Glioblastoma Multiforme: Correlation between gene mutation status and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.

Summary

Testing the association between mutation status of 181 genes and 5 clinical features across 276 patients, 2 significant findings detected with Q value < 0.25.

  • IDH1 mutation correlated to 'AGE'.

  • ANO2 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 181 genes and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		RADIATIONS
RADIATION
REGIMENINDICATION
nMutated (%) nWild-Type logrank test t-test Fisher's exact test t-test Fisher's exact test
IDH1 14 (5%) 262 0.00261
(1.00) 		7.95e-05
(0.0686) 		0.269
(1.00) 		0.0319
(1.00) 		0.00287
(1.00)
ANO2 5 (2%) 271 4.75e-09
(4.1e-06) 		0.0702
(1.00) 		0.0617
(1.00) 		0.363
(1.00) 		0.0512
(1.00)
EGFR 59 (21%) 217 0.59
(1.00) 		0.196
(1.00) 		0.0956
(1.00) 		0.34
(1.00) 		0.647
(1.00)
TP53 57 (21%) 219 0.281
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.876
(1.00)
PTEN 65 (24%) 211 0.514
(1.00) 		0.24
(1.00) 		0.557
(1.00) 		0.244
(1.00) 		1
(1.00)
PIK3R1 30 (11%) 246 0.775
(1.00) 		0.503
(1.00) 		0.548
(1.00) 		0.561
(1.00) 		0.686
(1.00)
RB1 18 (7%) 258 0.407
(1.00) 		0.313
(1.00) 		1
(1.00) 		0.0189
(1.00) 		0.615
(1.00)
NF1 25 (9%) 251 0.813
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.449
(1.00) 		0.379
(1.00)
PIK3CA 24 (9%) 252 0.925
(1.00) 		0.676
(1.00) 		1
(1.00) 		0.922
(1.00) 		0.372
(1.00)
SPTA1 26 (9%) 250 0.56
(1.00) 		0.228
(1.00) 		0.141
(1.00) 		0.572
(1.00) 		0.396
(1.00)
FLG 23 (8%) 253 0.262
(1.00) 		0.326
(1.00) 		1
(1.00) 		0.835
(1.00) 		0.494
(1.00)
GABRA6 10 (4%) 266 0.848
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.58
(1.00) 		1
(1.00)
RPL5 8 (3%) 268 0.897
(1.00) 		0.846
(1.00) 		0.47
(1.00) 		0.881
(1.00) 		0.718
(1.00)
KEL 11 (4%) 265 0.796
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.158
(1.00) 		1
(1.00)
RBM47 8 (3%) 268 0.893
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.414
(1.00) 		1
(1.00)
PCLO 22 (8%) 254 0.143
(1.00) 		0.967
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.351
(1.00)
TCHH 14 (5%) 262 0.307
(1.00) 		0.277
(1.00) 		0.584
(1.00) 		0.322
(1.00) 		0.392
(1.00)
SEMA3C 9 (3%) 267 0.0616
(1.00) 		0.745
(1.00) 		0.494
(1.00) 		0.751
(1.00) 		0.284
(1.00)
OR8K3 6 (2%) 270 0.704
(1.00) 		0.882
(1.00) 		0.42
(1.00) 		0.566
(1.00) 		0.668
(1.00)
PRB2 5 (2%) 271 0.928
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.000758
(0.653) 		1
(1.00)
RYR2 20 (7%) 256 0.845
