Correlation between gene mutation status and selected clinical features
Brain Lower Grade Glioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1BZ654Z
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1BZ654Z
Overview
Introduction

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

Summary

Testing the association between mutation status of 143 genes and 8 clinical features across 473 patients, 25 significant findings detected with Q value < 0.25.

  • IDH1 mutation correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • TP53 mutation correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • ATRX mutation correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • CIC mutation correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • NOTCH1 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • EGFR mutation correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • IDH2 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • NF1 mutation correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • PTEN mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • FUBP1 mutation correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • ZNF292 mutation correlated to 'YEARS_TO_BIRTH'.

  • PLCG1 mutation correlated to 'Time to Death'.

  • TMEM184A mutation correlated to 'Time to Death'.

  • HCFC1 mutation correlated to 'GENDER'.

  • TNFSF14 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 143 genes and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 25 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
TP53 226 (48%) 247 0.03
(0.621) 		1.74e-11
(6.65e-09) 		0.228
(0.923) 		0.188
(0.833) 		1e-05
(0.00104) 		0.00536
(0.245) 		0.0532
(0.771) 		0.633
(1.00)
PTEN 23 (5%) 450 2.57e-05
(0.00226) 		0.00441
(0.219) 		0.399
(1.00) 		0.509
(1.00) 		0.00126
(0.0861) 		0.419
(1.00) 		0.254
(0.945) 		1
(1.00)
IDH1 367 (78%) 106 6.57e-14
(7.52e-11) 		4.24e-07
(6.92e-05) 		0.74
(1.00) 		0.0146
(0.47) 		0.00655
(0.268) 		0.679
(1.00) 		0.0831
(0.826) 		0.567
(1.00)
ATRX 181 (38%) 292 0.147
(0.831) 		1.63e-11
(6.65e-09) 		0.703
(1.00) 		0.588
(1.00) 		1e-05
(0.00104) 		0.012
(0.428) 		0.428
(1.00) 		0.629
(1.00)
CIC 100 (21%) 373 0.00433
(0.219) 		0.0432
(0.756) 		0.497
(1.00) 		0.457
(1.00) 		1e-05
(0.00104) 		0.0869
(0.826) 		0.822
(1.00) 		0.775
(1.00)
EGFR 30 (6%) 443 6.3e-09
(1.44e-06) 		4.56e-09
(1.3e-06) 		0.85
(1.00) 		0.0242
(0.579) 		0.0248
(0.579) 		0.235
(0.923) 		0.368
(1.00) 		0.622
(1.00)
NF1 31 (7%) 442 2.17e-05
(0.00207) 		0.0189
(0.54) 		0.581
(1.00) 		0.435
(1.00) 		0.0039
(0.215) 		0.096
(0.826) 		0.276
(0.971) 		0.353
(1.00)
FUBP1 46 (10%) 427 0.262
(0.947) 		0.00493
(0.235) 		0.535
(1.00) 		0.268
(0.966) 		1e-05
(0.00104) 		1
(1.00) 		0.735
(1.00) 		0.24
(0.929)
NOTCH1 42 (9%) 431 0.231
(0.923) 		0.0436
(0.756) 		0.627
(1.00) 		0.488
(1.00) 		3e-05
(0.00245) 		1
(1.00) 		0.431
(1.00) 		0.675
(1.00)
IDH2 19 (4%) 454 0.104
(0.831) 		0.12
(0.831) 		0.815
(1.00) 		0.881
(1.00) 		0.00128
(0.0861) 		0.773
(1.00) 		0.645
(1.00) 		0.165
(0.832)
ZNF292 13 (3%) 460 0.614
(1.00) 		0.00395
(0.215) 		0.258
(0.947) 		0.612
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.157
(0.831) 		1
(1.00)
PLCG1 6 (1%) 467 5.98e-08
(1.14e-05) 		0.0153
(0.47) 		0.411
(1.00) 		0.642
(1.00) 		0.347
(1.00) 		0.331
(1.00) 		0.276
(0.971) 		1
(1.00)
TMEM184A 3 (1%) 470 0.000413
(0.0315) 		0.154
(0.831) 		1
