Correlation between gene mutation status and selected clinical features
Glioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1G73CQX
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/C1G73CQX
Overview
Introduction

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

Summary

Testing the association between mutation status of 187 genes and 9 clinical features across 751 patients, 95 significant findings detected with Q value < 0.25.

  • IDH1 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • TP53 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • ATRX mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

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

  • CIC mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

  • PIK3R1 mutation correlated to 'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • NOTCH1 mutation correlated to 'Time to Death',  'PRIMARY_SITE_OF_DISEASE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • FUBP1 mutation correlated to 'Time to Death',  'PRIMARY_SITE_OF_DISEASE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • RB1 mutation correlated to 'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • IDH2 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.

  • ARID1A mutation correlated to 'Time to Death',  'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.

  • NIPBL mutation correlated to 'Time to Death'.

  • SMARCA4 mutation correlated to 'Time to Death',  'PRIMARY_SITE_OF_DISEASE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • ZNF709 mutation correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • STAG2 mutation correlated to 'PRIMARY_SITE_OF_DISEASE' and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • REN mutation correlated to 'Time to Death'.

  • PLCG1 mutation correlated to 'Time to Death'.

  • SLC26A3 mutation correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • ZBTB20 mutation correlated to 'Time to Death',  'PRIMARY_SITE_OF_DISEASE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • DNMT3A mutation correlated to 'Time to Death'.

  • BRAF mutation correlated to 'HISTOLOGICAL_TYPE'.

  • EGFR mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PRIMARY_SITE_OF_DISEASE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • SEMG2 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'PRIMARY_SITE_OF_DISEASE'.

  • FAM83D mutation correlated to 'Time to Death'.

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

  • HTRA2 mutation correlated to 'YEARS_TO_BIRTH'.

  • PDHA1 mutation correlated to 'GENDER'.

  • DSG3 mutation correlated to 'PRIMARY_SITE_OF_DISEASE'.

  • CCDC110 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • ATF7IP2 mutation correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • QKI mutation correlated to 'Time to Death'.

  • CCDC135 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • SEMA3C mutation correlated to 'Time to Death',  'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.