(1.00) 		0.645
(1.00) 		0.811
(1.00) 		0.0862
(1.00) 		0.466
(1.00)
TPTE2 7 (3%) 269 0.191
(1.00) 		0.908
(1.00) 		0.709
(1.00) 		0.0356
(1.00) 		0.697
(1.00)
LZTR1 8 (3%) 268 0.284
(1.00) 		0.496
(1.00) 		0.265
(1.00) 		0.579
(1.00) 		0.131
(1.00)
DCAF12L2 6 (2%) 270 0.117
(1.00) 		0.972
(1.00) 		0.42
(1.00) 		0.629
(1.00) 		1
(1.00)
RIMS2 10 (4%) 266 0.379
(1.00) 		0.00133
(1.00) 		0.0985
(1.00) 		0.0356
(1.00) 		1
(1.00)
PSPH 5 (2%) 271 0.219
(1.00) 		0.362
(1.00) 		0.655
(1.00) 		0.914
(1.00) 		0.661
(1.00)
PDGFRA 9 (3%) 267 0.378
(1.00) 		0.0637
(1.00) 		1
(1.00) 		0.507
(1.00) 		0.284
(1.00)
SPRYD5 5 (2%) 271 0.555
(1.00) 		0.862
(1.00) 		1
(1.00) 		0.84
(1.00) 		1
(1.00)
LRFN5 7 (3%) 269 0.0281
(1.00) 		0.399
(1.00) 		0.264
(1.00) 		0.323
(1.00) 		0.00797
(1.00)
MUC16 34 (12%) 242 0.166
(1.00) 		0.925
(1.00) 		1
(1.00) 		0.939
(1.00) 		0.702
(1.00)
CALN1 5 (2%) 271 0.152
(1.00) 		0.817
(1.00) 		1
(1.00) 		0.663
(1.00) 		1
(1.00)
HCN1 7 (3%) 269 0.318
(1.00) 		0.897
(1.00) 		0.264
(1.00) 		0.661
(1.00) 		0.697
(1.00)
KIF2B 7 (3%) 269 0.271
(1.00) 		0.873
(1.00) 		0.709
(1.00) 		0.247
(1.00) 		0.242
(1.00)
AZGP1 4 (1%) 272 0.644
(1.00) 		0.84
(1.00) 		1
(1.00) 		1
(1.00)
MUC17 16 (6%) 260 0.997
(1.00) 		0.818
(1.00) 		0.597
(1.00) 		0.725
(1.00) 		1
(1.00)
AFM 6 (2%) 270 0.271
(1.00) 		0.398
(1.00) 		0.672
(1.00) 		0.363
(1.00) 		1
(1.00)
OR5D13 5 (2%) 271 0.461
(1.00) 		0.434
(1.00) 		0.655
(1.00) 		0.661
(1.00)
DRD5 6 (2%) 270 0.389
(1.00) 		0.425
(1.00) 		1
(1.00) 		0.668
(1.00)
SEMG1 6 (2%) 270 0.487
(1.00) 		0.0963
(1.00) 		1
(1.00) 		0.0886
(1.00) 		0.187
(1.00)
SULT1B1 5 (2%) 271 0.174
(1.00) 		0.635
(1.00) 		0.655
(1.00) 		0.981
(1.00) 		0.661
(1.00)
OR5D18 5 (2%) 271 0.225
(1.00) 		0.768
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.661
(1.00)
TRPV6 7 (3%) 269 0.702
(1.00) 		0.217
(1.00) 		0.709
(1.00) 		0.479
(1.00) 		0.1
(1.00)
POM121L12 5 (2%) 271 0.347
(1.00) 		0.216
(1.00) 		0.359
(1.00) 		0.661
(1.00) 		1
(1.00)
COL1A2 8 (3%) 268 0.907
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.0241
(1.00) 		0.131
(1.00)
LRRC55 5 (2%) 271 0.0742
(1.00) 		0.963
(1.00) 		0.359
(1.00) 		0.113
(1.00) 		0.661
(1.00)
CNTNAP2 8 (3%) 268 0.68
(1.00) 		0.516
(1.00) 		0.0545
(1.00) 		0.661
(1.00) 		0.718
(1.00)
HEATR7B2 9 (3%) 267 0.655
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.821
(1.00) 		0.284
(1.00)
OR4D5 5 (2%) 271 0.601
(1.00) 		0.143
(1.00) 		0.162
(1.00) 		0.378
(1.00) 		0.346
(1.00)
WNT2 5 (2%) 271 0.376
