Correlation between gene mutation status and selected clinical features
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1XD113Q
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1XD113Q
Overview
Introduction

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

Summary

Testing the association between mutation status of 171 genes and 9 clinical features across 795 patients, 91 significant findings detected with Q value < 0.25.

  • IDH1 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

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

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

  • CIC mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

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

  • PIK3R1 mutation correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

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

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

  • RB1 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • FUBP1 mutation correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

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

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

  • NIPBL mutation correlated to 'Time to Death'.

  • NUDT11 mutation correlated to 'TUMOR_TISSUE_SITE'.

  • PLCG1 mutation correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • PDGFRA mutation correlated to 'Time to Death'.

  • STAG2 mutation correlated to 'TUMOR_TISSUE_SITE'.

  • REN mutation correlated to 'Time to Death'.

  • HTRA2 mutation correlated to 'YEARS_TO_BIRTH'.

  • BRAF mutation correlated to 'HISTOLOGICAL_TYPE'.

  • MX2 mutation correlated to 'YEARS_TO_BIRTH'.

  • EGFR mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • WRN mutation correlated to 'ETHNICITY'.

  • ZNF41 mutation correlated to 'GENDER'.

  • ATF7IP2 mutation correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • ZBTB20 mutation correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • PDHA1 mutation correlated to 'GENDER'.

  • FAM123C mutation correlated to 'YEARS_TO_BIRTH'.

  • DNMT3A mutation correlated to 'Time to Death' and 'TUMOR_TISSUE_SITE'.

  • QKI mutation correlated to 'Time to Death'.

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

  • GRHL3 mutation correlated to 'GENDER'.

  • TNFRSF9 mutation correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • PASD1 mutation correlated to 'GENDER'.

  • IL4R mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'TUMOR_TISSUE_SITE'.

  • GABRA6 mutation correlated to 'TUMOR_TISSUE_SITE'.

  • AK7 mutation correlated to 'Time to Death'.

  • DSP mutation correlated to 'YEARS_TO_BIRTH'.