  • PAN3 mutation correlated to 'PRIMARY_SITE_OF_DISEASE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 187 genes and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 95 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PRIMARY
SITE
OF
DISEASE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
IDH1 381 (51%) 370 0
(0) 		4.19e-51
(1.41e-48) 		3.82e-94
(1.61e-91) 		0.373
(0.932) 		5.59e-17
(7.84e-15) 		1e-05
(0.000526) 		1.49e-18
(2.51e-16) 		0.0593
(0.5) 		0.508
(1.00)
PTEN 108 (14%) 643 0
(0) 		4.22e-13
(4.74e-11) 		1.19e-21
(2.5e-19) 		0.527
(1.00) 		0.000551
(0.0189) 		1e-05
(0.000526) 		1.31e-05
(0.000668) 		0.543
(1.00) 		0.755
(1.00)
CIC 101 (13%) 650 1.26e-10
(1.25e-08) 		0.00321
(0.0819) 		5.95e-21
(1.11e-18) 		0.232
(0.798) 		0.000639
(0.0203) 		1e-05
(0.000526) 		6e-08
(4.81e-06) 		0.574
(1.00) 		1
(1.00)
EGFR 103 (14%) 648 0
(0) 		6.05e-13
(6.36e-11) 		6e-14
(7.22e-12) 		0.197
(0.761) 		1.57e-05
(0.000776) 		1e-05
(0.000526) 		0.000634
(0.0203) 		0.134
(0.697) 		0.0945
(0.585)
TP53 304 (40%) 447 1.52e-10
(1.42e-08) 		1.48e-17
(2.26e-15) 		9.74e-08
(7.45e-06) 		0.763
(1.00) 		0.000195
(0.00783) 		1e-05
(0.000526) 		1
(1.00) 		0.41
(0.963) 		0.369
(0.932)
ATRX 197 (26%) 554 6.11e-15
(7.91e-13) 		2.19e-32
(6.13e-30) 		9.88e-26
(2.37e-23) 		0.556
(1.00) 		3.86e-06
(0.000271) 		1e-05
(0.000526) 		0.0202
(0.299) 		0.889
(1.00) 		0.321
(0.878)
FUBP1 46 (6%) 705 0.000397
(0.0145) 		0.29
(0.85) 		3.25e-10
(2.88e-08) 		0.878
(1.00) 		0.00673
(0.147) 		1e-05
(0.000526) 		0.0114
(0.215) 		1
(1.00) 		0.389
(0.956)
PIK3R1 52 (7%) 699 0.193
(0.757) 		0.00446
(0.109) 		0.000273
(0.0105) 		0.0792
(0.551) 		0.218
(0.789) 		0.00629
(0.145) 		0.00257
(0.0697) 		0.162
(0.708) 		0.389
(0.956)
NOTCH1 42 (6%) 709 0.000299
(0.0112) 		0.188
(0.745) 		2.12e-09
(1.79e-07) 		0.42
(0.966) 		0.0195
(0.29) 		1e-05
(0.000526) 		0.0132
(0.234) 		0.349
(0.916) 		0.367
(0.932)
RB1 28 (4%) 723 0.0684
(0.514) 		0.00149
(0.0439) 		8.28e-07
(6.06e-05) 		1
(1.00) 		0.991
(1.00) 		6e-05
(0.00273) 		0.00102
(0.0307) 		1
(1.00) 		1
(1.00)
IDH2 19 (3%) 732 0.00256
(0.0697) 		0.000852
(0.0266) 		0.00016
(0.00675) 		0.639
(1.00) 		0.227
(0.793) 		2e-05
(0.000962) 		0.228
(0.793) 		0.714
(1.00) 		0.108
(0.616)
SMARCA4 25 (3%) 726 0.000609
(0.0201) 		0.187
(0.741) 		0.000188
(0.00771) 		0.413
(0.964) 		0.0121
(0.219) 		0.00682
(0.147) 		1
(1.00) 		0.105
(0.616) 		0.481
(1.00)
ZBTB20 20 (3%) 731 0.0115
(0.215) 		0.162
(0.708) 		0.00163
(0.0465) 		0.651
(1.00) 		0.203
(0.761) 		0.00868
(0.176) 		0.00947
(0.187) 		0.471
(1.00) 		0.463
(0.996)
NF1 60 (8%) 691 2.89e-05
(0.00135) 		0.000971
(0.0297) 		0.0696
(0.521) 		0.784
(1.00) 		0.111
(0.621) 		0.00867
(0.176) 		0.125
(0.681) 		0.908
(1.00) 		0.673
(1.00)
ARID1A 21 (3%) 730 0.0036
(0.0905) 		0.0159
(0.268) 		0.00976
(0.191) 		0.27
(0.843) 		0.522
(1.00) 		0.00475
(0.113) 		0.108
(0.616) 		0.746
(1.00) 		0.498
(1.00)
SEMG2 13 (2%) 738 0.00275
(0.0722) 		0.000494
(0.0177) 		0.000551
(0.0189) 		0.779
(1.00) 		0.623
(1.00) 		0.0252
(0.348) 		0.249
(0.83) 		0.204
(0.761) 		1
(1.00)
SEMA3C 12 (2%) 739 0.000255
(0.01) 		0.0702
(0.523) 		0.000127
(0.00546) 		0.77
(1.00) 		0.173
(0.727) 		0.00685
(0.147) 		0.139
(0.697) 		0.0594
(0.5) 		0.301
(0.85)
STAG2 16 (2%) 735 0.0557
(0.494) 		0.104
(0.609) 		0.00263
(0.0701) 		0.454
(0.984) 		0.00901
(0.18) 		0.0244
(0.34) 		0.302
(0.85) 		0.624
(1.00) 		1
(1.00)
PDGFRA 20 (3%) 731 0.00162
(0.0465) 		0.0123
(0.22) 		0.0361
(0.421) 		1
(1.00) 		0.0334
(0.415) 		0.139
(0.697) 		0.486
(1.00) 		1
(1.00) 		0.445
(0.982)
NIPBL 19 (3%) 732 0.000564
(0.019) 		0.0184
(0.278) 		0.0151
(0.261) 		0.816
(1.00) 		0.462
(0.996) 		0.0256
(0.35) 		0.0565
(0.494) 		0.0815
(0.551) 		0.119
(0.651)
ZNF709 7 (1%) 744 0.485
(1.00) 		0.824
(1.00) 		0.714
(1.00) 		0.0455
(0.474) 		0.292
(0.85) 		0.494
(1.00) 		0.012
(0.219) 		0.364
(0.931) 		0.149
(0.697)
REN 7 (1%) 744 9.27e-05
(0.0041) 		0.0894
(0.567) 		0.108
(0.616) 		0.25
(0.83) 		0.329
(0.888) 		0.0384
(0.431) 		0.433
(0.966) 		1
(1.00) 		1
(1.00)
PLCG1 11 (1%) 740 0.00444
(0.109) 		0.0144
(0.253) 		0.547
(1.00) 		1
(1.00) 		0.172
(0.727) 		0.587
(1.00) 		0.547
(1.00) 		0.511
(1.00) 		1
(1.00)
SLC26A3 10 (1%) 741 0.656
(1.00) 		0.564
(1.00) 		0.185
(0.741) 		0.212
(0.778) 		0.209
(0.773) 		0.147
(0.697) 		0.00683
(0.147) 		0.478
(1.00) 		1
(1.00)
DNMT3A 10 (1%) 741 0.00864
(0.176) 		0.463
(0.996) 		0.0163
(0.269) 		1
(1.00) 		0.3
(0.85) 		0.0401
(0.447) 		0.101
(0.603) 		0.477
(1.00) 		0.278
(0.847)
BRAF 11 (1%) 740 0.846
(1.00) 		0.521
(1.00) 		0.345
(0.912) 		1
(1.00) 		0.746
(1.00) 		0.00193
(0.0541) 		0.547
(1.00) 		0.479
(1.00) 		1
(1.00)
FAM83D 4 (1%) 747 0.0101
(0.195) 		0.201
(0.761) 		0.629
(1.00) 		0.649
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.229
(0.793) 		1
(1.00)
HTRA2 5 (1%) 746 0.213
(0.778) 		0.00686
(0.147) 		0.164
(0.708) 		1
(1.00) 		0.156
(0.702) 		0.164
(0.708) 		1
(1.00) 		0.149
(0.697)
PDHA1 6 (1%) 745 0.59
(1.00) 		0.508
(1.00) 		0.421
(0.966) 		0.00453
(0.109) 		0.131
(0.695) 		0.283
(0.85) 		0.421
(0.966) 		1
(1.00) 		1
(1.00)
DSG3 11 (1%) 740 0.3
(0.85) 		0.0335
(0.415) 		0.003
(0.0778) 		0.0324
(0.407) 		0.669
(1.00) 		0.0823
(0.551) 		0.023
(0.322) 		1
(1.00) 		1
(1.00)
CCDC110 6 (1%) 745 0.886
(1.00) 		0.933
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.527
(1.00) 		0.00548
(0.128) 		1
(1.00) 		0.324
(0.88) 		1
(1.00)
ATF7IP2 8 (1%) 743 0.0619
(0.51) 		0.219
(0.791) 		0.154
(0.698) 		1
(1.00) 		0.00688
(0.147) 		0.645
(1.00) 		0.477
(1.00) 		0.0272
(0.37) 		1
(1.00)
QKI 6 (1%) 745 0.0112
(0.214) 		0.305
(0.85) 		0.0283
(0.378) 		0.693
(1.00) 		0.239
(0.809) 		0.174
(0.727) 		0.201
(0.761) 		1
(1.00) 		1
(1.00)
CCDC135 7 (1%) 744 0.205
(0.761) 		0.443
(0.979) 		0.269
(0.843) 		0.452
(0.984) 		0.00747
(0.157) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PAN3 7 (1%) 744 0.432
(0.966) 		0.286
(0.85) 		0.012
(0.219) 		1
(1.00) 		0.268
(0.843) 		0.126
(0.682) 		0.108
(0.616) 		1
(1.00) 		1
(1.00)
PIK3CA 70 (9%) 681 0.161
(0.708) 		0.126
(0.682) 		0.605
(1.00) 		1
(1.00) 		0.191
(0.752) 		0.056
(0.494) 		0.796
(1.00) 		0.711
(1.00) 		0.711
(1.00)
TCF12 18 (2%) 733 0.183
(0.741) 		1
(1.00) 		0.0849
(0.551) 		0.811
(1.00) 		0.515
(1.00) 		0.466
(1) 		0.224
(0.793) 		1
(1.00) 		1
(1.00)
STK19 11 (1%) 740 0.262
(0.843) 		0.104
(0.609) 		0.0621
(0.51) 		0.135
(0.697) 		0.228
(0.793) 		0.0539
(0.491) 		0.228
(0.793) 		1
(1.00) 		0.0445
(0.472)
CREBZF 8 (1%) 743 0.573
(1.00) 		0.39
(0.956) 		0.717
(1.00) 		0.722
(1.00) 		0.916
(1.00) 		0.221
(0.793) 		1
(1.00) 		0.0546
(0.494) 		1
(1.00)
EMG1 7 (1%) 744 0.488
(1.00) 		0.843
(1.00) 		0.0506
(0.477) 		0.452
(0.984) 		0.131
(0.695) 		0.139
(0.697) 		0.269
(0.843) 		1
(1.00) 		1
(1.00)
RPL5 10 (1%) 741 0.833
(1.00) 		0.0315
(0.402) 		0.0442
(0.472) 		0.332
(0.894) 		0.0593
(0.5) 		0.211
(0.776) 		0.0442
(0.472) 		0.133
(0.696) 		1
(1.00)
IRS4 10 (1%) 741 0.0875
(0.56) 		0.713
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.746
(1.00) 		0.374