(1.00) 		0.237
(1.00) 		0.0617
(1.00) 		0.717
(1.00) 		1
(1.00)
GABRA1 4 (1%) 272 0.947
(1.00) 		0.189
(1.00) 		1
(1.00) 		0.247
(1.00) 		1
(1.00)
OR5W2 4 (1%) 272 0.324
(1.00) 		0.0738
(1.00) 		0.625
(1.00) 		0.302
(1.00)
SLC1A6 6 (2%) 270 0.595
(1.00) 		0.806
(1.00) 		0.42
(1.00) 		0.0271
(1.00) 		0.668
(1.00)
DOCK5 10 (4%) 266 0.175
(1.00) 		0.967
(1.00) 		0.335
(1.00) 		0.804
(1.00) 		0.743
(1.00)
HMCN1 15 (5%) 261 0.62
(1.00) 		0.0247
(1.00) 		0.583
(1.00) 		0.635
(1.00) 		0.404
(1.00)
STAG2 8 (3%) 268 0.000953
(0.814) 		0.866
(1.00) 		0.47
(1.00) 		0.0722
(1.00) 		0.455
(1.00)
UGT2A3 5 (2%) 271 0.731
(1.00) 		0.0186
(1.00) 		0.655
(1.00) 		0.716
(1.00) 		0.167
(1.00)
CDKN2C 3 (1%) 273 0.731
(1.00) 		0.576
(1.00) 		0.301
(1.00) 		1
(1.00)
REN 5 (2%) 271 0.565
(1.00) 		0.969
(1.00) 		0.655
(1.00) 		0.146
(1.00) 		1
(1.00)
CDC27 5 (2%) 271 0.201
(1.00) 		0.701
(1.00) 		0.359
(1.00) 		1
(1.00)
WBSCR17 5 (2%) 271 0.00139
(1.00) 		0.117
(1.00) 		0.0617
(1.00) 		0.0512
(1.00)
GRM3 7 (3%) 269 0.726
(1.00) 		0.638
(1.00) 		0.709
(1.00) 		0.447
(1.00) 		0.428
(1.00)
FOXG1 3 (1%) 273 0.127
(1.00) 		0.697
(1.00) 		0.556
(1.00) 		1
(1.00)
KLF17 5 (2%) 271 0.00218
(1.00) 		0.3
(1.00) 		0.162
(1.00) 		0.446
(1.00) 		1
(1.00)
SLCO6A1 6 (2%) 270 0.513
(1.00) 		0.91
(1.00) 		0.42
(1.00) 		0.0486
(1.00) 		0.0952
(1.00)
UGT2B28 5 (2%) 271 0.779
(1.00) 		0.889
(1.00) 		0.655
(1.00) 		0.414
(1.00) 		1
(1.00)
HIST1H2BE 3 (1%) 273 0.732
(1.00) 		0.192
(1.00) 		0.301
(1.00) 		0.5
(1.00) 		1
(1.00)
AP3S1 3 (1%) 273 0.247
(1.00) 		0.351
(1.00) 		0.301
(1.00) 		0.247
(1.00) 		0.554
(1.00)
DSG3 7 (3%) 269 0.233
(1.00) 		0.966
(1.00) 		0.0501
(1.00) 		0.342
(1.00) 		0.697
(1.00)
PROKR2 5 (2%) 271 0.957
(1.00) 		0.0495
(1.00) 		1
(1.00) 		0.663
(1.00) 		0.167
(1.00)
QKI 4 (1%) 272 0.692
(1.00) 		0.836
(1.00) 		0.625
(1.00) 		0.014
(1.00)
TAS2R41 3 (1%) 273 0.876
(1.00) 		0.13
(1.00) 		0.556
(1.00) 		0.278
(1.00)
PCDHA3 7 (3%) 269 0.247
(1.00) 		0.275
(1.00) 		0.104
(1.00) 		0.0659
(1.00) 		0.697
(1.00)
PAN3 6 (2%) 270 0.284
(1.00) 		0.47
(1.00) 		1
(1.00) 		0.763
(1.00) 		0.668
(1.00)
COL6A3 12 (4%) 264 0.958
(1.00) 		0.264
(1.00) 		0.366
(1.00) 		0.192
(1.00) 		0.352
(1.00)
CYP3A5 5 (2%) 271 0.313
(1.00) 		0.699
(1.00) 		0.359
(1.00) 		0.363
(1.00) 		1
(1.00)
OR5D16 4 (1%) 272 0.0653
(1.00) 		0.205
(1.00) 		0.625
(1.00) 		0.837
(1.00) 		1
(1.00)
PLCXD3 4 (1%) 272 0.0039
(1.00) 		0.721
(1.00) 		0.625
(1.00) 		0.612
(1.00)
NOX4 5 (2%) 271 0.996
(1.00) 		0.426
(1.00) 		0.359
