
(1.00) 		0.606
(1.00) 		0.517
(1.00) 		0.875
(1.00)
ADAM29 9 (3%) 282 0.821
(1.00) 		0.73
(1.00) 		0.676
(1.00) 		0.793
(1.00) 		0.835
(1.00) 		0.487
(1.00) 		0.434
(1.00) 		0.519
(1.00) 		0.214
(1.00)
HEATR7B2 12 (4%) 279 0.0805
(1.00) 		0.46
(1.00) 		0.407
(1.00) 		0.212
(1.00) 		0.614
(1.00) 		0.355
(1.00) 		0.363
(1.00) 		0.842
(1.00) 		0.943
(1.00) 		0.631
(1.00)
COL1A2 12 (4%) 279 0.476
(1.00) 		0.123
(1.00) 		0.358
(1.00) 		0.69
(1.00) 		0.872
(1.00) 		0.829
(1.00) 		0.487
(1.00) 		0.832
(1.00) 		0.0572
(1.00) 		0.0693
(1.00)
ABCC9 11 (4%) 280 0.12
(1.00) 		0.317
(1.00) 		0.235
(1.00) 		0.735
(1.00) 		0.504
(1.00) 		0.0162
(1.00) 		0.45
(1.00) 		0.179
(1.00) 		0.187
(1.00) 		0.66
(1.00)
NLRP5 12 (4%) 279 0.862
(1.00) 		0.929
(1.00) 		0.901
(1.00) 		0.375
(1.00) 		0.548
(1.00) 		0.477
(1.00) 		0.347
(1.00) 		0.425
(1.00) 		0.521
(1.00) 		0.0234
(1.00)
CALCR 8 (3%) 283 0.254
(1.00) 		0.875
(1.00) 		0.93
(1.00) 		0.735
(1.00) 		0.208
(1.00) 		1
(1.00) 		0.279
(1.00) 		0.727
(1.00)
LZTR1 10 (3%) 281 0.707
(1.00) 		0.796
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.138
(1.00) 		0.771
(1.00) 		0.215
(1.00) 		0.459
(1.00) 		0.758
(1.00)
QKI 5 (2%) 286 0.0439
(1.00) 		0.313
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.738
(1.00) 		0.173
(1.00) 		0.494
(1.00) 		1
(1.00)
ZPBP 5 (2%) 286 0.166
(1.00) 		0.288
(1.00) 		0.0807
(1.00) 		0.454
(1.00) 		0.23
(1.00) 		0.742
(1.00) 		0.81
(1.00)
PSPH 5 (2%) 286 0.329
(1.00) 		0.617
(1.00) 		0.87
(1.00) 		0.459
(1.00) 		0.0139
(1.00) 		0.106
(1.00) 		0.0926
(1.00) 		0.606
(1.00) 		0.818
(1.00) 		0.61
(1.00)
UGT2A3 6 (2%) 285 1
(1.00) 		0.617
(1.00) 		0.767
(1.00) 		0.459
(1.00) 		0.673
(1.00) 		0.788
(1.00) 		0.57
(1.00) 		0.832
(1.00)
WNT2 5 (2%) 286 0.0212
(1.00) 		0.00339
(1.00) 		1
(1.00) 		0.79
(1.00) 		1
(1.00) 		0.0395
(1.00) 		0.629
(1.00)
OR5D18 6 (2%) 285 0.218
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.554
(1.00) 		0.515
(1.00) 		0.531
(1.00) 		0.725
(1.00) 		0.832
(1.00) 		0.114
(1.00) 		0.758
(1.00)
ABCB1 10 (3%) 281 0.702
(1.00) 		0.0988
(1.00) 		0.311
(1.00) 		0.265
(1.00) 		0.435
(1.00) 		0.613
(1.00) 		0.93
(1.00) 		0.842
(1.00) 		0.794
(1.00) 		0.364
(1.00)
CXORF22 9 (3%) 282 0.601
(1.00) 		0.905
(1.00) 		0.0456
(1.00) 		1
(1.00) 		0.721
(1.00) 		0.506
(1.00) 		0.606
(1.00) 		0.651
(1.00) 		0.282
(1.00) 		0.988
(1.00)
C1ORF150 3 (1%) 288 0.379
(1.00) 		0.613
(1.00) 		0.892
(1.00) 		0.606
(1.00)
GPX5 4 (1%) 287 0.329
(1.00) 		0.124
(1.00) 		0.386
(1.00) 		0.183
(1.00) 		0.193
(1.00) 		0.447
(1.00) 		0.832
(1.00) 		0.705
(1.00) 		0.829
(1.00)
LRRC55 6 (2%) 285 0.329
(1.00) 		0.45
(1.00) 		0.509
(1.00) 		0.142
(1.00) 		0.328
(1.00)
DCAF12L2 8 (3%) 283 0.868
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.68