(0.933) 		0.512
(1.00) 		1
(1.00) 		0.0303
(0.395)
TNRC18 12 (2%) 739 0.152
(0.698) 		0.453
(0.984) 		0.227
(0.793) 		0.136
(0.697) 		0.376
(0.933) 		0.117
(0.645) 		0.227
(0.793) 		0.543
(1.00) 		1
(1.00)
NRAS 5 (1%) 746 0.252
(0.832) 		0.868
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.137
(0.697) 		0.656
(1.00) 		1
(1.00) 		1
(1.00)
TRERF1 7 (1%) 744 0.327
(0.886) 		0.227
(0.793) 		0.269
(0.843) 		0.0207
(0.304) 		0.583
(1.00) 		0.151
(0.698) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MX2 9 (1%) 742 0.449
(0.984) 		0.0173
(0.278) 		0.303
(0.85) 		1
(1.00) 		0.529
(1.00) 		0.101
(0.603) 		0.733
(1.00) 		0.444
(0.981) 		1
(1.00)
ZMIZ1 11 (1%) 740 0.0685
(0.514) 		0.334
(0.898) 		0.755
(1.00) 		0.371
(0.932) 		0.806
(1.00) 		0.811
(1.00) 		0.755
(1.00) 		0.235
(0.798) 		0.0371
(0.422)
DDX5 8 (1%) 743 0.75
(1.00) 		0.411
(0.963) 		1
(1.00) 		0.482
(1.00) 		0.414
(0.966) 		0.171
(0.727) 		0.477
(1.00) 		1
(1.00) 		0.203
(0.761)
PTPN11 11 (1%) 740 0.304
(0.85) 		0.101
(0.603) 		1
(1.00) 		0.766
(1.00) 		0.75
(1.00) 		0.552
(1.00) 		0.547
(1.00) 		0.478
(1.00) 		1
(1.00)
ZNF292 16 (2%) 735 0.765
(1.00) 		0.0977
(0.592) 		0.19
(0.747) 		0.0363
(0.421) 		0.186
(0.741) 		0.596
(1.00) 		0.19
(0.747) 		0.18
(0.738) 		1
(1.00)
DSP 18 (2%) 733 0.375
(0.933) 		0.0305
(0.395) 		0.136
(0.697) 		0.472
(1.00) 		0.515
(1.00) 		0.524
(1.00) 		0.0457
(0.474) 		1
(1.00) 		1
(1.00)
RBPJ 7 (1%) 744 0.336
(0.903) 		0.68
(1.00) 		0.0506
(0.477) 		1
(1.00) 		0.558
(1.00) 		0.0819
(0.551) 		0.269
(0.843) 		1
(1.00) 		1
(1.00)
ARID2 13 (2%) 738 0.0811
(0.551) 		0.737
(1.00) 		0.147
(0.697) 		0.779
(1.00) 		0.392
(0.96) 		0.204
(0.761) 		0.777
(1.00) 		0.31
(0.856) 		0.345
(0.912)
ANKRD36 7 (1%) 744 0.902
(1.00) 		0.45
(0.984) 		0.0506
(0.477) 		0.452
(0.984) 		0.017
(0.278) 		0.0573
(0.494) 		1
(1.00) 		0.0735
(0.537) 		1
(1.00)
SRPX 3 (0%) 748 0.821
(1.00) 		0.547
(1.00) 		0.3
(0.85) 		0.0679
(0.514) 		0.276
(0.847) 		1
(1.00) 		1
(1.00) 		1
(1.00)
AK7 8 (1%) 743 0.0484
(0.477) 		0.591
(1.00) 		0.477
(1.00) 		1
(1.00) 		0.268
(0.843) 		0.201
(0.761) 		0.154
(0.698) 		0.404
(0.962) 		0.229
(0.793)
GAGE2D 5 (1%) 746 0.214
(0.78) 		0.485
(1.00) 		0.164
(0.708) 		0.654
(1.00) 		0.271
(0.843) 		0.656
(1.00) 		0.278
(0.847) 		0.149
(0.697)
SETD2 11 (1%) 740 0.269
(0.843) 		0.264
(0.843) 		0.755
(1.00) 		1
(1.00) 		0.287
(0.85) 		0.789
(1.00) 		0.547
(1.00) 		0.51
(1.00) 		1
(1.00)
HDAC2 7 (1%) 744 0.748
(1.00) 		0.0869
(0.558) 		0.714
(1.00) 		0.707
(1.00) 		0.725
(1.00) 		0.651
(1.00) 		0.108
(0.616) 		1
(1.00) 		1
(1.00)
TYRP1 6 (1%) 745 0.469
(1.00) 		0.146
(0.697) 		1
(1.00) 		1
(1.00) 		0.411
(0.963) 		0.0368
(0.421) 		0.675
(1.00) 		1
(1.00) 		1
(1.00)
BCOR 21 (3%) 730 0.384
(0.947) 		0.4
(0.962) 		0.821
(1.00) 		0.368
(0.932) 		0.08
(0.551) 		0.055
(0.494) 		0.497
(1.00) 		1
(1.00) 		1
(1.00)
FAM47C 23 (3%) 728 0.0708
(0.525) 		0.778
(1.00) 		0.187
(0.741) 		0.135
(0.697) 		0.322
(0.878) 		0.515
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.481
(1.00)
NEU2 7 (1%) 744 0.345
(0.912) 		0.42
(0.966) 		0.714
(1.00) 		0.707
(1.00) 		0.742
(1.00) 		0.855
(1.00) 		0.433
(0.966) 		1
(1.00) 		1
(1.00)
SERPING1 3 (0%) 748 0.401
(0.962) 		0.181
(0.741) 		1
(1.00) 		1
(1.00) 		0.705
(1.00) 		1
(1.00) 		1
(1.00)
NOTCH2 13 (2%) 738 0.533
(1.00) 		0.615
(1.00) 		1
(1.00) 		0.0854
(0.551) 		0.0321
(0.406) 		0.913
(1.00) 		0.0824
(0.551) 		1
(1.00) 		0.301
(0.85)
NKD2 4 (1%) 747 0.61
(1.00) 		0.72
(1.00) 		0.303
(0.85) 		1
(1.00) 		0.133
(0.696) 		0.303
(0.85) 		1
(1.00) 		1
(1.00)
TPX2 5 (1%) 746 0.138
(0.697) 		0.623
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.187
(0.741) 		0.836
(1.00) 		0.0654
(0.512) 		1
(1.00) 		1
(1.00)
ZNF512B 4 (1%) 747 0.067
(0.514) 		0.2
(0.761) 		0.303
(0.85) 		1
(1.00) 		0.215
(0.78) 		0.629
(1.00) 		1
(1.00) 		1
(1.00)
SPTAN1 8 (1%) 743 0.16
(0.708) 		0.841
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.81
(1.00) 		0.401
(0.962) 		0.154
(0.698) 		1
(1.00) 		0.229
(0.793)
THRA 5 (1%) 746 0.117
(0.645) 		0.769
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.433
(0.966) 		1
(1.00) 		0.107
(0.616) 		1
(1.00)
RGS3 7 (1%) 744 0.42
(0.966) 		0.453
(0.984) 		1
(1.00) 		0.452
(0.984) 		0.834
(1.00) 		0.094
(0.585) 		1
(1.00) 		1
(1.00) 		0.203
(0.761)
PROKR2 9 (1%) 742 0.0942
(0.585) 		0.0212
(0.308) 		0.0837
(0.551) 		0.744
(1.00) 		0.999
(1.00) 		0.306
(0.851) 		0.303
(0.85) 		1
(1.00) 		1
(1.00)
SLC6A14 7 (1%) 744 0.381
(0.941) 		0.0752
(0.543) 		0.108
(0.616) 		0.452
(0.984) 		0.375
(0.933) 		0.0581
(0.499) 		0.433
(0.966) 		1
(1.00) 		0.177
(0.727)
MST1 6 (1%) 745 0.222
(0.793) 		0.833
(1.00) 		1
(1.00) 		0.233
(0.798) 		0.907
(1.00) 		0.825
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.177
(0.727)
NUP210L 11 (1%) 740 0.559
(1.00) 		0.909
(1.00) 		0.111
(0.621) 		1
(1.00) 		0.819
(1.00) 		0.0737
(0.537) 		0.023
(0.322) 		0.512
(1.00) 		1
(1.00)
MED9 3 (0%) 748 0.969
(1.00) 		0.39
(0.956) 		0.3
(0.85) 		0.274
(0.845) 		0.0303
(0.395) 		0.3
(0.85) 		1
(1.00) 		1
(1.00)
ZDHHC4 3 (0%) 748 0.552
(1.00) 		0.784
(1.00) 		0.559
(1.00) 		0.571
(1.00) 		0.794
(1.00) 		0.0504
(0.477) 		0.176
(0.727) 		1
(1.00)
MATK 8 (1%) 743 0.549
(1.00) 		0.345
(0.912) 		1
(1.00) 		1
(1.00) 		0.0473
(0.474) 		0.122
(0.666) 		0.0572
(0.494) 		1
(1.00) 		1
(1.00)
KDR 13 (2%) 738 0.448
(0.984) 		0.0641
(0.512) 		0.0824
(0.551) 		1
(1.00) 		0.465
(0.999) 		0.136
(0.697) 		0.0824
(0.551) 		1
(1.00) 		1
(1.00)
WRN 3 (0%) 748 0.266
(0.843) 		0.56
(1.00) 		1
(1.00) 		0.0679
(0.514) 		1
(1.00) 		0.559
(1.00) 		1
(1.00) 		1
(1.00)
G6PC 6 (1%) 745 0.833
(1.00) 		0.353
(0.925) 		0.421
(0.966) 		0.409
(0.963) 		0.364
(0.931) 		0.675
(1.00) 		1
(1.00) 		0.177
(0.727)
TMEM184A 3 (0%) 748 0.204
(0.761) 		0.501
(1.00) 		0.3
(0.85) 		1
(1.00) 		0.37
(0.932) 		1
(1.00) 		0.176
(0.727) 		1
(1.00)
TMEM229B 4 (1%) 747 0.248
(0.83) 		0.09
(0.567) 		0.146
(0.697) 		0.649
(1.00) 		0.0712
(0.525) 		0.629
(1.00) 		1
(1.00) 		1
(1.00)
CD44 6 (1%) 745 0.339
(0.908) 		0.154
(0.698) 		0.675
(1.00) 		0.233
(0.798) 		0.953
(1.00) 		0.201
(0.761) 		1
(1.00) 		1
(1.00)
BCLAF1 11 (1%) 740 0.954
(1.00) 		0.985
(1.00) 		0.345
(0.912) 		0.539
(1.00) 		0.827
(1.00) 		0.273
(0.845) 		0.023
(0.322) 		0.516
(1.00) 		1
(1.00)
POM121 6 (1%) 745 0.843
(1.00) 		0.218
(0.789) 		1
(1.00) 		1
(1.00) 		0.832
(1.00) 		0.344
(0.912) 		0.675
(1.00) 		1
(1.00) 		1
(1.00)
SLC6A3 12 (2%) 739 0.847
(1.00) 		0.855
(1.00) 		0.55
(1.00) 		0.245
(0.822) 		0.74
(1.00) 		0.55
(1.00) 		1
(1.00) 		0.254
(0.832)
SMOC1 4 (1%) 747 0.765
(1.00) 		0.509
(1.00) 		1
(1.00) 		0.649
(1.00) 		0.725
(1.00) 		0.418
(0.966) 		0.629
(1.00) 		0.084
(0.551) 		1
(1.00)
MYT1 6 (1%) 745 0.0654
(0.512) 		0.057
(0.494) 		0.09
(0.567) 		0.693
(1.00) 		0.326
(0.885) 		0.0459
(0.474) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DOCK5 19 (3%) 732 0.813
(1.00) 		0.0959
(0.585) 		0.158
(0.708) 		0.816
(1.00) 		0.714
(1.00) 		0.16
(0.708) 		0.346
(0.912) 		1
(1.00) 		0.426
(0.966)
SLFN11 4 (1%) 747 0.269