(1.00) 		0.566
(1.00) 		1
(1.00)
KLK6 3 (1%) 273 0.248
(1.00) 		0.224
(1.00) 		0.556
(1.00) 		0.554
(1.00)
OR5AR1 3 (1%) 273 0.817
(1.00) 		0.075
(1.00) 		0.556
(1.00) 		0.286
(1.00) 		1
(1.00)
PODNL1 4 (1%) 272 0.102
(1.00) 		0.174
(1.00) 		0.625
(1.00) 		0.506
(1.00) 		0.123
(1.00)
TMPRSS6 6 (2%) 270 0.828
(1.00) 		0.207
(1.00) 		0.672
(1.00) 		0.342
(1.00) 		0.668
(1.00)
CALCR 5 (2%) 271 0.0432
(1.00) 		0.0821
(1.00) 		0.655
(1.00) 		0.663
(1.00) 		0.661
(1.00)
PCDHA1 7 (3%) 269 0.601
(1.00) 		0.311
(1.00) 		0.104
(1.00) 		0.981
(1.00) 		0.242
(1.00)
ADCY5 6 (2%) 270 0.99
(1.00) 		0.346
(1.00) 		0.42
(1.00) 		0.422
(1.00)
TGFA 3 (1%) 273 0.501
(1.00) 		0.477
(1.00) 		0.556
(1.00) 		1
(1.00)
GABRB2 5 (2%) 271 0.524
(1.00) 		0.0841
(1.00) 		0.359
(1.00) 		0.323
(1.00) 		0.346
(1.00)
ADAMTS16 6 (2%) 270 0.482
(1.00) 		0.894
(1.00) 		0.42
(1.00) 		0.414
(1.00) 		0.668
(1.00)
POTEH 3 (1%) 273 0.0221
(1.00) 		0.334
(1.00) 		1
(1.00) 		0.000758
(0.653) 		0.554
(1.00)
OR52M1 4 (1%) 272 0.966
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.743
(1.00) 		1
(1.00)
BCOR 6 (2%) 270 0.183
(1.00) 		0.585
(1.00) 		0.672
(1.00) 		0.187
(1.00)
PSG1 3 (1%) 273 0.0842
(1.00) 		0.283
(1.00) 		0.556
(1.00) 		1
(1.00)
TSHZ2 6 (2%) 270 0.449
(1.00) 		0.656
(1.00) 		0.672
(1.00) 		0.629
(1.00) 		0.422
(1.00)
FGD5 7 (3%) 269 0.0467
(1.00) 		0.962
(1.00) 		1
(1.00) 		0.0519
(1.00)
CDH18 6 (2%) 270 0.0502
(1.00) 		0.592
(1.00) 		0.42
(1.00) 		0.479
(1.00) 		0.668
(1.00)
KDELC2 4 (1%) 272 0.556
(1.00) 		0.904
(1.00) 		0.625
(1.00) 		0.548
(1.00) 		1
(1.00)
TREML2 3 (1%) 273 0.412
(1.00) 		0.158
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.278
(1.00)
FOXR2 4 (1%) 272 0.124
(1.00) 		0.813
(1.00) 		0.625
(1.00) 		0.716
(1.00) 		1
(1.00)
ADAM29 6 (2%) 270 0.734
(1.00) 		0.00818
(1.00) 		0.089
(1.00) 		0.000758
(0.653) 		0.668
(1.00)
DPP10 6 (2%) 270 0.851
(1.00) 		0.737
(1.00) 		0.672
(1.00) 		0.167
(1.00) 		1
(1.00)
KPRP 5 (2%) 271 0.281
(1.00) 		0.956
(1.00) 		1
(1.00) 		0.84
(1.00) 		1
(1.00)
OR13C5 4 (1%) 272 0.0612
(1.00) 		0.669
(1.00) 		0.141
(1.00) 		0.548
(1.00) 		0.302
(1.00)
OR5A1 4 (1%) 272 0.837
(1.00) 		0.212
(1.00) 		0.141
(1.00) 		0.914
(1.00) 		0.302
(1.00)
SERPINB4 3 (1%) 273 0.51
(1.00) 		0.869
(1.00) 		0.556
(1.00) 		0.278
(1.00)
LUM 4 (1%) 272 0.0826
(1.00) 		0.853
(1.00) 		1
(1.00) 		0.765
(1.00) 		0.612
(1.00)
GNAT3 4 (1%) 272 0.685
(1.00) 		0.295
(1.00) 		0.3
(1.00) 		0.247
(1.00) 		0.302
(1.00)
PCDH19 6 (2%) 270 0.618
(1.00) 		0.579