  • PAN3 mutation correlated to 'TUMOR_TISSUE_SITE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 171 genes and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 91 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		GENDER RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
IDH1 414 (52%) 381 0
(0) 		3.8e-55
(1.17e-52) 		1.34e-97
(5.16e-95) 		0.172
(0.715) 		2.67e-08
(1.96e-06) 		1.89e-16
(2.65e-14) 		1e-05
(0.000481) 		0.0597
(0.503) 		0.0542
(0.482)
TP53 330 (42%) 465 8.87e-10
(8.03e-08) 		9.18e-19
(1.41e-16) 		5.04e-08
(3.53e-06) 		1
(1.00) 		0.005
(0.108) 		0.00118
(0.0343) 		1e-05
(0.000481) 		0.283
(0.844) 		0.294
(0.855)
CIC 109 (14%) 686 1.84e-12
(1.77e-10) 		0.00112
(0.0334) 		2.84e-21
(4.85e-19) 		0.117
(0.624) 		2.15e-09
(1.74e-07) 		0.000469
(0.0154) 		1e-05
(0.000481) 		0.66
(1.00) 		0.216
(0.785)
EGFR 108 (14%) 687 0
(0) 		1.9e-14
(2.09e-12) 		2.5e-13
(2.56e-11) 		0.172
(0.715) 		0.0017
(0.0468) 		2.1e-05
(0.000949) 		1e-05
(0.000481) 		0.0504
(0.47) 		0.109
(0.609)
ATRX 213 (27%) 582 5.77e-15
(7.4e-13) 		6.85e-34
(1.76e-31) 		1.48e-26
(3.26e-24) 		0.516
(0.998) 		0.657
(1.00) 		0.000108
(0.00448) 		1e-05
(0.000481) 		0.925
(1.00) 		0.44
(0.955)
FUBP1 47 (6%) 748 0.000234
(0.00856) 		0.43
(0.947) 		1.03e-09
(8.8e-08) 		1
(1.00) 		0.00374
(0.0913) 		0.0102
(0.184) 		1e-05
(0.000481) 		1
(1.00) 		0.262
(0.83)
PTEN 110 (14%) 685 0
(0) 		1.74e-14
(2.07e-12) 		4.34e-23
(8.36e-21) 		0.467
(0.96) 		0.0639
(0.504) 		0.0017
(0.0468) 		1e-05
(0.000481) 		0.483
(0.971) 		0.607
(1.00)
IDH2 20 (3%) 775 0.00169
(0.0468) 		0.000505
(0.0162) 		0.000192
(0.00722) 		0.82
(1.00) 		0.135
(0.657) 		0.121
(0.635) 		3e-05
(0.00132) 		0.491
(0.971) 		0.0627
(0.504)
RB1 30 (4%) 765 0.0105
(0.187) 		0.000292
(0.0105) 		4.04e-07
(2.71e-05) 		1
(1.00) 		0.304
(0.864) 		0.484
(0.971) 		1e-05
(0.000481) 		1
(1.00) 		0.634
(1.00)
PIK3R1 54 (7%) 741 0.157
(0.705) 		0.00293
(0.0739) 		0.000307
(0.0107) 		0.0853
(0.55) 		0.158
(0.705) 		0.13
(0.651) 		0.00448
(0.101) 		0.126
(0.65) 		0.159
(0.705)
NOTCH1 42 (5%) 753 0.000471
(0.0154) 		0.248
(0.809) 		1.1e-08
(8.44e-07) 		0.426
(0.947) 		0.0824
(0.549) 		0.207
(0.764) 		1e-05
(0.000481) 		0.31
(0.872) 		1
(1.00)
ARID1A 22 (3%) 773 0.00409
(0.0979) 		0.0158
(0.251) 		0.0108
(0.187) 		0.388
(0.92) 		0.162
(0.712) 		0.268
(0.834) 		0.00538
(0.113) 		0.747
(1.00) 		1
(1.00)
SMARCA4 27 (3%) 768 0.000115
(0.00467) 		0.134
(0.657) 		0.000137
(0.00541) 		0.431
(0.947) 		0.661
(1.00) 		0.08
(0.549) 		0.00603
(0.125) 		0.0897
(0.566) 		0.28
(0.844)
IL4R 10 (1%) 785 6.81e-05
(0.00291) 		0.000403
(0.0138) 		0.0048
(0.107) 		0.0201
(0.285) 		1
(1.00) 		0.0526
(0.476) 		0.102
(0.596) 		0.501
(0.978) 		1
(1.00)
NF1 62 (8%) 733 1.07e-05
(0.000501) 		0.000558
(0.0175) 		0.0529
(0.476) 		0.688
(1.00) 		0.658
(1.00) 		0.0482
(0.458) 		0.0235
(0.304) 		0.685
(1.00) 		0.325
(0.877)
PLCG1 11 (1%) 784 0.00257
(0.0659) 		0.0117
(0.199) 		0.531
(1.00) 		1
(1.00) 		0.187
(0.718) 		0.79
(1.00) 		0.579
(1.00) 		0.534
(1.00) 		1
(1.00)
ZBTB20 22 (3%) 773 0.0261
(0.329) 		0.211
(0.773) 		0.00113
(0.0334) 		0.388
(0.92) 		0.0524
(0.476) 		0.352
(0.893) 		0.00747
(0.146) 		0.157
(0.705) 		0.28
(0.844)
DNMT3A 11 (1%) 784 0.00429
(0.0986) 		0.336
(0.877) 		0.0101
(0.184) 		0.77
(1.00) 		1
(1.00) 		0.336
(0.877) 		0.0293
(0.346) 		0.533
(1.00) 		0.431