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.147
(0.831) 		1
(1.00)
HCFC1 7 (1%) 466 0.286
(0.989) 		0.58
(1.00) 		0.0029
(0.184) 		0.499
(1.00) 		0.0301
(0.621) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TNFSF14 5 (1%) 468 0.00346
(0.208) 		0.0554
(0.79) 		1
(1.00) 		0.097
(0.826) 		1
(1.00) 		0.588
(1.00) 		1
(1.00) 		1
(1.00)
PIK3R1 20 (4%) 453 0.14
(0.831) 		0.1
(0.831) 		0.253
(0.945) 		0.684
(1.00) 		0.479
(1.00) 		0.0842
(0.826) 		0.119
(0.831) 		1
(1.00)
ARID1A 19 (4%) 454 0.0364
(0.686) 		0.695
(1.00) 		0.348
(1.00) 		0.526
(1.00) 		0.347
(1.00) 		0.773
(1.00) 		1
(1.00) 		0.557
(1.00)
PIK3CA 42 (9%) 431 0.563
(1.00) 		0.0459
(0.771) 		1
(1.00) 		0.116
(0.831) 		0.0163
(0.48) 		0.838
(1.00) 		0.839
(1.00) 		1
(1.00)
STK19 10 (2%) 463 0.426
(1.00) 		0.312
(1.00) 		0.113
(0.831) 		0.176
(0.832) 		0.0674
(0.826) 		0.695
(1.00) 		1
(1.00) 		0.0591
(0.795)
NIPBL 17 (4%) 456 0.00599
(0.254) 		0.201
(0.853) 		0.32
(1.00) 		0.415
(1.00) 		0.0743
(0.826) 		0.545
(1.00) 		0.0799
(0.826) 		0.151
(0.831)
CREBZF 6 (1%) 467 0.659
(1.00) 		0.116
(0.831) 		0.411
(1.00) 		0.112
(0.831) 		0.113
(0.831) 		1
(1.00) 		0.273
(0.971) 		1
(1.00)
TCF12 15 (3%) 458 0.88
(1.00) 		0.232
(0.923) 		0.598
(1.00) 		0.773
(1.00) 		0.945
(1.00) 		0.323
(1.00) 		1
(1.00) 		1
(1.00)
TRERF1 6 (1%) 467 0.697
(1.00) 		0.285
(0.989) 		0.0909
(0.826) 		0.627
(1.00) 		0.147
(0.831) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SRPX 3 (1%) 470 0.232
(0.923) 		0.0998
(0.831) 		0.0831
(0.826) 		0.787
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00)
SMARCA4 24 (5%) 449 0.0234
(0.579) 		0.387
(1.00) 		0.399
(1.00) 		0.117
(0.831) 		0.932
(1.00) 		0.107
(0.831) 		0.131
(0.831) 		0.576
(1.00)
EMG1 7 (1%) 466 0.467
(1.00) 		0.0651
(0.82) 		0.704
(1.00) 		0.462
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
FAM47C 18 (4%) 455 0.177
(0.832) 		0.571
(1.00) 		0.339
(1.00) 		0.877
(1.00) 		0.623
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.517
(1.00)
TNRC18 10 (2%) 463 0.75
(1.00) 		0.648
(1.00) 		0.198
(0.843) 		0.812
(1.00) 		0.0655
(0.82) 		0.695
(1.00) 		1
(1.00) 		1
(1.00)
DNMT3A 10 (2%) 463 0.0629
(0.82) 		0.486
(1.00) 		1
(1.00) 		0.804
(1.00) 		0.304
(1.00) 		0.695
(1.00) 		0.416
(1.00) 		0.346
(1.00)
HTRA2 5 (1%) 468 0.348
(1.00) 		0.028
(0.621) 		1
(1.00) 		0.378
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.19
(0.833)
ZNF709 4 (1%) 469 0.0638
(0.82) 		0.597
(1.00) 		0.135
(0.831) 		0.302
(1.00) 		0.0246
(0.579) 		0.193
(0.833) 		0.155
(0.831)
RBPJ 7 (1%) 466 0.936
(1.00) 		0.0559
(0.79) 		1
(1.00) 		0.29
(0.995) 		0.306
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
NRAS 4 (1%) 469 0.289
(0.993) 		0.892
(1.00) 		1
(1.00) 		0.505
(1.00) 		0.0424
(0.756) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
PTPN11 7 (1%) 466 0.208
(0.869) 		0.342
(1.00) 		1
(1.00) 		0.428
(1.00) 		0.272
(0.971) 		0.626
(1.00) 		0.313
(1.00) 		1
(1.00)
GAGE2D 5 (1%) 468 0.648
(1.00) 		0.55
(1.00) 		0.392
(1.00) 		1
(1.00) 		1
(1.00) 		0.237
(0.923) 		0.19
(0.833)
ARID2 11 (2%) 462 0.407
(1.00) 		0.114
(0.831) 		1
(1.00) 		0.942
(1.00) 		0.187
(0.833) 		0.454
(1.00) 		0.236
(0.923) 		1
(1.00)
ZMIZ1 8 (2%) 465 0.0472
(0.771) 		0.904
(1.00) 		0.306
(1.00) 		0.868
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.145
(0.831) 		0.0297
(0.621)
PDGFRA 8 (2%) 465 0.118
(0.831) 		0.7
(1.00) 		0.734