(1.00) 		0.196
(1.00) 		0.661
(1.00) 		0.422
(1.00)
OR5M3 4 (1%) 272 0.659
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.661
(1.00) 		0.612
(1.00)
ALPPL2 4 (1%) 272 0.325
(1.00) 		0.141
(1.00) 		1
(1.00) 		1
(1.00)
RELN 10 (4%) 266 0.477
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.84
(1.00) 		0.743
(1.00)
MSL3 3 (1%) 273 0.899
(1.00) 		0.342
(1.00) 		1
(1.00) 		1
(1.00)
GLT1D1 3 (1%) 273 0.419
(1.00) 		0.0397
(1.00) 		1
(1.00) 		1
(1.00)
ABCB1 7 (3%) 269 0.493
(1.00) 		0.0432
(1.00) 		0.264
(1.00) 		0.0659
(1.00) 		0.242
(1.00)
ELTD1 5 (2%) 271 0.908
(1.00) 		0.83
(1.00) 		0.655
(1.00) 		0.113
(1.00) 		1
(1.00)
TRAT1 3 (1%) 273 0.0111
(1.00) 		0.084
(1.00) 		1
(1.00) 		0.278
(1.00)
MAGEB4 4 (1%) 272 0.152
(1.00) 		0.114
(1.00) 		0.141
(1.00) 		0.166
(1.00) 		1
(1.00)
SLC5A7 4 (1%) 272 0.0445
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.0886
(1.00) 		1
(1.00)
BRAF 3 (1%) 273 0.879
(1.00) 		0.0474
(1.00) 		1
(1.00) 		0.000758
(0.653) 		0.278
(1.00)
DAO 4 (1%) 272 0.933
(1.00) 		0.975
(1.00) 		1
(1.00) 		0.765
(1.00) 		0.612
(1.00)
KRT37 4 (1%) 272 0.947
(1.00) 		0.813
(1.00) 		1
(1.00) 		0.123
(1.00)
PRDM9 6 (2%) 270 0.959
(1.00) 		0.0709
(1.00) 		0.672
(1.00) 		0.604
(1.00) 		1
(1.00)
ZNF181 4 (1%) 272 0.378
(1.00) 		0.498
(1.00) 		0.141
(1.00) 		0.247
(1.00) 		1
(1.00)
IL18RAP 4 (1%) 272 0.945
(1.00) 		0.178
(1.00) 		0.141
(1.00) 		0.286
(1.00) 		1
(1.00)
POTEG 4 (1%) 272 0.874
(1.00) 		0.646
(1.00) 		0.141
(1.00) 		0.612
(1.00)
PCDH11Y 6 (2%) 270 0.282
(1.00) 		0.948
(1.00) 		0.089
(1.00) 		0.479
(1.00) 		0.422
(1.00)
RSPO3 3 (1%) 273 0.397
(1.00) 		0.766
(1.00) 		0.556
(1.00) 		0.278
(1.00)
SEMA3E 5 (2%) 271 0.43
(1.00) 		0.416
(1.00) 		0.655
(1.00) 		0.166
(1.00) 		0.167
(1.00)
SLC27A2 5 (2%) 271 0.374
(1.00) 		0.292
(1.00) 		0.359
(1.00) 		0.661
(1.00) 		0.661
(1.00)
CKMT1A 3 (1%) 273 0.491
(1.00) 		0.0428
(1.00) 		0.301
(1.00) 		0.861
(1.00) 		1
(1.00)
CYP2D6 4 (1%) 272 0.0603
(1.00) 		0.201
(1.00) 		0.625
(1.00) 		0.123
(1.00)
GABRB3 4 (1%) 272 0.939
(1.00) 		0.715
(1.00) 		0.141
(1.00) 		1
(1.00)
TAF1L 8 (3%) 268 0.12
(1.00) 		0.137
(1.00) 		0.0289
(1.00) 		0.137
(1.00) 		0.455
(1.00)
TNFSF9 3 (1%) 273 0.816
(1.00) 		0.638
(1.00) 		0.301
(1.00) 		0.548
(1.00) 		0.554
(1.00)
ZDHHC4 3 (1%) 273 0.802
(1.00) 		0.764
(1.00) 		1
(1.00) 		1
(1.00)
FBLN2 5 (2%) 271 0.773
(1.00) 		0.0178
(1.00) 		1
(1.00) 		0.348
(1.00) 		0.661
(1.00)
SYT16 5 (2%) 271 0.368
(1.00) 		0.367
(1.00) 		0.162
(1.00) 		0.116
(1.00) 		0.346
