Correlation between gene mutation status and selected clinical features
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.

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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