(1.00) 		0.119
(0.831) 		0.141
(0.831) 		0.0499
(0.771) 		1
(1.00) 		0.287
(0.989)
ZNF512B 4 (1%) 469 0.152
(0.831) 		0.592
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.172
(0.832) 		1
(1.00) 		1
(1.00)
PPL 5 (1%) 468 0.0746
(0.826) 		0.824
(1.00) 		0.658
(1.00) 		0.965
(1.00) 		0.453
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PRX 10 (2%) 463 0.924
(1.00) 		0.468
(1.00) 		0.345
(1.00) 		0.755
(1.00) 		0.718
(1.00) 		0.695
(1.00) 		1
(1.00) 		0.346
(1.00)
NKD2 4 (1%) 469 0.552
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.376
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
IRS4 7 (1%) 466 0.225
(0.915) 		0.494
(1.00) 		1
(1.00) 		0.552
(1.00) 		0.113
(0.831) 		0.626
(1.00) 		1
(1.00) 		0.256
(0.945)
SPTAN1 5 (1%) 468 0.0867
(0.826) 		0.452
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.224
(0.915) 		0.251
(0.945) 		1
(1.00) 		0.19
(0.833)
CIB1 4 (1%) 469 0.42
(1.00) 		0.996
(1.00) 		1
(1.00) 		0.868
(1.00) 		0.839
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
EIF1AX 4 (1%) 469 0.346
(1.00) 		0.93
(1.00) 		0.135
(0.831) 		0.94
(1.00) 		0.193
(0.833) 		0.172
(0.832) 		1
(1.00) 		1
(1.00)
SCN4A 6 (1%) 467 0.283
(0.988) 		0.261
(0.947) 		0.411
(1.00) 		0.255
(0.945) 		1
(1.00) 		0.0909
(0.826) 		1
(1.00) 		1
(1.00)
DLC1 5 (1%) 468 0.882
(1.00) 		0.983
(1.00) 		0.658
(1.00) 		0.549
(1.00) 		0.0528
(0.771) 		1
(1.00) 		1
(1.00)
TMEM216 3 (1%) 470 0.78
(1.00) 		0.832
(1.00) 		0.0831
(0.826) 		0.474
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MYT1 6 (1%) 467 0.372
(1.00) 		0.403
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.147
(0.831) 		0.331
(1.00) 		1
(1.00) 		1
(1.00)
SMARCB1 4 (1%) 469 0.432
(1.00) 		0.807
(1.00) 		0.635
(1.00) 		0.868
(1.00) 		0.839
(1.00) 		0.0246
(0.579) 		1
(1.00) 		1
(1.00)
RIPK4 8 (2%) 465 0.845
(1.00) 		0.325
(1.00) 		0.734
(1.00) 		0.959
(1.00) 		0.754
(1.00) 		0.656
(1.00) 		0.0728
(0.826) 		1
(1.00)
NEU2 4 (1%) 469 0.72
(1.00) 		0.138
(0.831) 		0.635
(1.00) 		0.68
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
PTPRH 8 (2%) 465 0.883
(1.00) 		0.0587
(0.795) 		0.734
(1.00) 		0.213
(0.88) 		0.431
(1.00) 		0.19
(0.833) 		1
(1.00) 		1
(1.00)
MAPK15 4 (1%) 469 0.0057
(0.251) 		0.489
(1.00) 		0.635
(1.00) 		0.459
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
TPX2 3 (1%) 470 0.14
(0.831) 		0.411
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
SLC12A7 5 (1%) 468 0.0967
(0.826) 		0.57
(1.00) 		0.658
(1.00) 		0.581
(1.00) 		0.647
(1.00) 		0.0528
(0.771) 		0.235
(0.923) 		1
(1.00)
PLXNA3 8 (2%) 465 0.13
(0.831) 		0.295
(1.00) 		0.146
(0.831) 		0.672
(1.00) 		1
(1.00) 		0.0499
(0.771) 		0.0486
(0.771) 		1
(1.00)
RET 6 (1%) 467 0.921
(1.00) 		0.76
(1.00) 		0.411
(1.00) 		0.419
(1.00) 		0.037
(0.686) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ZNF148 4 (1%) 469 0.14
(0.831) 		0.661
(1.00) 		1
(1.00) 		0.455
(1.00) 		0.58
(1.00) 		0.0818
(0.826) 		1
(1.00)
HDAC2 4 (1%) 469 0.518
(1.00) 		0.199
(0.845) 		1
(1.00) 		0.456
(1.00) 		0.0246
(0.579) 		1
(1.00) 		1
(1.00)
RBBP6 6 (1%) 467 0.273
(0.971) 		0.324
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.125
(0.831) 		1
(1.00)
MED9 3 (1%) 470 0.196
(0.84) 		0.86
(1.00) 		0.26
(0.947) 		0.0152
(0.47) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DDX5 5 (1%) 468 0.156
(0.831) 		0.852
(1.00) 		1
(1.00) 		0.263
(0.948) 		0.647
(1.00) 		0.251
(0.945) 		1