(0.843) 		0.202
(0.761) 		1
(1.00) 		0.649
(1.00) 		0.917
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00)
DLC1 8 (1%) 743 0.974
(1.00) 		0.582
(1.00) 		1
(1.00) 		0.283
(0.85) 		0.63
(1.00) 		0.762
(1.00) 		0.0572
(0.494) 		1
(1.00) 		1
(1.00)
PPL 8 (1%) 743 0.0352
(0.421) 		0.934
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.75
(1.00) 		0.699
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CMA1 3 (0%) 748 0.226
(0.793) 		0.941
(1.00) 		1
(1.00) 		1
(1.00) 		0.426
(0.966) 		0.0504
(0.477) 		1
(1.00) 		1
(1.00)
PRKCD 3 (0%) 748 0.337
(0.904) 		0.873
(1.00) 		0.0504
(0.477) 		1
(1.00) 		0.318
(0.872) 		0.559
(1.00) 		0.179
(0.735) 		1
(1.00)
ANO1 9 (1%) 742 0.26
(0.843) 		0.235
(0.798) 		1
(1.00) 		0.498
(1.00) 		0.776
(1.00) 		0.971
(1.00) 		0.497
(1.00) 		1
(1.00) 		1
(1.00)
PLXNA3 9 (1%) 742 0.0982
(0.592) 		0.935
(1.00) 		0.165
(0.708) 		0.0363
(0.421) 		0.646
(1.00) 		0.462
(0.996) 		0.303
(0.85) 		0.11
(0.62) 		1
(1.00)
NAP1L2 6 (1%) 745 0.488
(1.00) 		0.174
(0.727) 		1
(1.00) 		0.693
(1.00) 		0.408
(0.963) 		0.454
(0.984) 		0.675
(1.00) 		1
(1.00) 		1
(1.00)
PLCH2 6 (1%) 745 0.0967
(0.587) 		0.537
(1.00) 		1
(1.00) 		0.233
(0.798) 		0.132
(0.696) 		0.345
(0.912) 		0.201
(0.761) 		0.13
(0.695) 		1
(1.00)
CD1D 4 (1%) 747 0.398
(0.962) 		0.0182
(0.278) 		0.0185
(0.278) 		1
(1.00) 		0.302
(0.85) 		0.16
(0.708) 		0.146
(0.697) 		1
(1.00) 		1
(1.00)
UBR3 5 (1%) 746 0.357
(0.93) 		0.803
(1.00) 		0.656
(1.00) 		0.654
(1.00) 		0.318
(0.872) 		0.43
(0.966) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CNOT1 8 (1%) 743 0.0451
(0.474) 		0.0831
(0.551) 		0.27
(0.843) 		0.482
(1.00) 		0.281
(0.85) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ESR2 6 (1%) 745 0.657
(1.00) 		0.32
(0.875) 		0.675
(1.00) 		1
(1.00) 		0.372
(0.932) 		0.952
(1.00) 		0.675
(1.00) 		1
(1.00) 		1
(1.00)
TNFRSF9 4 (1%) 747 0.764
(1.00) 		0.194
(0.757) 		1
(1.00) 		0.31
(0.856) 		0.0473
(0.474) 		0.916
(1.00) 		0.629
(1.00) 		0.228
(0.793) 		1
(1.00)
USP11 9 (1%) 742 0.142
(0.697) 		0.718
(1.00) 		1
(1.00) 		0.0363
(0.421) 		0.412
(0.964) 		0.665
(1.00) 		0.733
(1.00) 		1
(1.00) 		0.254
(0.832)
CYP11A1 5 (1%) 746 0.207
(0.767) 		0.0745
(0.54) 		0.365
(0.931) 		1
(1.00) 		0.551
(1.00) 		0.5
(1.00) 		0.365
(0.931) 		1
(1.00) 		1
(1.00)
NCAPH2 4 (1%) 747 0.0718
(0.527) 		0.714
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00) 		0.0185
(0.278) 		1
(1.00) 		1
(1.00)
PRB3 3 (0%) 748 0.183
(0.741) 		0.995
(1.00) 		1
(1.00) 		0.274
(0.845) 		0.426
(0.966) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TRPV6 13 (2%) 738 0.819
(1.00) 		0.998
(1.00) 		0.249
(0.83) 		0.398
(0.962) 		0.25
(0.83) 		0.709
(1.00) 		0.0824
(0.551) 		0.13
(0.695) 		1
(1.00)
AOX1 7 (1%) 744 0.691
(1.00) 		0.749
(1.00) 		0.433
(0.966) 		0.707
(1.00) 		0.0384
(0.431) 		0.381
(0.941) 		0.433
(0.966) 		1
(1.00) 		1
(1.00)
EEF1A1 8 (1%) 743 0.322
(0.878) 		0.0446
(0.472) 		0.477
(1.00) 		0.283
(0.85) 		0.0896
(0.567) 		0.935
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ZZZ3 3 (0%) 748 0.0599
(0.501) 		0.306
(0.851) 		1
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.0504
(0.477) 		1
(1.00) 		1
(1.00)
PAK1 3 (0%) 748 0.0802
(0.551) 		0.303
(0.85) 		1
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.559
(1.00) 		1
(1.00) 		1
(1.00)
RASGRF2 6 (1%) 745 0.143
(0.697) 		0.361
(0.931) 		1
(1.00) 		0.693
(1.00) 		0.747
(1.00) 		0.907
(1.00) 		0.201
(0.761) 		1
(1.00) 		1
(1.00)
WWC3 9 (1%) 742 0.348
(0.914) 		0.896
(1.00) 		1
(1.00) 		0.0363
(0.421) 		0.67
(1.00) 		0.971
(1.00) 		0.733
(1.00) 		1
(1.00) 		1
(1.00)
TTC30B 7 (1%) 744 0.0628
(0.512) 		0.116
(0.645) 		0.269
(0.843) 		1
(1.00) 		0.257
(0.837) 		0.41
(0.963) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ROBO3 4 (1%) 747 0.37
(0.932) 		0.354
(0.925) 		0.303
(0.85) 		0.31
(0.856) 		0.502
(1.00) 		0.214
(0.78) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SOX13 5 (1%) 746 0.985
(1.00) 		0.992
(1.00) 		0.365
(0.931) 		0.654
(1.00) 		0.408
(0.963) 		0.599
(1.00) 		0.0654
(0.512) 		1
(1.00) 		1
(1.00)
ST3GAL6 5 (1%) 746 0.889
(1.00) 		0.381
(0.941) 		1
(1.00) 		0.404
(0.962) 		0.15
(0.698) 		0.834
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CLCN7 7 (1%) 744 0.69
(1.00) 		0.162
(0.708) 		0.433
(0.966) 		0.707
(1.00) 		0.0954
(0.585) 		0.885
(1.00) 		0.108
(0.616) 		1
(1.00) 		1
(1.00)
CD99L2 4 (1%) 747 0.185
(0.741) 		0.29
(0.85) 		1
(1.00) 		0.31
(0.856) 		0.786
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00)
KRAS 4 (1%) 747 0.679
(1.00) 		0.67
(1.00) 		0.629
(1.00) 		1
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.146
(0.697) 		1
(1.00) 		1
(1.00)
PRG4 9 (1%) 742 0.438
(0.973) 		0.744
(1.00) 		0.497
(1.00) 		0.744
(1.00) 		0.243
(0.817) 		0.114
(0.635) 		0.497
(1.00) 		0.443
(0.979) 		0.254
(0.832)
USP6 10 (1%) 741 0.131
(0.695) 		0.972
(1.00) 		0.512
(1.00) 		0.539
(1.00) 		0.145
(0.697) 		0.571
(1.00) 		0.185
(0.741) 		0.477
(1.00) 		1
(1.00)
TP63 9 (1%) 742 0.373
(0.932) 		0.578
(1.00) 		0.0837
(0.551) 		1
(1.00) 		0.765
(1.00) 		0.304
(0.85) 		0.303
(0.85) 		1
(1.00) 		0.203
(0.761)
OR52M1 8 (1%) 743 0.531
(1.00) 		0.845
(1.00) 		0.477
(1.00) 		1
(1.00) 		0.94
(1.00) 		0.258
(0.838) 		0.477
(1.00) 		0.182
(0.741) 		1
(1.00)
TNFSF9 4 (1%) 747 0.11
(0.619) 		0.622
(1.00) 		0.146
(0.697) 		0.649
(1.00) 		0.102
(0.604) 		0.533
(1.00) 		0.146
(0.697) 		1
(1.00) 		1
(1.00)
HEATR3 4 (1%) 747 0.9
(1.00) 		0.142
(0.697) 		0.629
(1.00) 		1
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.229
(0.793) 		1
(1.00)
USP28 4 (1%) 747 0.686
(1.00) 		0.148
(0.697) 		0.146
(0.697) 		0.31
(0.856) 		0.533
(1.00) 		0.0185
(0.278) 		1
(1.00) 		1
(1.00)
ACADS 5 (1%) 746 0.341
(0.91) 		0.0286
(0.379) 		0.365
(0.931) 		0.654
(1.00) 		0.939
(1.00) 		0.478
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
RGL2 4 (1%) 747 0.0429
(0.472) 		0.768
(1.00) 		0.303
(0.85) 		1
(1.00) 		0.0536
(0.491) 		0.0949
(0.585) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MYO5A 5 (1%) 746 0.361
(0.931) 		0.747
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.0654
(0.512) 		1
(1.00) 		1
(1.00)
TMPRSS6 9 (1%) 742 0.972
(1.00) 		0.0602
(0.501) 		0.0837
(0.551) 		0.498
(1.00) 		0.89
(1.00) 		0.187
(0.741) 		0.0152
(0.261) 		1
(1.00) 		1
(1.00)
DYNC1I1 10 (1%) 741 0.783
(1.00) 		0.979
(1.00) 		0.0442
(0.472) 		0.539
(1.00) 		0.3
(0.85) 		0.212
(0.777) 		0.0442
(0.472) 		0.0833
(0.551) 		0.254
(0.832)
PASD1 9 (1%) 742 0.628
(1.00) 		0.596
(1.00) 		0.303
(0.85) 		0.0363
(0.421) 		0.679
(1.00) 		0.395
(0.962) 		0.733
(1.00) 		1
(1.00) 		1
(1.00)
RPL7 3 (0%) 748 0.243
(0.817) 		0.629
(1.00) 		1
(1.00) 		0.571
(1.00) 		0.427
(0.966) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CES3 3 (0%) 748 0.519
(1.00) 		0.399
(0.962) 		1
(1.00) 		0.0679
(0.514) 		0.709
(1.00) 		1
(1.00) 		0.175
(0.727) 		1
(1.00)
CLEC12A 5 (1%) 746 0.372
(0.932) 		0.762
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.241
(0.814) 		0.365
(0.931) 		1
(1.00) 		1
(1.00)
CACNA1S 14 (2%) 737 0.609