(1.00)
F9 4 (1%) 272 0.0203
(1.00) 		0.559
(1.00) 		0.625
(1.00) 		1
(1.00)
CD33 4 (1%) 272 0.52
(1.00) 		0.0328
(1.00) 		0.141
(1.00) 		1
(1.00)
CXORF22 6 (2%) 270 0.856
(1.00) 		0.49
(1.00) 		0.026
(1.00) 		0.661
(1.00) 		0.668
(1.00)
CARD6 6 (2%) 270 0.03
(1.00) 		0.00839
(1.00) 		0.42
(1.00) 		0.113
(1.00) 		0.422
(1.00)
PLEKHG4B 6 (2%) 270 0.36
(1.00) 		0.059
(1.00) 		0.196
(1.00) 		0.716
(1.00) 		0.422
(1.00)
CPNE8 4 (1%) 272 0.901
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.612
(1.00)
MRGPRE 3 (1%) 273 0.585
(1.00) 		0.447
(1.00) 		0.0481
(1.00) 		0.247
(1.00) 		0.554
(1.00)
RBMS3 4 (1%) 272 0.556
(1.00) 		0.842
(1.00) 		0.625
(1.00) 		0.853
(1.00) 		0.302
(1.00)
NLRP12 6 (2%) 270 0.985
(1.00) 		0.477
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.187
(1.00)
OR4P4 3 (1%) 273 0.749
(1.00) 		0.477
(1.00) 		1
(1.00) 		1
(1.00)
SDK1 9 (3%) 267 0.502
(1.00) 		0.215
(1.00) 		0.494
(1.00) 		0.231
(1.00) 		0.0295
(1.00)
CFHR4 3 (1%) 273 0.574
(1.00) 		0.838
(1.00) 		0.556
(1.00) 		0.716
(1.00) 		1
(1.00)
DPPA4 3 (1%) 273 0.515
(1.00) 		0.552
(1.00) 		0.301
(1.00) 		0.716
(1.00) 		1
(1.00)
LPAR3 3 (1%) 273 0.124
(1.00) 		0.847
(1.00) 		1
(1.00) 		0.0412
(1.00)
FBN3 10 (4%) 266 0.246
(1.00) 		0.393
(1.00) 		0.505
(1.00) 		0.456
(1.00) 		1
(1.00)
CD1D 3 (1%) 273 0.0527
(1.00) 		0.235
(1.00) 		1
(1.00) 		0.000758
(0.653) 		0.554
(1.00)
POTEF 5 (2%) 271 0.971
(1.00) 		0.718
(1.00) 		1
(1.00) 		1
(1.00)
ACSM2B 4 (1%) 272 0.276
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.302
(1.00)
ZNF618 5 (2%) 271 0.066
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.505
(1.00) 		0.346
(1.00)
FBXL12 3 (1%) 273 0.844
(1.00) 		0.71
(1.00) 		1
(1.00) 		1
(1.00)
CHD8 7 (3%) 269 0.678
(1.00) 		0.424
(1.00) 		0.264
(1.00) 		0.539
(1.00) 		0.242
(1.00)
NLRP5 6 (2%) 270 0.989
(1.00) 		0.318
(1.00) 		0.42
(1.00) 		0.283
(1.00) 		1
(1.00)
OR5P2 3 (1%) 273 0.295
(1.00) 		0.32
(1.00) 		0.301
(1.00) 		0.000758
(0.653) 		1
(1.00)
CLYBL 3 (1%) 273 0.833
(1.00) 		0.356
(1.00) 		1
(1.00) 		1
(1.00)
MMP13 4 (1%) 272 0.847
(1.00) 		0.307
(1.00) 		0.625
(1.00) 		0.116
(1.00) 		0.302
(1.00)
SLCO5A1 4 (1%) 272 0.931
(1.00) 		0.724
(1.00) 		0.141
(1.00) 		0.612
(1.00)
OR4C11 3 (1%) 273 0.481
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.278
(1.00)
TRIML1 4 (1%) 272 0.0651
(1.00) 		0.283
(1.00) 		0.141
(1.00) 		0.612
(1.00)
FRMD7 5 (2%) 271 0.355
(1.00) 		0.527
(1.00) 		0.655
(1.00) 		0.921
(1.00) 		1
(1.00)
GRIN2A 7 (3%) 269 0.319