(1.00) 		0.155
(0.831)
ZC3H11A 5 (1%) 468 0.131
(0.831) 		0.162
(0.832) 		0.392
(1.00) 		0.179
(0.833) 		0.155
(0.831) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SLC6A3 9 (2%) 464 0.856
(1.00) 		0.383
(1.00) 		0.514
(1.00) 		0.759
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.256
(0.945)
TPTE2 5 (1%) 468 0.412
(1.00) 		0.543
(1.00) 		0.658
(1.00) 		0.177
(0.832) 		0.0509
(0.771) 		0.588
(1.00) 		1
(1.00) 		1
(1.00)
C4BPA 4 (1%) 469 0.494
(1.00) 		0.717
(1.00) 		0.323
(1.00) 		0.65
(1.00) 		0.142
(0.831) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
MATK 5 (1%) 468 0.431
(1.00) 		0.446
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.0528
(0.771) 		1
(1.00) 		1
(1.00)
SMOC1 3 (1%) 470 0.506
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.94
(1.00) 		0.362
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
NAP1L2 4 (1%) 469 0.285
(0.989) 		0.181
(0.833) 		1
(1.00) 		0.3
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
CD99L2 3 (1%) 470 0.168
(0.832) 		0.308
(1.00) 		0.0831
(0.826) 		0.787
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00)
SELE 6 (1%) 467 0.824
(1.00) 		0.168
(0.832) 		0.411
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.331
(1.00) 		1
(1.00) 		1
(1.00)
FHOD1 6 (1%) 467 0.245
(0.945) 		0.175
(0.832) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
HTR3A 7 (1%) 466 0.581
(1.00) 		0.545
(1.00) 		0.047
(0.771) 		1
(1.00) 		1
(1.00) 		0.0079
(0.292) 		1
(1.00)
RB1 5 (1%) 468 0.968
(1.00) 		0.389
(1.00) 		0.173
(0.832) 		0.222
(0.915) 		0.0528
(0.771) 		0.235
(0.923) 		1
(1.00)
FGD6 4 (1%) 469 0.771
(1.00) 		0.96
(1.00) 		0.0361
(0.686) 		0.428
(1.00) 		0.565
(1.00) 		0.0246
(0.579) 		1
(1.00) 		1
(1.00)
CD72 3 (1%) 470 0.483
(1.00) 		0.968
(1.00) 		0.584
(1.00) 		0.428
(1.00) 		0.0659
(0.82) 		1
(1.00) 		1
(1.00) 		1
(1.00)
NKPD1 3 (1%) 470 0.158
(0.831) 		0.0823
(0.826) 		0.584
(1.00) 		0.628
(1.00) 		1
(1.00) 		1
(1.00) 		0.119
(0.831)
MTMR1 4 (1%) 469 0.472
(1.00) 		0.171
(0.832) 		0.323
(1.00) 		0.681
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
GPR133 3 (1%) 470 0.128
(0.831) 		0.584
(1.00) 		1
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.119
(0.831)
CNOT4 5 (1%) 468 0.131
(0.831) 		0.666
(1.00) 		1
(1.00) 		0.119
(0.831) 		0.648
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ZBTB20 19 (4%) 454 0.203
(0.856) 		0.53
(1.00) 		0.64
(1.00) 		0.938
(1.00) 		0.176
(0.832) 		0.552
(1.00) 		0.193
(0.833) 		0.537
(1.00)
ROBO3 4 (1%) 469 0.646
(1.00) 		0.808
(1.00) 		0.323
(1.00) 		0.147
(0.831) 		0.681
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
PDE8A 6 (1%) 467 0.62
(1.00) 		0.0304
(0.621) 		1
(1.00) 		0.455
(1.00) 		0.331
(1.00) 		1
(1.00) 		1
(1.00)
EEF1D 3 (1%) 470 0.36
(1.00) 		0.101
(0.831) 		0.584
(1.00) 		1
(1.00) 		0.00717
(0.283) 		1
(1.00) 		1
(1.00)
MET 7 (1%) 466 0.259
(0.947) 		0.446
(1.00) 		1
(1.00) 		0.554
(1.00) 		0.562
(1.00) 		0.137
(0.831) 		1
(1.00) 		1
(1.00)
CUL4B 10 (2%) 463 0.341
(1.00) 		0.815
(1.00) 		0.113
(0.831) 		0.817
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.212
(0.88) 		1
(1.00)
SNX31 4 (1%) 469 0.0939
(0.826) 		0.465
(1.00) 		0.323
(1.00) 		0.839
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
PHF3 8 (2%) 465 0.903
(1.00) 		0.617
(1.00) 		0.734
(1.00) 		0.213
(0.88) 		0.539
(1.00) 		0.19
(0.833) 		0.35
(1.00) 		0.256
(0.945)
G6PC 5 (1%) 468 0.868
(1.00) 		0.112