(0.947)
NIPBL 20 (3%) 775 0.00485
(0.107) 		0.0157
(0.251) 		0.0166
(0.256) 		0.649
(1.00) 		0.118
(0.624) 		0.0889
(0.565) 		0.0315
(0.354) 		0.09
(0.566) 		0.0713
(0.541)
NUDT11 11 (1%) 784 0.0854
(0.55) 		0.567
(1.00) 		0.0101
(0.184) 		0.377
(0.917) 		0.747
(1.00) 		0.178
(0.715) 		0.0761
(0.548) 		1
(1.00) 		1
(1.00)
PDGFRA 21 (3%) 774 0.00428
(0.0986) 		0.0713
(0.541) 		0.108
(0.609) 		0.656
(1.00) 		1
(1.00) 		0.015
(0.25) 		0.182
(0.715) 		0.743
(1.00) 		0.261
(0.829)
STAG2 16 (2%) 779 0.0301
(0.351) 		0.0865
(0.554) 		0.00213
(0.0566) 		0.61
(1.00) 		0.591
(1.00) 		0.0292
(0.346) 		0.0175
(0.261) 		0.649
(1.00) 		1
(1.00)
REN 7 (1%) 788 0.000159
(0.00611) 		0.0776
(0.549) 		0.103
(0.596) 		0.249
(0.81) 		0.445
(0.955) 		0.37
(0.902) 		0.0309
(0.352) 		1
(1.00) 		1
(1.00)
HTRA2 5 (1%) 790 0.222
(0.792) 		0.00731
(0.146) 		0.168
(0.712) 		1
(1.00) 		0.311
(0.872) 		0.179
(0.715) 		1
(1.00) 		0.225
(0.792)
BRAF 11 (1%) 784 0.929
(1.00) 		0.549
(1.00) 		0.208
(0.769) 		1
(1.00) 		0.287
(0.844) 		0.481
(0.969) 		0.00312
(0.0774) 		0.5
(0.978) 		1
(1.00)
MX2 9 (1%) 786 0.391
(0.925) 		0.0145
(0.245) 		0.291
(0.85) 		1
(1.00) 		1
(1.00) 		0.263
(0.83) 		0.0867
(0.554) 		0.465
(0.959) 		1
(1.00)
WRN 6 (1%) 789 0.0729
(0.541) 		0.363
(0.902) 		0.671
(1.00) 		0.241
(0.801) 		1
(1.00) 		0.135
(0.657) 		0.585
(1.00) 		0.339
(0.878) 		0.00202
(0.0545)
ZNF41 8 (1%) 787 0.113
(0.615) 		0.965
(1.00) 		0.719
(1.00) 		0.0107
(0.187) 		0.063
(0.504) 		0.36
(0.897) 		0.278
(0.844) 		0.1
(0.594) 		1
(1.00)
ATF7IP2 8 (1%) 787 0.0848
(0.55) 		0.194
(0.731) 		0.138
(0.661) 		1
(1.00) 		0.445
(0.955) 		0.00992
(0.184) 		0.64
(1.00) 		0.0264
(0.33) 		1
(1.00)
PDHA1 6 (1%) 789 0.648
(1.00) 		0.469
(0.96) 		0.671
(1.00) 		0.00507
(0.108) 		0.178
(0.715) 		0.0502
(0.47) 		0.315
(0.872) 		1
(1.00) 		1
(1.00)
FAM123C 11 (1%) 784 0.0466
(0.448) 		0.00254
(0.0659) 		0.0587
(0.499) 		0.0307
(0.352) 		0.036
(0.387) 		0.347
(0.893) 		0.194
(0.731) 		0.533
(1.00) 		1
(1.00)
QKI 6 (1%) 789 0.00714
(0.145) 		0.279
(0.844) 		0.0226
(0.302) 		0.697
(1.00) 		0.672
(1.00) 		0.278
(0.844) 		0.144
(0.678) 		1
(1.00) 		1
(1.00)
GRHL3 8 (1%) 787 0.363
(0.902) 		0.708
(1.00) 		0.462
(0.955) 		0.000859
(0.0264) 		0.382
(0.92) 		0.412
(0.942) 		0.426
(0.947) 		1
(1.00)
TNFRSF9 4 (1%) 791 0.81
(1.00) 		0.181
(0.715) 		1
(1.00) 		0.313
(0.872) 		1
(1.00) 		0.00962
(0.183) 		0.921
(1.00) 		0.242
(0.801) 		1
(1.00)
PASD1 8 (1%) 787 0.617
(1.00) 		0.893
(1.00) 		0.462
(0.955) 		0.0107
(0.187) 		0.683
(1.00) 		0.781
(1.00) 		0.389
(0.92) 		1
(1.00) 		1
(1.00)
GABRA6 15 (2%) 780 0.112
(0.615) 		0.0229
(0.302) 		0.00414
(0.0979) 		0.793
(1.00) 		0.117
(0.624) 		0.0283
(0.341) 		0.0417
(0.422) 		1
(1.00) 		1
(1.00)
AK7 8 (1%) 787 0.00746
(0.146) 		0.54
(1.00) 		0.462
(0.955) 		1
(1.00) 		0.446
(0.955) 		0.496
(0.976) 		0.217
(0.786) 		0.423
(0.947) 		0.336
(0.877)
DSP 20 (3%) 775 0.655
(1.00) 		0.00655
(0.134) 		0.0939
(0.583) 		0.495
(0.975) 		0.454
(0.955) 		0.567
(1.00) 		0.324
(0.877) 		0.715
(1.00) 		0.604
(1.00)
PAN3 7 (1%) 788 0.365
(0.902) 		0.263
(0.83) 		0.00906
(0.174) 		1
(1.00) 		1
(1.00) 		0.0599
(0.503) 		0.0841
(0.549) 		1
(1.00) 		1
(1.00)
TCF12 19 (2%) 776 0.24
(0.801) 		0.678
(1.00) 		0.231
(0.801) 		0.643
(1.00) 		1
(1.00) 		0.956
(1.00) 		0.26
(0.829) 		0.733
(1.00) 		0.617
(1.00)