(1.00) 		0.311
(1.00) 		0.697
(1.00) 		0.55
(1.00) 		0.727
(1.00) 		0.954
(1.00) 		0.947
(1.00)
LRFN5 7 (2%) 284 0.897
(1.00) 		0.62
(1.00) 		0.43
(1.00) 		1
(1.00) 		1
(1.00) 		0.817
(1.00) 		0.331
(1.00) 		0.434
(1.00) 		0.839
(1.00) 		0.947
(1.00)
LUM 5 (2%) 286 0.418
(1.00) 		0.475
(1.00) 		0.512
(1.00) 		1
(1.00) 		0.33
(1.00)
MMP13 6 (2%) 285 0.744
(1.00) 		0.727
(1.00) 		0.543
(1.00) 		0.454
(1.00) 		0.88
(1.00) 		0.201
(1.00) 		0.323
(1.00) 		0.259
(1.00) 		0.66
(1.00)
UGT2B28 6 (2%) 285 1
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.249
(1.00) 		0.515
(1.00)
OR5D13 5 (2%) 286 0.0767
(1.00) 		1
(1.00) 		0.297
(1.00) 		0.832
(1.00) 		0.33
(1.00) 		0.434
(1.00) 		0.109
(1.00)
ZNF99 6 (2%) 285 1
(1.00) 		0.821
(1.00) 		0.443
(1.00) 		0.616
(1.00) 		0.385
(1.00) 		0.402
(1.00) 		0.241
(1.00) 		0.234
(1.00)
SLC5A7 7 (2%) 284 0.0844
(1.00) 		0.205
(1.00) 		0.361
(1.00) 		0.832
(1.00) 		0.385
(1.00) 		0.765
(1.00) 		0.682
(1.00) 		0.359
(1.00)
TRPV6 8 (3%) 283 0.513
(1.00) 		0.488
(1.00) 		0.0843
(1.00) 		0.43
(1.00) 		0.432
(1.00) 		0.57
(1.00) 		0.832
(1.00) 		0.404
(1.00) 		0.287
(1.00)
SEMA3E 8 (3%) 283 0.167
(1.00) 		0.171
(1.00) 		0.543
(1.00) 		0.37
(1.00) 		0.819
(1.00) 		0.0529
(1.00) 		0.00903
(1.00) 		0.0589
(1.00) 		0.31
(1.00) 		0.123
(1.00)
SLC26A3 7 (2%) 284 0.45
(1.00) 		0.875
(1.00) 		0.557
(1.00) 		0.767
(1.00) 		0.801
(1.00) 		0.205
(1.00) 		0.0155
(1.00) 		0.682
(1.00) 		0.357
(1.00)
OR4D5 5 (2%) 286 0.107
(1.00) 		0.617
(1.00) 		0.364
(1.00) 		0.847
(1.00) 		0.738
(1.00) 		0.539
(1.00) 		0.645
(1.00)
TCHH 16 (5%) 275 0.275
(1.00) 		0.131
(1.00) 		0.422
(1.00) 		0.148
(1.00) 		0.446
(1.00) 		0.354
(1.00) 		0.581
(1.00) 		0.359
(1.00) 		0.007
(1.00) 		0.3
(1.00)
CFHR4 5 (2%) 286 0.744
(1.00) 		0.853
(1.00) 		0.83
(1.00) 		0.68
(1.00) 		0.524
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.667
(1.00)
GABRB2 6 (2%) 285 0.782
(1.00) 		0.0949
(1.00) 		0.136
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.153
(1.00) 		0.02
(1.00) 		0.234
(1.00) 		0.197
(1.00) 		0.319
(1.00)
IL18RAP 6 (2%) 285 0.329
(1.00) 		0.0598
(1.00) 		0.231
(1.00) 		0.183
(1.00) 		0.88
(1.00) 		0.138
(1.00) 		0.527
(1.00) 		0.538
(1.00) 		0.437
(1.00) 		0.284
(1.00)
OGDH 3 (1%) 288 1
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.351
(1.00) 		0.521
(1.00)
PCDH11X 9 (3%) 282 0.544
(1.00) 		0.48
(1.00) 		0.206
(1.00) 		0.035
(1.00) 		0.117
(1.00) 		0.0223
(1.00) 		0.328
(1.00) 		0.684
(1.00) 		0.44
(1.00)
SPRYD5 6 (2%) 285 0.874
(1.00) 		1
(1.00) 		0.196
(1.00) 		0.511
(1.00) 		0.587
(1.00) 		1
(1.00) 		0.434
(1.00) 		0.481
(1.00) 		0.0647
(1.00)
TGFA 4 (1%) 287 0.688
(1.00) 		1
(1.00) 		0.434
(1.00)
OR5P2 4 (1%) 287 0.534
(1.00) 		0.791