(0.831) 		0.392
(1.00) 		0.377
(1.00) 		0.251
(0.945) 		1
(1.00) 		0.19
(0.833)
FOXQ1 3 (1%) 470 0.5
(1.00) 		0.252
(0.945) 		0.584
(1.00) 		1
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
AEBP1 4 (1%) 469 0.429
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.457
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SETD2 8 (2%) 465 0.826
(1.00) 		0.0314
(0.63) 		0.734
(1.00) 		0.565
(1.00) 		0.752
(1.00) 		0.19
(0.833) 		0.349
(1.00) 		1
(1.00)
DST 11 (2%) 462 0.0775
(0.826) 		0.397
(1.00) 		0.763
(1.00) 		0.875
(1.00) 		0.0925
(0.826) 		1
(1.00) 		1
(1.00) 		0.0705
(0.826)
USP6 5 (1%) 468 0.0788
(0.826) 		0.237
(0.923) 		1
(1.00) 		0.356
(1.00) 		0.379
(1.00) 		0.251
(0.945) 		0.235
(0.923) 		1
(1.00)
TPM1 5 (1%) 468 0.127
(0.831) 		0.381
(1.00) 		1
(1.00) 		0.851
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
GLYAT 4 (1%) 469 0.0789
(0.826) 		0.583
(1.00) 		0.635
(1.00) 		0.839
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
DIAPH1 4 (1%) 469 0.146
(0.831) 		0.489
(1.00) 		1
(1.00) 		0.142
(0.831) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
ZMYM2 6 (1%) 467 0.283
(0.988) 		0.309
(1.00) 		0.7
(1.00) 		0.704
(1.00) 		0.776
(1.00) 		0.331
(1.00) 		1
(1.00) 		1
(1.00)
MST1 4 (1%) 469 0.12
(0.831) 		0.321
(1.00) 		0.0361
(0.686) 		0.94
(1.00) 		0.681
(1.00) 		0.58
(1.00) 		1
(1.00) 		0.155
(0.831)
DNAH7 10 (2%) 463 0.776
(1.00) 		0.0571
(0.795) 		1
(1.00) 		0.104
(0.831) 		0.477
(1.00) 		0.417
(1.00) 		1
(1.00) 		1
(1.00)
ENGASE 3 (1%) 470 0.344
(1.00) 		0.668
(1.00) 		0.584
(1.00) 		0.628
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00)
MYH8 11 (2%) 462 0.0635
(0.82) 		0.716
(1.00) 		0.224
(0.915) 		0.519
(1.00) 		0.186
(0.833) 		0.454
(1.00) 		0.0808
(0.826) 		0.373
(1.00)
VSIG4 6 (1%) 467 0.75
(1.00) 		0.947
(1.00) 		0.411
(1.00) 		1
(1.00) 		0.602
(1.00) 		1
(1.00) 		1
(1.00)
KRT3 4 (1%) 469 0.0709
(0.826) 		0.865
(1.00) 		0.635
(1.00) 		0.428
(1.00) 		0.681
(1.00) 		0.172
(0.832) 		1
(1.00) 		0.155
(0.831)
STAG2 4 (1%) 469 0.104
(0.831) 		0.659
(1.00) 		0.323
(1.00) 		0.139
(0.831) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
MUC17 24 (5%) 449 0.699
(1.00) 		0.15
(0.831) 		0.3
(1.00) 		0.653
(1.00) 		0.233
(0.923) 		1
(1.00) 		0.269
(0.966) 		0.614
(1.00)
ABCA7 9 (2%) 464 0.98
(1.00) 		0.163
(0.832) 		0.738
(1.00) 		0.415
(1.00) 		0.487
(1.00) 		0.689
(1.00) 		1
(1.00) 		1
(1.00)
FOXK1 4 (1%) 469 0.0924
(0.826) 		0.336
(1.00) 		0.323
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.155
(0.831)
SLFN11 3 (1%) 470 0.175
(0.832) 		0.0681
(0.826) 		1
(1.00) 		1
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00)
MX2 4 (1%) 469 0.323
(1.00) 		0.0297
(0.621) 		1
(1.00) 		0.683
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SLC6A4 4 (1%) 469 0.158
(0.831) 		0.449
(1.00) 		0.323
(1.00) 		0.14
(0.831) 		0.172
(0.832) 		1
(1.00) 		1
(1.00)
KRT15 6 (1%) 467 0.695
(1.00) 		0.117
(0.831) 		0.7
(1.00) 		0.34
(1.00) 		0.773
(1.00) 		0.602
(1.00) 		0.277
(0.971) 		1
(1.00)
F8 8 (2%) 465 0.382
(1.00) 		0.116
(0.831) 		0.024
(0.579) 		0.205
(0.859) 		0.54
(1.00) 		0.19
(0.833) 		0.0468
(0.771) 		1
(1.00)
HOOK1 3 (1%) 470 0.125
(0.831) 		0.904
(1.00) 		0.584
(1.00) 		0.628
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
FMR1 5 (1%) 468 0.104
(0.831) 		0.182
(0.833) 		1
(1.00) 		0.428
(1.00) 		0.0966
(0.826) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SON 8 (2%) 465 0.97