PIK3CA 70 (9%) 725 0.321
(0.877) 		0.196
(0.735) 		0.793
(1.00) 		1
(1.00) 		0.497
(0.977) 		0.379
(0.92) 		0.113
(0.615) 		0.546
(1.00) 		1
(1.00)
STK19 11 (1%) 784 0.223
(0.792) 		0.114
(0.615) 		0.108
(0.609) 		0.216
(0.785) 		0.683
(1.00) 		0.257
(0.828) 		0.0719
(0.541) 		1
(1.00) 		0.0992
(0.592)
ZMIZ1 12 (2%) 783 0.152
(0.698) 		0.235
(0.801) 		0.555
(1.00) 		0.568
(1.00) 		1
(1.00) 		0.359
(0.897) 		0.674
(1.00) 		0.118
(0.624) 		0.0181
(0.265)
GAGE2A 8 (1%) 787 0.136
(0.657) 		0.258
(0.828) 		0.056
(0.491) 		1
(1.00) 		0.683
(1.00) 		0.834
(1.00) 		0.218
(0.786) 		0.0568
(0.491) 		0.336
(0.877)
CREBZF 9 (1%) 786 0.337
(0.878) 		0.321
(0.877) 		0.505
(0.982) 		0.502
(0.978) 		1
(1.00) 		0.8
(1.00) 		0.132
(0.657) 		0.0709
(0.541) 		0.369
(0.902)
SLC26A3 11 (1%) 784 0.451
(0.955) 		0.283
(0.844) 		0.0587
(0.499) 		0.134
(0.657) 		0.063
(0.504) 		0.045
(0.438) 		0.0326
(0.36) 		0.535
(1.00) 		1
(1.00)
SEMG1 11 (1%) 784 0.593
(1.00) 		0.0158
(0.251) 		0.0204
(0.285) 		1
(1.00) 		0.728
(1.00) 		0.89
(1.00) 		0.0613
(0.504) 		0.536
(1.00) 		1
(1.00)
NUP210L 12 (2%) 783 0.946
(1.00) 		0.712
(1.00) 		0.0308
(0.352) 		1
(1.00) 		0.187
(0.718) 		0.742
(1.00) 		0.0156
(0.251) 		0.565
(1.00) 		1
(1.00)
MED9 3 (0%) 792 0.861
(1.00) 		0.411
(0.942) 		0.556
(1.00) 		0.27
(0.835) 		0.556
(1.00) 		0.0324
(0.36) 		1
(1.00) 		1
(1.00)
NKD2 4 (1%) 791 0.367
(0.902) 		0.746
(1.00) 		0.303
(0.864) 		1
(1.00) 		0.092
(0.573) 		0.173
(0.715) 		1
(1.00) 		1
(1.00)
IRS4 11 (1%) 784 0.0567
(0.491) 		0.984
(1.00) 		0.755
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.408
(0.942) 		0.266
(0.833) 		1
(1.00) 		0.0837
(0.549)
MUC17 50 (6%) 745 0.259
(0.829) 		0.0405
(0.415) 		0.221
(0.79) 		0.555
(1.00) 		0.744
(1.00) 		0.824
(1.00) 		0.568
(1.00) 		0.474
(0.965) 		1
(1.00)
RPL5 10 (1%) 785 0.951
(1.00) 		0.0267
(0.331) 		0.0388
(0.412) 		0.334
(0.877) 		0.0637
(0.504) 		0.0756
(0.548) 		0.189
(0.72) 		0.147
(0.687) 		1
(1.00)
KDR 13 (2%) 782 0.489
(0.971) 		0.0542
(0.482) 		0.0741
(0.541) 		1
(1.00) 		0.359
(0.897) 		0.592
(1.00) 		0.129
(0.65) 		1
(1.00) 		1
(1.00)
RBPJ 7 (1%) 788 0.302
(0.864) 		0.625
(1.00) 		0.0562
(0.491) 		1
(1.00) 		0.382
(0.92) 		0.583
(1.00) 		0.0953
(0.584) 		1
(1.00) 		1
(1.00)
NRAS 5 (1%) 790 0.537
(1.00) 		0.834
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.178
(0.715) 		0.544
(1.00) 		0.134
(0.657) 		1
(1.00) 		1
(1.00)
TRERF1 7 (1%) 788 0.118
(0.624) 		0.242
(0.801) 		0.431
(0.947) 		0.023
(0.302) 		0.683
(1.00) 		0.549
(1.00) 		0.18
(0.715) 		1
(1.00) 		1
(1.00)
BCOR 22 (3%) 773 0.456
(0.955) 		0.444
(0.955) 		0.824
(1.00) 		0.273
(0.838) 		1
(1.00) 		0.344
(0.888) 		0.0991
(0.592) 		1
(1.00) 		1
(1.00)
PTPN11 11 (1%) 784 0.276
(0.844) 		0.0904
(0.566) 		1
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.461
(0.955) 		0.572
(1.00) 		0.501
(0.978) 		1
(1.00)
FAM47C 24 (3%) 771 0.0382
(0.409) 		0.697
(1.00) 		0.192
(0.727) 		0.0974
(0.588) 		0.487
(0.971) 		0.234
(0.801) 		0.609
(1.00) 		0.756
(1.00) 		1
(1.00)
DDX5 9 (1%) 786 0.699
(1.00) 		0.194
(0.731) 		0.727
(1.00) 		0.318
(0.873) 		1
(1.00) 		0.152
(0.698) 		0.0222
(0.302) 		1
(1.00) 		0.336
(0.877)
SETD2 13 (2%) 782 0.571
(1.00) 		0.153
(0.7) 		0.559
(1.00) 		0.574
(1.00) 		0.764
(1.00) 		0.221
(0.79) 		0.542
(1.00) 		0.594
(1.00) 		1
(1.00)
ZNF709 5 (1%) 790 0.904