(1.00) 		0.68
(1.00) 		0.403
(0.962) 		0.174
(0.727) 		0.93
(1.00) 		0.792
(1.00) 		0.16
(0.708) 		0.333
(0.898) 		1
(1.00)
SON 9 (1%) 742 0.265
(0.843) 		0.822
(1.00) 		0.165
(0.708) 		1
(1.00) 		0.779
(1.00) 		0.256
(0.835) 		0.497
(1.00) 		1
(1.00) 		0.229
(0.793)
SLC35A2 3 (0%) 748 0.705
(1.00) 		0.433
(0.966) 		1
(1.00) 		1
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.0924
(0.578)
OR2A12 7 (1%) 744 0.695
(1.00) 		0.289
(0.85) 		0.433
(0.966) 		0.452
(0.984) 		0.438
(0.973) 		0.0524
(0.485) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PLCG2 10 (1%) 741 0.933
(1.00) 		0.268
(0.843) 		0.752
(1.00) 		0.539
(1.00) 		0.0215
(0.31) 		0.561
(1.00) 		0.752
(1.00) 		1
(1.00) 		1
(1.00)
HTT 5 (1%) 746 0.0516
(0.483) 		0.378
(0.936) 		0.164
(0.708) 		0.404
(0.962) 		0.102
(0.604) 		0.656
(1.00) 		1
(1.00) 		1
(1.00)
MAP3K1 9 (1%) 742 0.598
(1.00) 		0.0461
(0.474) 		0.0837
(0.551) 		0.744
(1.00) 		0.238
(0.809) 		0.304
(0.85) 		0.733
(1.00) 		1
(1.00) 		1
(1.00)
BBS9 3 (0%) 748 0.737
(1.00) 		0.769
(1.00) 		1
(1.00) 		1
(1.00) 		0.426
(0.966) 		0.559
(1.00) 		1
(1.00) 		1
(1.00)
CSNK2B 3 (0%) 748 0.869
(1.00) 		0.92
(1.00) 		0.559
(1.00) 		0.0679
(0.514) 		0.883
(1.00) 		0.559
(1.00) 		0.061
(0.506) 		1
(1.00)
CD72 3 (0%) 748 0.203
(0.761) 		0.442
(0.979) 		0.3
(0.85) 		0.571
(1.00) 		0.152
(0.698) 		0.0669
(0.514) 		0.3
(0.85) 		1
(1.00) 		1
(1.00)
SPINT1 5 (1%) 746 0.0158
(0.268) 		0.257
(0.837) 		0.0654
(0.512) 		0.165
(0.708) 		0.0473
(0.474) 		0.351
(0.919) 		0.656
(1.00) 		0.279
(0.849) 		1
(1.00)
EGR1 5 (1%) 746 0.966
(1.00) 		0.303
(0.85) 		0.365
(0.931) 		0.404
(0.962) 		0.372
(0.932) 		0.478
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
OR2A25 5 (1%) 746 0.194
(0.757) 		0.287
(0.85) 		1
(1.00) 		0.404
(0.962) 		0.401
(0.962) 		0.933
(1.00) 		1
(1.00) 		0.277
(0.847) 		1
(1.00)
PDGFRB 3 (0%) 748 0.109
(0.619) 		0.537
(1.00) 		0.0504
(0.477) 		1
(1.00) 		0.318
(0.872) 		0.0504
(0.477) 		1
(1.00) 		1
(1.00)
MTMR12 4 (1%) 747 0.913
(1.00) 		0.0851
(0.551) 		0.629
(1.00) 		1
(1.00) 		0.63
(1.00) 		0.493
(1.00) 		0.146
(0.697) 		1
(1.00) 		1
(1.00)
AMBRA1 6 (1%) 745 0.143
(0.697) 		0.723
(1.00) 		1
(1.00) 		1
(1.00) 		0.052
(0.483) 		0.755
(1.00) 		0.201
(0.761) 		1
(1.00) 		0.177
(0.727)
BTNL2 4 (1%) 747 0.951
(1.00) 		0.504
(1.00) 		0.629
(1.00) 		1
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.226
(0.793) 		1
(1.00)
RPTN 7 (1%) 744 0.911
(1.00) 		0.65
(1.00) 		0.433
(0.966) 		0.707
(1.00) 		0.15
(0.698) 		0.674
(1.00) 		0.433
(0.966) 		0.363
(0.931) 		1
(1.00)
ZNF148 5 (1%) 746 0.0472
(0.474) 		0.183
(0.741) 		0.656
(1.00) 		0.404
(0.962) 		0.433
(0.966) 		1
(1.00) 		0.106
(0.616) 		1
(1.00)
GFRA4 3 (0%) 748 0.0959
(0.585) 		0.497
(1.00) 		0.559
(1.00) 		0.274
(0.845) 		0.411
(0.963) 		0.794
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SLC6A4 5 (1%) 746 0.147
(0.697) 		0.144
(0.697) 		0.656
(1.00) 		0.165
(0.708) 		0.242
(0.817) 		0.365
(0.931) 		1
(1.00) 		1
(1.00)
RUVBL2 4 (1%) 747 0.371
(0.932) 		0.47
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00)
PYGL 4 (1%) 747 0.279
(0.849) 		0.777
(1.00) 		1
(1.00) 		1
(1.00) 		0.408
(0.963) 		0.917
(1.00) 		0.629
(1.00) 		0.0851
(0.551) 		1
(1.00)
ASXL2 3 (0%) 748 0.0819
(0.551) 		0.129
(0.695) 		0.3
(0.85) 		0.571
(1.00) 		0.275
(0.845) 		0.559
(1.00) 		1
(1.00) 		1
(1.00)
CIB1 5 (1%) 746 0.458
(0.99) 		0.899
(1.00) 		0.656
(1.00) 		0.404
(0.962) 		0.988
(1.00) 		0.741
(1.00) 		0.656
(1.00) 		1
(1.00) 		1
(1.00)
REXO1 7 (1%) 744 0.956
(1.00) 		0.14
(0.697) 		0.433
(0.966) 		0.452
(0.984) 		0.268
(0.843) 		0.115
(0.638) 		0.714
(1.00) 		0.366
(0.931) 		1
(1.00)
SOX4 6 (1%) 745 0.034
(0.418) 		0.676
(1.00) 		0.421
(0.966) 		0.233
(0.798) 		0.725
(1.00) 		1
(1.00) 		1
(1.00) 		0.177
(0.727)
GLYAT 5 (1%) 746 0.0644
(0.512) 		0.838
(1.00) 		0.656
(1.00) 		0.654
(1.00) 		0.659
(1.00) 		0.744
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
LYPD4 5 (1%) 746 0.724
(1.00) 		0.368
(0.932) 		0.365
(0.931) 		0.404
(0.962) 		0.479
(1.00) 		0.365
(0.931) 		1
(1.00) 		0.149
(0.697)
EPS8L1 4 (1%) 747 0.155
(0.702) 		0.455
(0.984) 		0.629
(1.00) 		1
(1.00) 		0.492
(1.00) 		0.0185
(0.278) 		1
(1.00) 		1
(1.00)
CNOT4 6 (1%) 745 0.0792
(0.551) 		0.992
(1.00) 		0.421
(0.966) 		0.693
(1.00) 		0.941
(1.00) 		0.533
(1.00) 		0.421
(0.966) 		1
(1.00) 		1
(1.00)
MYH8 17 (2%) 734 0.063
(0.512) 		0.432
(0.966) 		1
(1.00) 		0.141
(0.697) 		0.27
(0.843) 		0.529
(1.00) 		0.205
(0.761) 		0.296
(0.85) 		0.407
(0.963)
DPYS 5 (1%) 746 0.701
(1.00) 		0.594
(1.00) 		0.656
(1.00) 		0.654
(1.00) 		0.587
(1.00) 		0.786
(1.00) 		0.365
(0.931) 		1
(1.00) 		0.149
(0.697)
TLR7 9 (1%) 742 0.228
(0.793) 		0.961
(1.00) 		0.733
(1.00) 		0.171
(0.727) 		0.227
(0.793) 		0.854
(1.00) 		0.733
(1.00) 		0.404
(0.962) 		1
(1.00)
MYH11 14 (2%) 737 0.547
(1.00) 		0.289
(0.85) 		1
(1.00) 		1
(1.00) 		0.0507
(0.477) 		0.204
(0.761) 		0.781
(1.00) 		1
(1.00) 		1
(1.00)
SLC9A4 10 (1%) 741 0.195
(0.758) 		0.147
(0.697) 		0.0442
(0.472) 		0.748
(1.00) 		0.404
(0.962) 		0.0368
(0.421) 		0.512
(1.00) 		0.476
(1.00) 		1
(1.00)
KRT15 8 (1%) 743 0.971
(1.00) 		0.274
(0.845) 		0.717
(1.00) 		0.482
(1.00) 		0.511
(1.00) 		0.783
(1.00) 		0.27
(0.843) 		0.405
(0.962) 		1
(1.00)
FMR1 5 (1%) 746 0.0362
(0.421) 		0.031
(0.399) 		0.164
(0.708) 		1
(1.00) 		0.152
(0.698) 		0.0594
(0.5) 		0.656
(1.00) 		1
(1.00) 		1
(1.00)
PPP2R5E 3 (0%) 748 0.283
(0.85) 		0.479
(1.00) 		1
(1.00) 		0.0679
(0.514) 		0.43
(0.966) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ZC3H11A 5 (1%) 746 0.798
(1.00) 		0.753
(1.00) 		0.164
(0.708) 		0.654
(1.00) 		0.654
(1.00) 		0.078
(0.551) 		0.656
(1.00) 		1
(1.00) 		1
(1.00)
DST 15 (2%) 736 0.132
(0.696) 		0.812
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.907
(1.00) 		0.254
(0.832) 		1
(1.00) 		0.598
(1.00) 		0.0787
(0.551)
NKPD1 3 (0%) 748 0.954
(1.00) 		0.435
(0.968) 		0.3
(0.85) 		0.571
(1.00) 		0.234
(0.798) 		0.3
(0.85) 		1
(1.00) 		0.0924
(0.578)
CTBP2 3 (0%) 748 0.811
(1.00) 		0.638
(1.00) 		0.559
(1.00) 		0.571
(1.00) 		0.777
(1.00) 		0.793
(1.00) 		0.559
(1.00) 		0.175
(0.727) 		1
(1.00)
SEC14L4 3 (0%) 748 0.586
(1.00) 		0.0176
(0.278) 		0.3
(0.85) 		0.274
(0.845) 		0.234
(0.798) 		0.559
(1.00) 		1
(1.00) 		1
(1.00)
KEL 24 (3%) 727 0.054
(0.491) 		0.0184
(0.278) 		0.0161
(0.268) 		0.675
(1.00) 		0.346
(0.912) 		0.131
(0.695) 		0.2
(0.761) 		0.763
(1.00) 		1
(1.00)
SSTR4 10 (1%) 741 0.429
(0.966) 		0.652
(1.00) 		1
(1.00) 		1
(1.00) 		0.329
(0.888) 		0.0786
(0.551) 		0.512
(1.00) 		1
(1.00) 		1
(1.00)
SMARCB1 4 (1%) 747 0.165
(0.708) 		0.25
(0.83) 		0.303
(0.85) 		0.649
(1.00) 		0.411
(0.963) 		0.275
(0.845) 		0.146
(0.697) 		1
(1.00) 		1
(1.00)
CAPN11 5 (1%) 746 0.591
(1.00) 		0.549
(1.00) 		1
(1.00) 		1
(1.00) 		0.315
(0.867) 		0.0654
(0.512) 		1
(1.00) 		1
(1.00)
SH3KBP1 4 (1%) 747 0.0567
(0.494) 		0.265
(0.843) 		0.303
(0.85) 		0.0276
(0.372) 		0.144
(0.697) 		1
(1.00) 		0.0842
(0.551) 		1
(1.00)
'IDH1 MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