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.193
(1.00)
FOXR2 5 (2%) 286 1
(1.00) 		0.685
(1.00) 		0.756
(1.00) 		0.0381
(1.00) 		0.39
(1.00)
PSG8 6 (2%) 285 1
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.362
(1.00) 		0.673
(1.00) 		0.788
(1.00) 		0.701
(1.00) 		0.798
(1.00) 		0.489
(1.00) 		0.612
(1.00)
CNTNAP2 13 (4%) 278 0.872
(1.00) 		0.554
(1.00) 		0.174
(1.00) 		0.466
(1.00) 		0.756
(1.00) 		0.676
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.591
(1.00)
GABRA1 6 (2%) 285 0.203
(1.00) 		0.727
(1.00) 		0.708
(1.00) 		0.37
(1.00) 		0.88
(1.00) 		0.434
(1.00) 		0.323
(1.00) 		0.373
(1.00) 		0.254
(1.00)
DYNC1I1 7 (2%) 284 0.377
(1.00) 		0.0442
(1.00) 		0.417
(1.00) 		0.211
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.682
(1.00)
KDR 9 (3%) 282 0.521
(1.00) 		0.318
(1.00) 		0.278
(1.00) 		0.0146
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.0997
(1.00) 		0.651
(1.00)
PODXL 3 (1%) 288 1
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.79
(1.00)
SCN9A 11 (4%) 280 0.686
(1.00) 		0.499
(1.00) 		0.963
(1.00) 		0.341
(1.00) 		0.688
(1.00) 		0.763
(1.00) 		0.842
(1.00) 		0.0407
(1.00) 		0.346
(1.00)
PIK3C2G 9 (3%) 282 0.227
(1.00) 		0.0356
(1.00) 		0.846
(1.00) 		0.577
(1.00) 		0.267
(1.00) 		0.703
(1.00) 		0.763
(1.00) 		0.727
(1.00)
AFM 6 (2%) 285 1
(1.00) 		0.617
(1.00) 		0.808
(1.00) 		0.454
(1.00) 		0.515
(1.00) 		0.79
(1.00) 		0.323
(1.00)
CARD6 7 (2%) 284 0.571
(1.00) 		0.434
(1.00) 		0.19
(1.00) 		0.616
(1.00) 		0.641
(1.00) 		0.647
(1.00) 		0.619
(1.00) 		0.682
(1.00) 		0.854
(1.00) 		0.412
(1.00)
OR5K4 4 (1%) 287 0.776
(1.00) 		1
(1.00) 		0.675
(1.00) 		0.616
(1.00) 		0.0397
(1.00) 		0.852
(1.00) 		0.667
(1.00)
KRTAP20-2 3 (1%) 288 0.418
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.616
(1.00) 		0.281
(1.00) 		0.434
(1.00) 		0.109
(1.00)
PODNL1 4 (1%) 287 0.0767
(1.00) 		0.364
(1.00) 		0.83
(1.00) 		1
(1.00) 		0.0397
(1.00) 		0.791
(1.00) 		0.667
(1.00)
POTEF 5 (2%) 286 0.0303
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.79
(1.00) 		0.0708
(1.00)
OTC 3 (1%) 288 0.312
(1.00) 		0.791
(1.00) 		0.194
(1.00)
TRAT1 4 (1%) 287 0.469
(1.00) 		0.685
(1.00) 		0.767
(1.00) 		0.79
(1.00) 		0.827
(1.00) 		0.256
(1.00) 		0.522
(1.00)
RBM47 9 (3%) 282 0.256
(1.00) 		0.117
(1.00) 		0.168
(1.00) 		0.43
(1.00) 		0.44
(1.00) 		1
(1.00) 		0.537
(1.00)
KLK6 4 (1%) 287 0.00654
(1.00) 		1
(1.00) 		1
(1.00)
KRTAP4-7 3 (1%) 288 0.208
(1.00) 		0.184
(1.00) 		0.379
(1.00) 		0.331
(1.00) 		0.434
(1.00)
CDH9 8 (3%) 283 0.404
(1.00) 		0.129
(1.00) 		0.589
(1.00) 		0.577
(1.00) 		0.801
(1.00) 		0.332
(1.00) 		0.1
(1.00) 		0.0842
(1.00) 		0.88
(1.00)
OR4P4 4 (1%) 287 0.193
(1.00)
OR52M1 4 (1%) 287 0.469
(1.00) 		1
(1.00) 		0.19
(1.00) 		0.0591
(1.00) 		0.106