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.0794
(0.549) 		1
(1.00) 		0.352
(0.893) 		0.635
(1.00) 		0.294
(0.855) 		1
(1.00)
FAM126B 8 (1%) 787 0.875
(1.00) 		0.491
(0.971) 		0.462
(0.955) 		1
(1.00) 		1
(1.00) 		0.407
(0.942) 		0.551
(1.00) 		1
(1.00) 		0.301
(0.864)
MYST4 12 (2%) 783 0.042
(0.422) 		0.695
(1.00) 		0.0656
(0.512) 		1
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.113
(0.615) 		0.197
(0.736) 		0.401
(0.942)
TLR6 8 (1%) 787 0.529
(1.00) 		0.148
(0.687) 		0.138
(0.661) 		0.725
(1.00) 		0.063
(0.504) 		0.122
(0.635) 		0.282
(0.844) 		0.1
(0.594) 		1
(1.00)
ACADS 5 (1%) 790 0.304
(0.864) 		0.0259
(0.329) 		0.351
(0.893) 		0.408
(0.942) 		0.332
(0.877) 		0.903
(1.00) 		0.465
(0.959) 		1
(1.00) 		1
(1.00)
TNRC18 12 (2%) 783 0.0759
(0.548) 		0.387
(0.92) 		0.231
(0.801) 		0.137
(0.66) 		0.359
(0.897) 		0.851
(1.00) 		0.385
(0.92) 		0.566
(1.00) 		1
(1.00)
SLC6A3 12 (2%) 783 0.997
(1.00) 		0.922
(1.00) 		0.555
(1.00) 		0.253
(0.817) 		0.332
(0.877) 		0.237
(0.801) 		0.749
(1.00) 		1
(1.00) 		0.369
(0.902)
ZNF292 17 (2%) 778 0.555
(1.00) 		0.128
(0.65) 		0.198
(0.738) 		0.0225
(0.302) 		0.108
(0.609) 		0.845
(1.00) 		0.596
(1.00) 		0.209
(0.771) 		0.561
(1.00)
ARID2 13 (2%) 782 0.118
(0.624) 		0.664
(1.00) 		0.155
(0.704) 		0.782
(1.00) 		0.359
(0.897) 		0.359
(0.897) 		0.257
(0.828) 		0.319
(0.873) 		0.487
(0.971)
KRTAP5-3 4 (1%) 791 0.129
(0.65) 		0.897
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.922
(1.00) 		0.244
(0.801) 		1
(1.00)
SRPX 4 (1%) 791 0.94
(1.00) 		0.382
(0.92) 		0.303
(0.864) 		0.0297
(0.349) 		1
(1.00) 		0.427
(0.947) 		0.157
(0.705) 		0.244
(0.801) 		1
(1.00)
NEU2 9 (1%) 786 0.762
(1.00) 		0.756
(1.00) 		1
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.419
(0.947) 		0.624
(1.00) 		1
(1.00) 		0.336
(0.877)
TMEM216 3 (0%) 792 0.517
(0.999) 		0.485
(0.971) 		0.556
(1.00) 		0.0718
(0.541) 		0.526
(1.00) 		0.18
(0.715) 		1
(1.00) 		1
(1.00)
KTELC1 5 (1%) 790 0.102
(0.596) 		0.53
(1.00) 		0.168
(0.712) 		0.408
(0.942) 		1
(1.00) 		0.24
(0.801) 		1
(1.00) 		1
(1.00)
SOX4 7 (1%) 788 0.0196
(0.282) 		0.768
(1.00) 		0.431
(0.947) 		0.459
(0.955) 		1
(1.00) 		0.628
(1.00) 		1
(1.00) 		0.0429
(0.423)
SERPING1 4 (1%) 791 0.915
(1.00) 		0.0904
(0.566) 		1
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.116
(0.624) 		0.923
(1.00) 		1
(1.00) 		1
(1.00)
RASGRF2 6 (1%) 789 0.119
(0.626) 		0.331
(0.877) 		1
(1.00) 		0.697
(1.00) 		0.185
(0.715) 		0.71
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
FAM83D 6 (1%) 789 0.734
(1.00) 		0.267
(0.833) 		1
(1.00) 		0.697
(1.00) 		0.332
(0.877) 		0.352
(0.893) 		0.702
(1.00) 		0.341
(0.882) 		1
(1.00)
ZNF512B 5 (1%) 790 0.0284
(0.341) 		0.0816
(0.549) 		0.168
(0.712) 		1
(1.00) 		1
(1.00) 		0.38
(0.92) 		1
(1.00) 		0.225
(0.792)
TPX2 7 (1%) 788 0.134
(0.657) 		0.767
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.544
(1.00) 		1
(1.00) 		1
(1.00) 		0.0429
(0.423)
C10ORF76 4 (1%) 791 0.318
(0.873) 		0.486
(0.971) 		1
(1.00) 		1
(1.00) 		0.316
(0.872) 		0.843
(1.00) 		1
(1.00) 		1
(1.00)
TRPV6 13 (2%) 782 0.969
(1.00) 		0.925
(1.00) 		0.239
(0.801) 		0.404
(0.942) 		0.764
(1.00) 		0.422
(0.947) 		0.67
(1.00) 		0.134
(0.657) 		1
(1.00)
ZDHHC4 4 (1%) 791 0.811
(1.00) 		0.336
(0.877) 		0.128
(0.65) 		0.313
(0.872) 		0.556
(1.00) 		0.0826
(0.549) 		0.243
(0.801) 		1
(1.00)