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

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
IDH1 MUTATED 379 57 0.0 - 182.3 (20.2)
IDH1 WILD-TYPE 370 247 0.1 - 211.2 (11.7)

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 = 4.19e-51 (Wilcoxon-test), Q value = 1.4e-48

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

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
IDH1 MUTATED 380 41.1 (12.6)
IDH1 WILD-TYPE 370 58.4 (14.1)

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

'IDH1 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 3.82e-94 (Fisher's exact test), Q value = 1.6e-91

Table S3.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
IDH1 MUTATED 14 367
IDH1 WILD-TYPE 264 106

Figure S3.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'IDH1 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 5.59e-17 (Wilcoxon-test), Q value = 7.8e-15

Table S4.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
IDH1 MUTATED 223 88.2 (11.9)
IDH1 WILD-TYPE 246 77.8 (15.7)

Figure S4.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'IDH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S5.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
IDH1 MUTATED 122 1 100 145 0 13
IDH1 WILD-TYPE 53 8 19 34 4 252

Figure S5.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'IDH1 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 1.49e-18 (Fisher's exact test), Q value = 2.5e-16

Table S6.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
IDH1 MUTATED 83 298
IDH1 WILD-TYPE 195 175

Figure S6.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'TP53 MUTATION STATUS' versus 'Time to Death'

P value = 1.52e-10 (logrank test), Q value = 1.4e-08

Table S7.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
TP53 MUTATED 303 90 0.0 - 211.2 (18.6)
TP53 WILD-TYPE 446 214 0.1 - 182.3 (14.2)

Figure S7.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'TP53 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 1.48e-17 (Wilcoxon-test), Q value = 2.3e-15

Table S8.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
TP53 MUTATED 304 43.8 (15.4)
TP53 WILD-TYPE 446 53.7 (14.9)

Figure S8.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TP53 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 9.74e-08 (Fisher's exact test), Q value = 7.5e-06

Table S9.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
TP53 MUTATED 78 226
TP53 WILD-TYPE 200 247

Figure S9.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'TP53 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000195 (Wilcoxon-test), Q value = 0.0078

Table S10.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
TP53 MUTATED 194 86.0 (12.2)
TP53 WILD-TYPE 275 80.5 (16.2)

Figure S10.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S11.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
TP53 MUTATED 116 1 69 41 0 77
TP53 WILD-TYPE 59 8 50 138 4 188

Figure S11.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'ATRX MUTATION STATUS' versus 'Time to Death'

P value = 6.11e-15 (logrank test), Q value = 7.9e-13

Table S12.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
ATRX MUTATED 196 42 0.0 - 211.2 (20.8)
ATRX WILD-TYPE 553 262 0.1 - 182.3 (14.1)

Figure S12.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ATRX MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 2.19e-32 (Wilcoxon-test), Q value = 6.1e-30

Table S13.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
ATRX MUTATED 197 38.3 (12.5)
ATRX WILD-TYPE 553 53.7 (15.0)

Figure S13.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'ATRX MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 9.88e-26 (Fisher's exact test), Q value = 2.4e-23

Table S14.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
ATRX MUTATED 16 181
ATRX WILD-TYPE 262 292

Figure S14.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'ATRX MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 3.86e-06 (Wilcoxon-test), Q value = 0.00027

Table S15.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
ATRX MUTATED 117 87.6 (12.5)
ATRX WILD-TYPE 352 81.2 (15.3)

Figure S15.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'ATRX MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S16.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
ATRX MUTATED 86 1 61 34 0 15
ATRX WILD-TYPE 89 8 58 145 4 250

Figure S16.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'PTEN MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S17.  Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
PTEN MUTATED 108 74 0.1 - 211.2 (10.6)
PTEN WILD-TYPE 641 230 0.0 - 182.3 (15.8)

Figure S17.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTEN MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 4.22e-13 (Wilcoxon-test), Q value = 4.7e-11

Table S18.  Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
PTEN MUTATED 108 60.0 (12.9)
PTEN WILD-TYPE 642 47.9 (15.7)

Figure S18.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PTEN MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.19e-21 (Fisher's exact test), Q value = 2.5e-19

Table S19.  Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
PTEN MUTATED 85 23
PTEN WILD-TYPE 193 450

Figure S19.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'PTEN MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000551 (Wilcoxon-test), Q value = 0.019

Table S20.  Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
PTEN MUTATED 74 77.8 (15.8)
PTEN WILD-TYPE 395 83.7 (14.6)

Figure S20.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'PTEN MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S21.  Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
PTEN MUTATED 17 0 3 3 2 83
PTEN WILD-TYPE 158 9 116 176 2 182

Figure S21.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'PTEN MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.00067

Table S22.  Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
PTEN MUTATED 61 47
PTEN WILD-TYPE 217 426

Figure S22.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'CIC MUTATION STATUS' versus 'Time to Death'

P value = 1.26e-10 (logrank test), Q value = 1.2e-08

Table S23.  Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
CIC MUTATED 101 11 0.1 - 211.2 (19.9)
CIC WILD-TYPE 648 293 0.0 - 172.8 (14.9)

Figure S23.  Get High-res Image Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CIC MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00321 (Wilcoxon-test), Q value = 0.082

Table S24.  Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
CIC MUTATED 101 45.3 (13.7)
CIC WILD-TYPE 649 50.3 (16.1)

Figure S24.  Get High-res Image Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'CIC MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 5.95e-21 (Fisher's exact test), Q value = 1.1e-18

Table S25.  Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
CIC MUTATED 1 100
CIC WILD-TYPE 277 373

Figure S25.  Get High-res Image Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'CIC MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000639 (Wilcoxon-test), Q value = 0.02

Table S26.  Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
CIC MUTATED 58 88.6 (11.0)
CIC WILD-TYPE 411 81.9 (15.2)

Figure S26.  Get High-res Image Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'CIC MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S27.  Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
CIC MUTATED 3 0 20 77 0 1
CIC WILD-TYPE 172 9 99 102 4 264

Figure S27.  Get High-res Image Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'CIC MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 6e-08 (Fisher's exact test), Q value = 4.8e-06

Table S28.  Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
CIC MUTATED 14 87
CIC WILD-TYPE 264 386

Figure S28.  Get High-res Image Gene #5: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'NF1 MUTATION STATUS' versus 'Time to Death'

P value = 2.89e-05 (logrank test), Q value = 0.0014

Table S29.  Gene #7: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
NF1 MUTATED 60 37 0.2 - 211.2 (12.5)
NF1 WILD-TYPE 689 267 0.0 - 182.3 (15.3)

Figure S29.  Get High-res Image Gene #7: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NF1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000971 (Wilcoxon-test), Q value = 0.03

Table S30.  Gene #7: 'NF1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
NF1 MUTATED 60 56.0 (15.2)
NF1 WILD-TYPE 690 49.1 (15.8)

Figure S30.  Get High-res Image Gene #7: 'NF1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'NF1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00867 (Fisher's exact test), Q value = 0.18

Table S31.  Gene #7: 'NF1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
NF1 MUTATED 20 1 6 5 0 28
NF1 WILD-TYPE 155 8 113 174 4 237

Figure S31.  Get High-res Image Gene #7: 'NF1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'PIK3R1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00446 (Wilcoxon-test), Q value = 0.11

Table S32.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
PIK3R1 MUTATED 52 55.6 (15.4)
PIK3R1 WILD-TYPE 698 49.2 (15.9)