(1.00) 		0.204
(0.859) 		1
(1.00) 		0.425
(1.00) 		0.433
(1.00) 		1
(1.00) 		1
(1.00) 		0.256
(0.945)
TTC30B 6 (1%) 467 0.164
(0.832) 		0.154
(0.831) 		0.7
(1.00) 		0.187
(0.833) 		0.587
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
FANCD2 7 (1%) 466 0.356
(1.00) 		0.0974
(0.826) 		0.704
(1.00) 		0.349
(1.00) 		0.626
(1.00) 		1
(1.00) 		0.256
(0.945)
RGL2 4 (1%) 469 0.126
(0.831) 		0.194
(0.833) 		1
(1.00) 		0.123
(0.831) 		0.139
(0.831) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
NR1H3 4 (1%) 469 0.131
(0.831) 		0.497
(1.00) 		0.323
(1.00) 		0.141
(0.831) 		0.172
(0.832) 		1
(1.00) 		0.155
(0.831)
TYRP1 4 (1%) 469 0.485
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.139
(0.831) 		0.172
(0.832) 		1
(1.00) 		1
(1.00)
SLC25A5 4 (1%) 469 0.0156
(0.47) 		0.581
(1.00) 		0.323
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.58
(1.00) 		0.193
(0.833) 		1
(1.00)
AGBL1 4 (1%) 469 0.65
(1.00) 		0.362
(1.00) 		0.635
(1.00) 		0.193
(0.833) 		1
(1.00) 		1
(1.00) 		1
(1.00)
AMPD1 4 (1%) 469 0.903
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.683
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
NGEF 5 (1%) 468 0.361
(1.00) 		0.904
(1.00) 		0.658
(1.00) 		0.41
(1.00) 		0.305
(1.00) 		1
(1.00) 		1
(1.00) 		0.0148
(0.47)
YIPF1 3 (1%) 470 0.17
(0.832) 		0.951
(1.00) 		0.0831
(0.826) 		0.629
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00)
PDHA1 5 (1%) 468 0.967
(1.00) 		0.188
(0.833) 		0.0156
(0.47) 		0.483
(1.00) 		0.304
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ASXL2 3 (1%) 470 0.163
(0.832) 		0.415
(1.00) 		0.584
(1.00) 		0.788
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
HLA-DRA 3 (1%) 470 0.448
(1.00) 		0.792
(1.00) 		0.0831
(0.826) 		0.0659
(0.82) 		0.0982
(0.826) 		0.149
(0.831) 		1
(1.00)
ALPP 4 (1%) 469 0.387
(1.00) 		0.913
(1.00) 		0.323
(1.00) 		0.85
(1.00) 		0.298
(1.00) 		0.58
(1.00) 		0.0213
(0.579) 		0.0806
(0.826)
CDH3 3 (1%) 470 0.429
(1.00) 		0.621
(1.00) 		0.0831
(0.826) 		0.789
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00)
NADSYN1 3 (1%) 470 0.17
(0.832) 		0.825
(1.00) 		0.584
(1.00) 		0.362
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00)
LHFPL1 4 (1%) 469 0.963
(1.00) 		0.0266
(0.609) 		0.635
(1.00) 		1
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
CXCR2 4 (1%) 469 0.823
(1.00) 		0.825
(1.00) 		0.635
(1.00) 		0.682
(1.00) 		0.172
(0.832) 		1
(1.00) 		1
(1.00)
SEC14L4 3 (1%) 470 0.638
(1.00) 		0.0378
(0.686) 		0.26
(0.947) 		0.627
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
ANKRD17 6 (1%) 467 0.154
(0.831) 		0.485
(1.00) 		0.7
(1.00) 		0.177
(0.832) 		1
(1.00) 		0.331
(1.00) 		0.276
(0.971) 		1
(1.00)
MAST3 5 (1%) 468 0.476
(1.00) 		0.689
(1.00) 		0.658
(1.00) 		0.0377
(0.686) 		0.452
(1.00) 		1
(1.00) 		0.235
(0.923) 		1
(1.00)
AMMECR1 3 (1%) 470 0.66
(1.00) 		0.937
(1.00) 		0.584
(1.00) 		0.868
(1.00) 		0.628
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
NEO1 7 (1%) 466 0.0579
(0.795) 		0.14
(0.831) 		0.248
(0.945) 		0.559
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
IGSF8 3 (1%) 470 0.157
(0.831) 		0.382
(1.00) 		0.584
(1.00) 		0.628
(1.00) 		0.0982
(0.826) 		1
(1.00) 		1
(1.00)
RGS3 5 (1%) 468 0.335
(1.00) 		0.487
(1.00) 		0.658
(1.00) 		0.303
(1.00) 		0.00772
(0.292) 		1
(1.00) 		1
(1.00) 		0.19
(0.833)
'IDH1 MUTATION STATUS' versus 'Time to Death'