CPEB4 7 (1%) 788 0.0818
(0.549) 		0.48
(0.968) 		0.431
(0.947) 		1
(1.00) 		0.683
(1.00) 		0.388
(0.92) 		0.518
(0.999) 		0.157
(0.705) 		1
(1.00)
EEF1A1 8 (1%) 787 0.406
(0.942) 		0.0394
(0.412) 		0.462
(0.955) 		0.288
(0.846) 		1
(1.00) 		0.112
(0.615) 		0.889
(1.00) 		1
(1.00) 		1
(1.00)
PROKR2 9 (1%) 786 0.0219
(0.301) 		0.0187
(0.271) 		0.0738
(0.541) 		0.742
(1.00) 		0.728
(1.00) 		0.479
(0.968) 		0.272
(0.837) 		1
(1.00) 		1
(1.00)
TMEM184A 3 (0%) 792 0.188
(0.718) 		0.476
(0.967) 		0.556
(1.00) 		1
(1.00) 		1
(1.00) 		0.503
(0.978) 		0.186
(0.718) 		1
(1.00)
G6PC 7 (1%) 788 0.714
(1.00) 		0.752
(1.00) 		0.431
(0.947) 		0.706
(1.00) 		0.445
(0.955) 		0.99
(1.00) 		0.384
(0.92) 		1
(1.00) 		0.0429
(0.423)
CYP11A1 7 (1%) 788 0.162
(0.712) 		0.114
(0.615) 		0.702
(1.00) 		1
(1.00) 		0.683
(1.00) 		0.408
(0.942) 		0.924
(1.00) 		0.385
(0.92) 		0.301
(0.864)
KRT15 8 (1%) 787 0.973
(1.00) 		0.25
(0.81) 		0.719
(1.00) 		0.48
(0.968) 		0.264
(0.831) 		0.905
(1.00) 		0.938
(1.00) 		0.424
(0.947) 		1
(1.00)
CMA1 3 (0%) 792 0.179
(0.715) 		0.916
(1.00) 		1
(1.00) 		1
(1.00) 		0.556
(1.00) 		0.558
(1.00) 		1
(1.00) 		1
(1.00)
MAP3K12 6 (1%) 789 0.0202
(0.285) 		0.868
(1.00) 		0.671
(1.00) 		1
(1.00) 		1
(1.00) 		0.313
(0.872) 		1
(1.00) 		1
(1.00)
TREML2 7 (1%) 788 0.934
(1.00) 		0.127
(0.65) 		0.25
(0.81) 		0.459
(0.955) 		1
(1.00) 		0.0842
(0.549) 		0.199
(0.74) 		0.339
(0.878) 		1
(1.00)
PRCP 5 (1%) 790 0.0168
(0.256) 		0.0414
(0.422) 		0.351
(0.893) 		0.654
(1.00) 		1
(1.00) 		0.37
(0.902) 		0.572
(1.00) 		1
(1.00) 		0.184
(0.715)
ESR2 6 (1%) 789 0.582
(1.00) 		0.3
(0.864) 		0.43
(0.947) 		1
(1.00) 		1
(1.00) 		0.427
(0.947) 		0.906
(1.00) 		1
(1.00) 		1
(1.00)
POM121 6 (1%) 789 0.675
(1.00) 		0.233
(0.801) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.781
(1.00) 		0.448
(0.955) 		1
(1.00) 		1
(1.00)
MACC1 8 (1%) 787 0.642
(1.00) 		0.0837
(0.549) 		0.462
(0.955) 		0.0729
(0.541) 		1
(1.00) 		0.908
(1.00) 		0.411
(0.942) 		0.426
(0.947) 		1
(1.00)
AOX1 8 (1%) 787 0.748
(1.00) 		0.623
(1.00) 		0.462
(0.955) 		0.48
(0.968) 		1
(1.00) 		0.109
(0.609) 		0.412
(0.942) 		1
(1.00) 		1
(1.00)
KRAS 4 (1%) 791 0.754
(1.00) 		0.709
(1.00) 		0.616
(1.00) 		1
(1.00) 		1
(1.00) 		0.338
(0.878) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TYRP1 6 (1%) 789 0.411
(0.942) 		0.163
(0.712) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.781
(1.00) 		0.0552
(0.489) 		1
(1.00) 		1
(1.00)
EMG1 5 (1%) 790 0.243
(0.801) 		0.686
(1.00) 		0.168
(0.712) 		0.167
(0.712) 		0.649
(1.00) 		0.0502
(0.47) 		0.243
(0.801) 		1
(1.00) 		1
(1.00)
HEATR3 4 (1%) 791 0.765
(1.00) 		0.134
(0.657) 		0.616
(1.00) 		1
(1.00) 		0.592
(1.00) 		1
(1.00) 		0.243
(0.801) 		1
(1.00)
CDKN2A 6 (1%) 789 0.424
(0.947) 		0.834
(1.00) 		1
(1.00) 		0.409
(0.942) 		0.0791
(0.549) 		0.0331
(0.363) 		1
(1.00) 		0.0606
(0.504) 		0.0217
(0.301)
SLC35A2 3 (0%) 792 0.669
(1.00) 		0.439
(0.955) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.71
(1.00) 		1
(1.00) 		0.142
(0.671)
MYH8 21 (3%) 774 0.139
(0.664) 		0.491
(0.971) 		1
(1.00) 		0.179
(0.715) 		0.454
(0.955) 		0.448
(0.955) 		0.162
(0.712) 		0.511
(0.99) 		0.261
(0.829)
DOCK5 20 (3%) 775 0.936
(1.00) 		0.166
(0.712) 		0.164
(0.712) 		1
(1.00) 		0.018
(0.265) 		0.564
(1.00) 		0.212
(0.775) 		0.729
(1.00) 		0.223
(0.792)
PAK1 3 (0%) 792 0.15