Figure S32.  Get High-res Image Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PIK3R1 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000273 (Fisher's exact test), Q value = 0.01

Table S33.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
PIK3R1 MUTATED 32 20
PIK3R1 WILD-TYPE 246 453

Figure S33.  Get High-res Image Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'PIK3R1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00629 (Fisher's exact test), Q value = 0.15

Table S34.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
PIK3R1 MUTATED 7 1 3 10 0 31
PIK3R1 WILD-TYPE 168 8 116 169 4 234

Figure S34.  Get High-res Image Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'PIK3R1 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00257 (Fisher's exact test), Q value = 0.07

Table S35.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
PIK3R1 MUTATED 30 22
PIK3R1 WILD-TYPE 248 451

Figure S35.  Get High-res Image Gene #8: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'NOTCH1 MUTATION STATUS' versus 'Time to Death'

P value = 0.000299 (logrank test), Q value = 0.011

Table S36.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
NOTCH1 MUTATED 41 7 0.3 - 211.2 (23.2)
NOTCH1 WILD-TYPE 708 297 0.0 - 182.3 (15.0)

Figure S36.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NOTCH1 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 2.12e-09 (Fisher's exact test), Q value = 1.8e-07

Table S37.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
NOTCH1 MUTATED 0 42
NOTCH1 WILD-TYPE 278 431

Figure S37.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'NOTCH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S38.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
NOTCH1 MUTATED 6 0 7 29 0 0
NOTCH1 WILD-TYPE 169 9 112 150 4 265

Figure S38.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'NOTCH1 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0132 (Fisher's exact test), Q value = 0.23

Table S39.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
NOTCH1 MUTATED 8 34
NOTCH1 WILD-TYPE 270 439

Figure S39.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'FUBP1 MUTATION STATUS' versus 'Time to Death'

P value = 0.000397 (logrank test), Q value = 0.015

Table S40.  Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
FUBP1 MUTATED 46 6 0.1 - 211.2 (16.6)
FUBP1 WILD-TYPE 703 298 0.0 - 182.3 (15.1)

Figure S40.  Get High-res Image Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'FUBP1 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 3.25e-10 (Fisher's exact test), Q value = 2.9e-08

Table S41.  Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
FUBP1 MUTATED 0 46
FUBP1 WILD-TYPE 278 427

Figure S41.  Get High-res Image Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'FUBP1 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00673 (Wilcoxon-test), Q value = 0.15

Table S42.  Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
FUBP1 MUTATED 27 89.6 (11.6)
FUBP1 WILD-TYPE 442 82.4 (15.0)

Figure S42.  Get High-res Image Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'FUBP1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S43.  Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
FUBP1 MUTATED 2 0 8 36 0 0
FUBP1 WILD-TYPE 173 9 111 143 4 265

Figure S43.  Get High-res Image Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'FUBP1 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0114 (Fisher's exact test), Q value = 0.21

Table S44.  Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
FUBP1 MUTATED 9 37
FUBP1 WILD-TYPE 269 436

Figure S44.  Get High-res Image Gene #10: 'FUBP1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'RB1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00149 (Wilcoxon-test), Q value = 0.044

Table S45.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
RB1 MUTATED 28 59.4 (14.5)
RB1 WILD-TYPE 722 49.3 (15.8)

Figure S45.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RB1 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 8.28e-07 (Fisher's exact test), Q value = 6.1e-05

Table S46.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
RB1 MUTATED 23 5
RB1 WILD-TYPE 255 468

Figure S46.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'RB1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0027

Table S47.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
RB1 MUTATED 4 1 0 1 0 22
RB1 WILD-TYPE 171 8 119 178 4 243

Figure S47.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'RB1 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00102 (Fisher's exact test), Q value = 0.031

Table S48.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
RB1 MUTATED 19 9
RB1 WILD-TYPE 259 464

Figure S48.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'IDH2 MUTATION STATUS' versus 'Time to Death'

P value = 0.00256 (logrank test), Q value = 0.07

Table S49.  Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
IDH2 MUTATED 19 1 0.1 - 78.2 (29.6)
IDH2 WILD-TYPE 730 303 0.0 - 211.2 (15.0)

Figure S49.  Get High-res Image Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'IDH2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000852 (Wilcoxon-test), Q value = 0.027

Table S50.  Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
IDH2 MUTATED 19 38.1 (9.8)
IDH2 WILD-TYPE 731 50.0 (15.9)

Figure S50.  Get High-res Image Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'IDH2 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00016 (Fisher's exact test), Q value = 0.0067

Table S51.  Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
IDH2 MUTATED 0 19
IDH2 WILD-TYPE 278 454

Figure S51.  Get High-res Image Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'IDH2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00096

Table S52.  Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
IDH2 MUTATED 1 0 4 14 0 0
IDH2 WILD-TYPE 174 9 115 165 4 265

Figure S52.  Get High-res Image Gene #12: 'IDH2 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'ARID1A MUTATION STATUS' versus 'Time to Death'

P value = 0.0036 (logrank test), Q value = 0.09

Table S53.  Gene #15: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
ARID1A MUTATED 21 3 6.7 - 211.2 (23.3)
ARID1A WILD-TYPE 728 301 0.0 - 182.3 (15.0)

Figure S53.  Get High-res Image Gene #15: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ARID1A MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00976 (Fisher's exact test), Q value = 0.19

Table S54.  Gene #15: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
ARID1A MUTATED 2 19
ARID1A WILD-TYPE 276 454

Figure S54.  Get High-res Image Gene #15: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'ARID1A MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00475 (Fisher's exact test), Q value = 0.11

Table S55.  Gene #15: 'ARID1A MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
ARID1A MUTATED 4 1 6 9 0 1
ARID1A WILD-TYPE 171 8 113 170 4 264

Figure S55.  Get High-res Image Gene #15: 'ARID1A MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'NIPBL MUTATION STATUS' versus 'Time to Death'

P value = 0.000564 (logrank test), Q value = 0.019

Table S56.  Gene #16: 'NIPBL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
NIPBL MUTATED 19 1 0.2 - 211.2 (23.5)
NIPBL WILD-TYPE 730 303 0.0 - 182.3 (15.1)

Figure S56.  Get High-res Image Gene #16: 'NIPBL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SMARCA4 MUTATION STATUS' versus 'Time to Death'

P value = 0.000609 (logrank test), Q value = 0.02

Table S57.  Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
SMARCA4 MUTATED 25 2 0.2 - 211.2 (25.0)
SMARCA4 WILD-TYPE 724 302 0.0 - 182.3 (15.0)

Figure S57.  Get High-res Image Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SMARCA4 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000188 (Fisher's exact test), Q value = 0.0077

Table S58.  Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
SMARCA4 MUTATED 1 24
SMARCA4 WILD-TYPE 277 449

Figure S58.  Get High-res Image Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'SMARCA4 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0121 (Wilcoxon-test), Q value = 0.22

Table S59.  Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
SMARCA4 MUTATED 14 91.4 (7.7)
SMARCA4 WILD-TYPE 455 82.5 (15.0)

Figure S59.  Get High-res Image Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'SMARCA4 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00682 (Fisher's exact test), Q value = 0.15

Table S60.  Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
SMARCA4 MUTATED 9 0 5 10 0 1
SMARCA4 WILD-TYPE 166 9 114 169 4 264

Figure S60.  Get High-res Image Gene #17: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'ZNF709 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.012 (Fisher's exact test), Q value = 0.22

Table S61.  Gene #20: 'ZNF709 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
ZNF709 MUTATED 6 1
ZNF709 WILD-TYPE 272 472

Figure S61.  Get High-res Image Gene #20: 'ZNF709 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'STAG2 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00263 (Fisher's exact test), Q value = 0.07

Table S62.  Gene #22: 'STAG2 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
STAG2 MUTATED 12 4
STAG2 WILD-TYPE 266 469

Figure S62.  Get High-res Image Gene #22: 'STAG2 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'STAG2 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00901 (Wilcoxon-test), Q value = 0.18

Table S63.  Gene #22: 'STAG2 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
STAG2 MUTATED 9 66.7 (19.4)
STAG2 WILD-TYPE 460 83.1 (14.7)

Figure S63.  Get High-res Image Gene #22: 'STAG2 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'REN MUTATION STATUS' versus 'Time to Death'

P value = 9.27e-05 (logrank test), Q value = 0.0041

Table S64.  Gene #24: 'REN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
REN MUTATED 7 5 1.0 - 15.0 (8.0)
REN WILD-TYPE 742 299 0.0 - 211.2 (15.3)

Figure S64.  Get High-res Image Gene #24: 'REN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PLCG1 MUTATION STATUS' versus 'Time to Death'

P value = 0.00444 (logrank test), Q value = 0.11

Table S65.  Gene #27: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
PLCG1 MUTATED 11 9 6.7 - 39.0 (14.8)
PLCG1 WILD-TYPE 738 295 0.0 - 211.2 (15.2)

Figure S65.  Get High-res Image Gene #27: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SLC26A3 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00683 (Fisher's exact test), Q value = 0.15

Table S66.  Gene #28: 'SLC26A3 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
SLC26A3 MUTATED 8 2
SLC26A3 WILD-TYPE 270 471

Figure S66.  Get High-res Image Gene #28: 'SLC26A3 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'ZBTB20 MUTATION STATUS' versus 'Time to Death'