(1.00) 		0.852
(1.00) 		0.667
(1.00)
ADAMTS16 9 (3%) 282 1
(1.00) 		1
(1.00) 		0.717
(1.00) 		1
(1.00) 		0.906
(1.00) 		0.211
(1.00) 		0.629
(1.00) 		0.329
(1.00) 		0.787
(1.00)
GLT8D2 4 (1%) 287 0.652
(1.00) 		0.107
(1.00) 		1
(1.00)
KLF17 5 (2%) 286 0.625
(1.00) 		0.45
(1.00) 		0.633
(1.00) 		0.832
(1.00) 		0.738
(1.00) 		0.41
(1.00) 		0.538
(1.00)
CDHR3 3 (1%) 288 0.312
(1.00) 		1
(1.00) 		0.194
(1.00)
CD3EAP 3 (1%) 288 1
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.616
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.667
(1.00)
OR8J3 4 (1%) 287 0.692
(1.00) 		0.821
(1.00) 		0.297
(1.00) 		0.128
(1.00) 		0.194
(1.00) 		0.494
(1.00) 		0.109
(1.00)
AP3S1 3 (1%) 288 0.652
(1.00) 		1
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.633
(1.00)
CKMT1A 3 (1%) 288 0.418
(1.00) 		0.475
(1.00) 		0.331
(1.00) 		0.616
(1.00) 		0.115
(1.00)
ST6GAL2 6 (2%) 285 1
(1.00) 		0.875
(1.00) 		0.34
(1.00) 		0.767
(1.00) 		0.863
(1.00) 		0.221
(1.00) 		0.101
(1.00)
F9 4 (1%) 287 0.776
(1.00) 		1
(1.00) 		0.151
(1.00) 		0.12
(1.00) 		1
(1.00)
SHB 3 (1%) 288 0.418
(1.00) 		0.475
(1.00) 		1
(1.00)
RSPO3 3 (1%) 288 0.781
(1.00)
TCN1 4 (1%) 287 0.692
(1.00) 		0.466
(1.00) 		0.675
(1.00) 		0.183
(1.00) 		0.391
(1.00) 		0.0529
(1.00) 		0.259
(1.00) 		0.66
(1.00)
CDKN2C 3 (1%) 288 0.534
(1.00) 		0.791
(1.00) 		0.675
(1.00) 		0.616
(1.00) 		0.781
(1.00) 		0.512
(1.00) 		0.521
(1.00)
DRD5 7 (2%) 284 0.897
(1.00) 		0.62
(1.00) 		0.624
(1.00) 		0.344
(1.00) 		0.432
(1.00) 		0.338
(1.00) 		0.682
(1.00) 		0.765
(1.00) 		0.643
(1.00)
FGA 6 (2%) 285 0.241
(1.00) 		0.533
(1.00) 		0.0846
(1.00) 		0.0642
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.441
(1.00)
FGG 5 (2%) 286 0.218
(1.00) 		0.288
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.434
(1.00)
HCN1 12 (4%) 279 0.739
(1.00) 		1
(1.00) 		0.218
(1.00) 		0.0532
(1.00) 		0.533
(1.00) 		0.953
(1.00) 		0.663
(1.00) 		0.864
(1.00)
PAN3 6 (2%) 285 0.868
(1.00) 		0.533
(1.00) 		0.509
(1.00) 		0.544
(1.00) 		0.772
(1.00)
OR10G8 4 (1%) 287 0.843
(1.00) 		1
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.701
(1.00) 		0.606
(1.00)
PROKR2 6 (2%) 285 0.534
(1.00) 		0.212
(1.00) 		0.865
(1.00) 		0.847
(1.00) 		0.112
(1.00) 		0.0446
(1.00) 		0.0537
(1.00)
AZGP1 5 (2%) 286 0.868
(1.00) 		0.533
(1.00) 		0.128
(1.00) 		0.128
(1.00) 		1
(1.00)
CYP3A5 5 (2%) 286 1
(1.00) 		0.475
(1.00) 		0.863
(1.00) 		0.765
(1.00) 		0.623
(1.00) 		0.109
(1.00) 		0.742
(1.00) 		0.667
(1.00)
HIST1H2BE 3 (1%) 288 0.208
(1.00) 		0.475
(1.00) 		0.0901
(1.00) 		0.616
(1.00) 		0.379
(1.00)
PCMTD1 4 (1%) 287 1
(1.00) 		0.685
(1.00) 		0.443
(1.00) 		0.79
(1.00) 		0.563
(1.00) 		0.672
(1.00) 		0.832
(1.00)
'EGFR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.087