P value = 6.57e-14 (logrank test), Q value = 7.5e-11

Table S1.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
IDH1 MUTATED 365 53 0.0 - 182.3 (20.1)
IDH1 WILD-TYPE 106 40 0.1 - 211.2 (14.6)

Figure S1.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'IDH1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 4.24e-07 (Wilcoxon-test), Q value = 6.9e-05

Table S2.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 472 43.0 (13.5)
IDH1 MUTATED 366 41.2 (12.5)
IDH1 WILD-TYPE 106 49.2 (14.8)

Figure S2.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TP53 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 1.74e-11 (Wilcoxon-test), Q value = 6.6e-09

Table S3.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 472 43.0 (13.5)
TP53 MUTATED 226 38.6 (11.5)
TP53 WILD-TYPE 246 47.0 (13.9)

Figure S3.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S4.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
TP53 MUTATED 116 69 41
TP53 WILD-TYPE 59 50 138

Figure S4.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00536 (Fisher's exact test), Q value = 0.25

Table S5.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 381
TP53 MUTATED 56 170
TP53 WILD-TYPE 36 211

Figure S5.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'ATRX MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 1.63e-11 (Wilcoxon-test), Q value = 6.6e-09

Table S6.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 472 43.0 (13.5)
ATRX MUTATED 181 37.9 (12.1)
ATRX WILD-TYPE 291 46.1 (13.3)

Figure S6.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'ATRX MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S7.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
ATRX MUTATED 86 61 34
ATRX WILD-TYPE 89 58 145

Figure S7.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'CIC MUTATION STATUS' versus 'Time to Death'

P value = 0.00433 (logrank test), Q value = 0.22

Table S8.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
CIC MUTATED 100 11 0.1 - 211.2 (20.2)
CIC WILD-TYPE 371 82 0.0 - 172.8 (18.5)

Figure S8.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CIC MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S9.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
CIC MUTATED 3 20 77
CIC WILD-TYPE 172 99 102

Figure S9.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'NOTCH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0025

Table S10.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
NOTCH1 MUTATED 6 7 29
NOTCH1 WILD-TYPE 169 112 150

Figure S10.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'EGFR MUTATION STATUS' versus 'Time to Death'

P value = 6.3e-09 (logrank test), Q value = 1.4e-06

Table S11.  Gene #6: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
EGFR MUTATED 30 14 0.5 - 211.2 (11.1)
EGFR WILD-TYPE 441 79 0.0 - 182.3 (19.2)

Figure S11.  Get High-res Image Gene #6: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'EGFR MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 4.56e-09 (Wilcoxon-test), Q value = 1.3e-06

Table S12.  Gene #6: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 472 43.0 (13.5)
EGFR MUTATED 30 57.3 (9.7)
EGFR WILD-TYPE 442 42.0 (13.1)

Figure S12.  Get High-res Image Gene #6: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'IDH2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00128 (Fisher's exact test), Q value = 0.086