P value = 0.0115 (logrank test), Q value = 0.22

Table S67.  Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
ZBTB20 MUTATED 19 3 4.6 - 211.2 (22.1)
ZBTB20 WILD-TYPE 730 301 0.0 - 182.3 (15.0)

Figure S67.  Get High-res Image Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ZBTB20 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00163 (Fisher's exact test), Q value = 0.047

Table S68.  Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
ZBTB20 MUTATED 1 19
ZBTB20 WILD-TYPE 277 454

Figure S68.  Get High-res Image Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'ZBTB20 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00868 (Fisher's exact test), Q value = 0.18

Table S69.  Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
ZBTB20 MUTATED 4 0 4 11 0 1
ZBTB20 WILD-TYPE 171 9 115 168 4 264

Figure S69.  Get High-res Image Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'ZBTB20 MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00947 (Fisher's exact test), Q value = 0.19

Table S70.  Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
ZBTB20 MUTATED 2 18
ZBTB20 WILD-TYPE 276 455

Figure S70.  Get High-res Image Gene #29: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'DNMT3A MUTATION STATUS' versus 'Time to Death'

P value = 0.00864 (logrank test), Q value = 0.18

Table S71.  Gene #34: 'DNMT3A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
DNMT3A MUTATED 10 0 13.3 - 211.2 (17.3)
DNMT3A WILD-TYPE 739 304 0.0 - 182.3 (15.0)

Figure S71.  Get High-res Image Gene #34: 'DNMT3A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'BRAF MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00193 (Fisher's exact test), Q value = 0.054

Table S72.  Gene #38: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
BRAF MUTATED 5 2 0 0 0 4
BRAF WILD-TYPE 170 7 119 179 4 261

Figure S72.  Get High-res Image Gene #38: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'EGFR MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S73.  Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
EGFR MUTATED 103 72 0.2 - 211.2 (11.5)
EGFR WILD-TYPE 646 232 0.0 - 182.3 (16.0)

Figure S73.  Get High-res Image Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'EGFR MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 6.05e-13 (Wilcoxon-test), Q value = 6.4e-11

Table S74.  Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
EGFR MUTATED 103 59.7 (11.1)
EGFR WILD-TYPE 647 48.1 (16.0)

Figure S74.  Get High-res Image Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'EGFR MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 6e-14 (Fisher's exact test), Q value = 7.2e-12

Table S75.  Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
EGFR MUTATED 73 30
EGFR WILD-TYPE 205 443

Figure S75.  Get High-res Image Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'EGFR MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.57e-05 (Wilcoxon-test), Q value = 0.00078

Table S76.  Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
EGFR MUTATED 71 75.9 (16.7)
EGFR WILD-TYPE 398 84.0 (14.2)

Figure S76.  Get High-res Image Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'EGFR MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00053

Table S77.  Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
EGFR MUTATED 18 1 6 6 0 72
EGFR WILD-TYPE 157 8 113 173 4 193

Figure S77.  Get High-res Image Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'EGFR MUTATION STATUS' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000634 (Fisher's exact test), Q value = 0.02

Table S78.  Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 278 473
EGFR MUTATED 54 49
EGFR WILD-TYPE 224 424

Figure S78.  Get High-res Image Gene #39: 'EGFR MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'SEMG2 MUTATION STATUS' versus 'Time to Death'

P value = 0.00275 (logrank test), Q value = 0.072

Table S79.  Gene #41: 'SEMG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
SEMG2 MUTATED 13 10 0.2 - 73.8 (9.5)
SEMG2 WILD-TYPE 736 294 0.0 - 211.2 (15.2)

Figure S79.  Get High-res Image Gene #41: 'SEMG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SEMG2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000494 (Wilcoxon-test), Q value = 0.018

Table S80.  Gene #41: 'SEMG2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
SEMG2 MUTATED 13 64.8 (10.2)
SEMG2 WILD-TYPE 737 49.4 (15.9)

Figure S80.  Get High-res Image Gene #41: 'SEMG2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'SEMG2 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000551 (Fisher's exact test), Q value = 0.019

Table S81.  Gene #41: 'SEMG2 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
SEMG2 MUTATED 11 2
SEMG2 WILD-TYPE 267 471

Figure S81.  Get High-res Image Gene #41: 'SEMG2 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'FAM83D MUTATION STATUS' versus 'Time to Death'

P value = 0.0101 (logrank test), Q value = 0.2

Table S82.  Gene #45: 'FAM83D MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
FAM83D MUTATED 4 2 0.1 - 15.1 (2.1)
FAM83D WILD-TYPE 745 302 0.0 - 211.2 (15.2)

Figure S82.  Get High-res Image Gene #45: 'FAM83D MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PDGFRA MUTATION STATUS' versus 'Time to Death'

P value = 0.00162 (logrank test), Q value = 0.047

Table S83.  Gene #52: 'PDGFRA MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
PDGFRA MUTATED 20 15 0.5 - 211.2 (11.8)
PDGFRA WILD-TYPE 729 289 0.0 - 182.3 (15.3)

Figure S83.  Get High-res Image Gene #52: 'PDGFRA MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PDGFRA MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0123 (Wilcoxon-test), Q value = 0.22

Table S84.  Gene #52: 'PDGFRA MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
PDGFRA MUTATED 20 58.4 (15.8)
PDGFRA WILD-TYPE 730 49.4 (15.8)

Figure S84.  Get High-res Image Gene #52: 'PDGFRA MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'HTRA2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00686 (Wilcoxon-test), Q value = 0.15

Table S85.  Gene #56: 'HTRA2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 750 49.7 (15.9)
HTRA2 MUTATED 5 31.2 (9.7)
HTRA2 WILD-TYPE 745 49.8 (15.9)

Figure S85.  Get High-res Image Gene #56: 'HTRA2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PDHA1 MUTATION STATUS' versus 'GENDER'

P value = 0.00453 (Fisher's exact test), Q value = 0.11

Table S86.  Gene #75: 'PDHA1 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 307 444
PDHA1 MUTATED 6 0
PDHA1 WILD-TYPE 301 444

Figure S86.  Get High-res Image Gene #75: 'PDHA1 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

'DSG3 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.003 (Fisher's exact test), Q value = 0.078

Table S87.  Gene #125: 'DSG3 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
DSG3 MUTATED 9 2
DSG3 WILD-TYPE 269 471

Figure S87.  Get High-res Image Gene #125: 'DSG3 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'CCDC110 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00548 (Fisher's exact test), Q value = 0.13

Table S88.  Gene #142: 'CCDC110 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
CCDC110 MUTATED 1 1 1 1 1 1
CCDC110 WILD-TYPE 174 8 118 178 3 264

Figure S88.  Get High-res Image Gene #142: 'CCDC110 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'ATF7IP2 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00688 (Wilcoxon-test), Q value = 0.15

Table S89.  Gene #143: 'ATF7IP2 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 469 82.8 (14.9)
ATF7IP2 MUTATED 7 70.0 (10.0)
ATF7IP2 WILD-TYPE 462 83.0 (14.9)

Figure S89.  Get High-res Image Gene #143: 'ATF7IP2 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'QKI MUTATION STATUS' versus 'Time to Death'

P value = 0.0112 (logrank test), Q value = 0.21

Table S90.  Gene #144: 'QKI MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
QKI MUTATED 6 6 10.4 - 36.8 (15.8)
QKI WILD-TYPE 743 298 0.0 - 211.2 (15.2)

Figure S90.  Get High-res Image Gene #144: 'QKI MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CCDC135 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00747 (Fisher's exact test), Q value = 0.16

Table S91.  Gene #157: 'CCDC135 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
CCDC135 MUTATED 4 0 1 1 1 0
CCDC135 WILD-TYPE 171 9 118 178 3 265

Figure S91.  Get High-res Image Gene #157: 'CCDC135 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'SEMA3C MUTATION STATUS' versus 'Time to Death'

P value = 0.000255 (logrank test), Q value = 0.01

Table S92.  Gene #173: 'SEMA3C MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 749 304 0.0 - 211.2 (15.2)
SEMA3C MUTATED 12 8 1.1 - 22.8 (9.1)
SEMA3C WILD-TYPE 737 296 0.0 - 211.2 (15.2)

Figure S92.  Get High-res Image Gene #173: 'SEMA3C MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SEMA3C MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000127 (Fisher's exact test), Q value = 0.0055

Table S93.  Gene #173: 'SEMA3C MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
SEMA3C MUTATED 11 1
SEMA3C WILD-TYPE 267 472

Figure S93.  Get High-res Image Gene #173: 'SEMA3C MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'SEMA3C MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00685 (Fisher's exact test), Q value = 0.15

Table S94.  Gene #173: 'SEMA3C MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 175 9 119 179 4 265
SEMA3C MUTATED 1 0 0 0 0 11
SEMA3C WILD-TYPE 174 9 119 179 4 254

Figure S94.  Get High-res Image Gene #173: 'SEMA3C MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'PAN3 MUTATION STATUS' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.012 (Fisher's exact test), Q value = 0.22

Table S95.  Gene #174: 'PAN3 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 278 473
PAN3 MUTATED 6 1
PAN3 WILD-TYPE 272 472

Figure S95.  Get High-res Image Gene #174: 'PAN3 MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

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/GBMLGG-TP/15650472/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBMLGG-TP/15078950/GBMLGG-TP.merged_data.txt

  • Number of patients = 751

  • Number of significantly mutated genes = 187

  • Number of selected clinical features = 9

  • 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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