(0.695) 		0.318
(0.873) 		1
(1.00) 		1
(1.00) 		0.556
(1.00) 		0.8
(1.00) 		1
(1.00) 		1
(1.00)
KRT13 6 (1%) 789 0.17
(0.715) 		0.921
(1.00) 		0.43
(0.947) 		0.241
(0.801) 		0.0791
(0.549) 		0.904
(1.00) 		0.335
(0.877) 		1
(1.00) 		1
(1.00)
MYO5A 5 (1%) 790 0.258
(0.828) 		0.715
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.332
(0.877) 		0.887
(1.00) 		1
(1.00) 		1
(1.00)
MORN5 3 (0%) 792 0.541
(1.00) 		0.0607
(0.504) 		1
(1.00) 		1
(1.00) 		0.23
(0.801) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KRT3 4 (1%) 791 0.824
(1.00) 		0.44
(0.955) 		0.303
(0.864) 		0.645
(1.00) 		1
(1.00) 		0.0524
(0.476) 		0.265
(0.833) 		1
(1.00) 		0.184
(0.715)
LGALS13 4 (1%) 791 0.537
(1.00) 		0.449
(0.955) 		1
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.388
(0.92) 		0.316
(0.872) 		0.242
(0.801) 		0.184
(0.715)
CD44 6 (1%) 789 0.301
(0.864) 		0.139
(0.664) 		0.43
(0.947) 		0.241
(0.801) 		0.672
(1.00) 		0.906
(1.00) 		1
(1.00) 		1
(1.00)
CD1D 4 (1%) 791 0.352
(0.893) 		0.0167
(0.256) 		0.0152
(0.251) 		1
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.143
(0.676) 		1
(1.00) 		1
(1.00)
CNOT1 8 (1%) 787 0.0397
(0.413) 		0.0945
(0.584) 		0.272
(0.837) 		0.48
(0.968) 		1
(1.00) 		0.71
(1.00) 		0.334
(0.877) 		1
(1.00) 		1
(1.00)
NAP1L2 6 (1%) 789 0.523
(1.00) 		0.157
(0.705) 		1
(1.00) 		0.697
(1.00) 		1
(1.00) 		0.442
(0.955) 		0.434
(0.951) 		1
(1.00) 		1
(1.00)
OR52M1 8 (1%) 787 0.472
(0.962) 		0.792
(1.00) 		0.462
(0.955) 		1
(1.00) 		0.446
(0.955) 		0.886
(1.00) 		0.242
(0.801) 		0.185
(0.715) 		1
(1.00)
OAS2 4 (1%) 791 0.0311
(0.352) 		0.99
(1.00) 		0.128
(0.65) 		0.645
(1.00) 		0.316
(0.872) 		0.37
(0.902) 		0.468
(0.96) 		1
(1.00) 		1
(1.00)
FMR1 5 (1%) 790 0.0235
(0.304) 		0.0341
(0.372) 		0.168
(0.712) 		1
(1.00) 		1
(1.00) 		0.147
(0.687) 		0.08
(0.549) 		1
(1.00) 		1
(1.00)
INF2 4 (1%) 791 0.68
(1.00) 		0.999
(1.00) 		1
(1.00) 		0.313
(0.872) 		1
(1.00) 		0.588
(1.00) 		0.24
(0.801) 		1
(1.00)
EPS8L1 4 (1%) 791 0.126
(0.65) 		0.436
(0.954) 		0.616
(1.00) 		1
(1.00) 		1
(1.00) 		0.625
(1.00) 		1
(1.00) 		1
(1.00)
CD209 10 (1%) 785 0.174
(0.715) 		0.112
(0.615) 		0.335
(0.877) 		0.334
(0.877) 		0.728
(1.00) 		0.19
(0.723) 		0.873
(1.00) 		1
(1.00) 		0.369
(0.902)
PRG4 10 (1%) 785 0.326
(0.877) 		0.467
(0.96) 		0.507
(0.985) 		1
(1.00) 		1
(1.00) 		0.22
(0.79) 		0.158
(0.705) 		0.501
(0.978) 		0.401
(0.942)
RFX4 6 (1%) 789 0.367
(0.902) 		0.345
(0.89) 		1
(1.00) 		0.697
(1.00) 		0.672
(1.00) 		0.129
(0.65) 		0.763
(1.00) 		1
(1.00) 		1
(1.00)
LUM 7 (1%) 788 0.889
(1.00) 		0.838
(1.00) 		0.103
(0.596) 		1
(1.00) 		0.672
(1.00) 		0.974
(1.00) 		0.0773
(0.549) 		0.383
(0.92) 		1
(1.00)
MYT1 6 (1%) 789 0.0577
(0.496) 		0.0648
(0.508) 		0.0957
(0.584) 		0.697
(1.00) 		0.185
(0.715) 		0.305
(0.865) 		0.0622
(0.504) 		1
(1.00) 		1
(1.00)
KCNJ15 4 (1%) 791 0.554
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.592
(1.00) 		0.922
(1.00) 		0.244
(0.801) 		1
(1.00)
GFRA4 3 (0%) 792 0.0789
(0.549) 		0.476
(0.967) 		0.285
(0.844) 		0.27
(0.835) 		0.556
(1.00) 		0.388
(0.92) 		0.882
(1.00) 		1
(1.00) 		1
(1.00)
DLC1 9 (1%) 786 0.456
(0.955) 		0.971
(1.00) 		1
(1.00) 		0.175
(0.715) 		0.0637
(0.504) 		0.659
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.369
(0.902)
TMPRSS6 9 (1%) 786 0.918
(1.00) 		0.052
(0.476) 		0.0738
(0.541) 		0.502