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.566
(1.00) 		1
(1.00)
KCNB2 4 (1%) 272 0.674
(1.00) 		0.8
(1.00) 		0.625
(1.00) 		0.123
(1.00)
SCN9A 8 (3%) 268 0.263
(1.00) 		0.538
(1.00) 		0.715
(1.00) 		0.84
(1.00) 		0.131
(1.00)
UGT2B10 4 (1%) 272 0.685
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.000758
(0.653) 		0.612
(1.00)
KDR 6 (2%) 270 0.14
(1.00) 		0.795
(1.00) 		0.42
(1.00) 		0.498
(1.00) 		0.668
(1.00)
NDST4 5 (2%) 271 0.934
(1.00) 		0.327
(1.00) 		0.359
(1.00) 		0.0899
(1.00) 		0.167
(1.00)
PIK3C2G 6 (2%) 270 0.541
(1.00) 		0.869
(1.00) 		0.672
(1.00) 		0.661
(1.00) 		0.422
(1.00)
CDH9 5 (2%) 271 0.763
(1.00) 		0.876
(1.00) 		0.359
(1.00) 		0.346
(1.00)
AHNAK2 14 (5%) 262 0.859
(1.00) 		0.446
(1.00) 		0.0429
(1.00) 		0.735
(1.00) 		0.569
(1.00)
SH3RF2 5 (2%) 271 0.392
(1.00) 		0.268
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.167
(1.00)
USH2A 14 (5%) 262 0.598
(1.00) 		0.642
(1.00) 		0.269
(1.00) 		0.918
(1.00) 		0.0866
(1.00)
PCDHB7 4 (1%) 272 0.686
(1.00) 		0.26
(1.00) 		0.3
(1.00) 		0.32
(1.00) 		1
(1.00)
TLR6 5 (2%) 271 0.745
(1.00) 		0.667
(1.00) 		0.655
(1.00) 		1
(1.00)
PAK4 3 (1%) 273 0.853
(1.00) 		0.337
(1.00) 		0.556
(1.00) 		0.765
(1.00) 		1
(1.00)
PTX4 4 (1%) 272 0.643
(1.00) 		0.983
(1.00) 		0.625
(1.00) 		0.363
(1.00) 		0.612
(1.00)
SIGLEC8 3 (1%) 273 0.861
(1.00) 		0.152
(1.00) 		1
(1.00) 		0.0469
(1.00) 		0.278
(1.00)
'IDH1 MUTATION STATUS' versus 'AGE'

P value = 7.95e-05 (t-test), Q value = 0.069

Table S1.  Gene #7: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 276 61.1 (12.6)
IDH1 MUTATED 14 40.7 (14.4)
IDH1 WILD-TYPE 262 62.2 (11.5)

Figure S1.  Get High-res Image Gene #7: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'ANO2 MUTATION STATUS' versus 'Time to Death'

P value = 4.75e-09 (logrank test), Q value = 4.1e-06

Table S2.  Gene #174: 'ANO2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 276 176 0.1 - 58.8 (8.4)
ANO2 MUTATED 5 5 0.2 - 4.7 (2.5)
ANO2 WILD-TYPE 271 171 0.1 - 58.8 (8.6)

Figure S2.  Get High-res Image Gene #174: 'ANO2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

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

  • Clinical data file = GBM-TP.clin.merged.picked.txt

  • Number of patients = 276

  • Number of significantly mutated genes = 181

  • Number of selected clinical features = 5

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] 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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