Table S13.  Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
IDH2 MUTATED 1 4 14
IDH2 WILD-TYPE 174 115 165

Figure S13.  Get High-res Image Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'NF1 MUTATION STATUS' versus 'Time to Death'

P value = 2.17e-05 (logrank test), Q value = 0.0021

Table S14.  Gene #9: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
NF1 MUTATED 31 14 0.2 - 211.2 (16.2)
NF1 WILD-TYPE 440 79 0.0 - 182.3 (18.7)

Figure S14.  Get High-res Image Gene #9: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NF1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.0039 (Fisher's exact test), Q value = 0.21

Table S15.  Gene #9: 'NF1 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
NF1 MUTATED 20 6 5
NF1 WILD-TYPE 155 113 174

Figure S15.  Get High-res Image Gene #9: 'NF1 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'PTEN MUTATION STATUS' versus 'Time to Death'

P value = 2.57e-05 (logrank test), Q value = 0.0023

Table S16.  Gene #10: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
PTEN MUTATED 23 11 0.5 - 211.2 (16.2)
PTEN WILD-TYPE 448 82 0.0 - 182.3 (18.8)

Figure S16.  Get High-res Image Gene #10: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTEN MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00441 (Wilcoxon-test), Q value = 0.22

Table S17.  Gene #10: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 472 43.0 (13.5)
PTEN MUTATED 23 50.4 (11.8)
PTEN WILD-TYPE 449 42.6 (13.4)

Figure S17.  Get High-res Image Gene #10: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PTEN MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00126 (Fisher's exact test), Q value = 0.086

Table S18.  Gene #10: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
PTEN MUTATED 17 3 3
PTEN WILD-TYPE 158 116 176

Figure S18.  Get High-res Image Gene #10: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'FUBP1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00493 (Wilcoxon-test), Q value = 0.23

Table S19.  Gene #11: 'FUBP1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 472 43.0 (13.5)
FUBP1 MUTATED 46 47.2 (9.6)
FUBP1 WILD-TYPE 426 42.5 (13.7)

Figure S19.  Get High-res Image Gene #11: 'FUBP1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'FUBP1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.001

Table S20.  Gene #11: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 175 119 179
FUBP1 MUTATED 2 8 36
FUBP1 WILD-TYPE 173 111 143

Figure S20.  Get High-res Image Gene #11: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'ZNF292 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00395 (Wilcoxon-test), Q value = 0.21

Table S21.  Gene #29: 'ZNF292 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 472 43.0 (13.5)
ZNF292 MUTATED 13 53.7 (12.0)
ZNF292 WILD-TYPE 459 42.7 (13.4)

Figure S21.  Get High-res Image Gene #29: 'ZNF292 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PLCG1 MUTATION STATUS' versus 'Time to Death'

P value = 5.98e-08 (logrank test), Q value = 1.1e-05

Table S22.  Gene #44: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
PLCG1 MUTATED 6 4 6.7 - 23.7 (11.3)
PLCG1 WILD-TYPE 465 89 0.0 - 211.2 (18.6)

Figure S22.  Get High-res Image Gene #44: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'TMEM184A MUTATION STATUS' versus 'Time to Death'

P value = 0.000413 (logrank test), Q value = 0.031

Table S23.  Gene #71: 'TMEM184A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
TMEM184A MUTATED 3 1 0.3 - 9.2 (6.5)
TMEM184A WILD-TYPE 468 92 0.0 - 211.2 (18.7)

Figure S23.  Get High-res Image Gene #71: 'TMEM184A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'HCFC1 MUTATION STATUS' versus 'GENDER'

P value = 0.0029 (Fisher's exact test), Q value = 0.18

Table S24.  Gene #99: 'HCFC1 MUTATION STATUS' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 207 266
HCFC1 MUTATED 7 0
HCFC1 WILD-TYPE 200 266

Figure S24.  Get High-res Image Gene #99: 'HCFC1 MUTATION STATUS' versus Clinical Feature #3: 'GENDER'

'TNFSF14 MUTATION STATUS' versus 'Time to Death'

P value = 0.00346 (logrank test), Q value = 0.21

Table S25.  Gene #101: 'TNFSF14 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 471 93 0.0 - 211.2 (18.6)
TNFSF14 MUTATED 5 3 0.1 - 49.5 (18.0)
TNFSF14 WILD-TYPE 466 90 0.0 - 211.2 (18.6)

Figure S25.  Get High-res Image Gene #101: 'TNFSF14 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

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/LGG-TP/15716584/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/15082624/LGG-TP.merged_data.txt

  • Number of patients = 473

  • Number of significantly mutated genes = 143

  • Number of selected clinical features = 8

  • 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

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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[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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