Table S1.  Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 87 83
EGFR MUTATED 21 13 37
EGFR WILD-TYPE 57 74 46

Figure S1.  Get High-res Image Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 9.19e-08 (Fisher's exact test), Q value = 8.1e-05

Table S2.  Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 111 81
EGFR MUTATED 16 50 9
EGFR WILD-TYPE 73 61 72

Figure S2.  Get High-res Image Gene #3: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 3.99e-05 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 54 31
EGFR MUTATED 6 25 6
EGFR WILD-TYPE 54 29 25

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 = 3.45e-07 (Fisher's exact test), Q value = 3e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 87 83
IDH1 MUTATED 0 14 0
IDH1 WILD-TYPE 78 73 83

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 = 1.17e-07 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 61 81
IDH1 MUTATED 0 0 14
IDH1 WILD-TYPE 106 61 67

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

'IDH1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 2.5e-06 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 84 50
IDH1 MUTATED 0 1 10
IDH1 WILD-TYPE 76 83 40

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

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.61e-05 (Fisher's exact test), Q value = 0.023

Table S7.  Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 111 81
IDH1 MUTATED 3 0 11
IDH1 WILD-TYPE 86 111 70

Figure S7.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Chi-square test), Q value = 0.2

Table S8.  Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 20 19 42
IDH1 MUTATED 7 0 1 0 0 0
IDH1 WILD-TYPE 23 3 32 20 19 42

Figure S8.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.051

Table S9.  Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 87 83
TP53 MUTATED 21 39 12
TP53 WILD-TYPE 57 48 71

Figure S9.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.098

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 111 81
TP53 MUTATED 35 17 30
TP53 WILD-TYPE 54 94 51

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

'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 8.02e-05 (Fisher's exact test), Q value = 0.07

Table S11.  Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 87 83
ATRX MUTATED 2 12 0
ATRX WILD-TYPE 76 75 83

Figure S11.  Get High-res Image Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.044

Table S12.  Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 61 81
ATRX MUTATED 2 0 12
ATRX WILD-TYPE 104 61 69

Figure S12.  Get High-res Image Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 3.46e-05 (Fisher's exact test), Q value = 0.03

Table S13.  Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 84 50
ATRX MUTATED 0 2 9
ATRX WILD-TYPE 76 82 41

Figure S13.  Get High-res Image Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 111 81
ATRX MUTATED 3 1 12
ATRX WILD-TYPE 86 110 69

Figure S14.  Get High-res Image Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000194 (Chi-square test), Q value = 0.17

Table S15.  Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 20 19 42
ATRX MUTATED 7 0 0 1 0 0
ATRX WILD-TYPE 23 3 33 19 19 42

Figure S15.  Get High-res Image Gene #36: 'ATRX MUTATION STATUS' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 291

  • Number of significantly mutated genes = 114

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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