(0.978) 		0.287
(0.844) 		1
(1.00) 		0.169
(0.712) 		1
(1.00) 		1
(1.00)
DLX6 5 (1%) 790 0.289
(0.847) 		0.58
(1.00) 		0.662
(1.00) 		0.408
(0.942) 		1
(1.00) 		0.512
(0.992) 		1
(1.00) 		1
(1.00)
MAP3K1 9 (1%) 786 0.84
(1.00) 		0.0402
(0.415) 		0.0738
(0.541) 		0.742
(1.00) 		0.287
(0.844) 		0.165
(0.712) 		0.275
(0.843) 		1
(1.00) 		1
(1.00)
ROBO3 5 (1%) 790 0.15
(0.693) 		0.185
(0.715) 		0.168
(0.712) 		0.654
(1.00) 		0.592
(1.00) 		0.856
(1.00) 		0.169
(0.712) 		1
(1.00) 		0.225
(0.792)
SGOL2 9 (1%) 786 0.268
(0.834) 		0.332
(0.877) 		1
(1.00) 		0.742
(1.00) 		0.471
(0.962) 		0.435
(0.953) 		0.973
(1.00) 		1
(1.00) 		0.301
(0.864)
HTT 5 (1%) 790 0.0282
(0.341) 		0.412
(0.942) 		0.168
(0.712) 		0.654
(1.00) 		0.649
(1.00) 		0.103
(0.596) 		1
(1.00) 		1
(1.00)
SON 9 (1%) 786 0.225
(0.792) 		0.887
(1.00) 		0.171
(0.715) 		1
(1.00) 		0.213
(0.776) 		0.502
(0.978) 		0.314
(0.872) 		1
(1.00) 		0.336
(0.877)
PLXNA3 10 (1%) 785 0.0473
(0.452) 		0.924
(1.00) 		0.109
(0.609) 		0.103
(0.596) 		0.287
(0.844) 		0.96
(1.00) 		0.429
(0.947) 		0.148
(0.687) 		1
(1.00)
AMPD1 7 (1%) 788 0.891
(1.00) 		0.424
(0.947) 		0.702
(1.00) 		0.459
(0.955) 		1
(1.00) 		0.834
(1.00) 		0.86
(1.00) 		1
(1.00) 		1
(1.00)
TNFSF9 5 (1%) 790 0.357
(0.897) 		0.934
(1.00) 		0.351
(0.893) 		0.408
(0.942) 		1
(1.00) 		0.451
(0.955) 		0.573
(1.00) 		1
(1.00) 		0.225
(0.792)
TJAP1 3 (0%) 792 0.267
(0.833) 		0.315
(0.872) 		0.285
(0.844) 		0.574
(1.00) 		1
(1.00) 		0.881
(1.00) 		1
(1.00) 		1
(1.00)
KLKB1 7 (1%) 788 0.218
(0.786) 		0.297
(0.863) 		1
(1.00) 		1
(1.00) 		0.445
(0.955) 		0.278
(0.844) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CHGB 8 (1%) 787 0.168
(0.712) 		0.713
(1.00) 		0.462
(0.955) 		0.725
(1.00) 		0.063
(0.504) 		0.926
(1.00) 		0.745
(1.00) 		1
(1.00) 		1
(1.00)
ALPK3 4 (1%) 791 0.49
(0.971) 		0.357
(0.897) 		0.616
(1.00) 		1
(1.00) 		1
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.184
(0.715)
MYO1B 10 (1%) 785 0.278
(0.844) 		0.181
(0.715) 		0.179
(0.715) 		1
(1.00) 		0.287
(0.844) 		0.388
(0.92) 		0.155
(0.704) 		0.0841
(0.549) 		0.369
(0.902)
SMOC1 4 (1%) 791 0.461
(0.955) 		0.486
(0.971) 		1
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.903
(1.00) 		0.585
(1.00) 		0.0826
(0.549) 		1
(1.00)
ACSM1 7 (1%) 788 0.412
(0.942) 		0.55
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.729
(1.00) 		0.704
(1.00) 		1
(1.00) 		1
(1.00)
CIB1 5 (1%) 790 0.493
(0.973) 		0.935
(1.00) 		0.662
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.974
(1.00) 		0.889
(1.00) 		1
(1.00) 		1
(1.00)
CDA 3 (0%) 792 0.718
(1.00) 		0.491
(0.971) 		0.285
(0.844) 		1
(1.00) 		1
(1.00) 		0.0815
(0.549) 		0.882
(1.00) 		1
(1.00) 		0.142
(0.671)
TTC30B 7 (1%) 788 0.0971
(0.588) 		0.126
(0.65) 		0.431
(0.947) 		1
(1.00) 		1
(1.00) 		0.239
(0.801) 		0.534
(1.00) 		1
(1.00) 		1
(1.00)
AGXT2L1 4 (1%) 791 0.229
(0.801) 		0.89
(1.00) 		1
(1.00) 		1
(1.00) 		0.316
(0.872) 		0.588
(1.00) 		0.082
(0.549) 		1
(1.00)
PRKCD 3 (0%) 792 0.308
(0.872) 		0.832
(1.00) 		0.0434
(0.425) 		1
(1.00) 		1
(1.00) 		0.247
(0.809) 		0.189
(0.72) 		1
(1.00)
ST3GAL6 5 (1%) 790 0.949
(1.00) 		0.354
(0.895) 		1
(1.00) 		0.654
(1.00) 		0.556
(1.00) 		0.176
(0.715) 		0.936
(1.00) 		1
(1.00) 		1
(1.00)
SOX13 5 (1%) 790 0.865
(1.00) 		0.939
(1.00) 		0.351
(0.893) 		0.408
(0.942) 		0.332
(0.877) 		0.442
(0.955) 		0.573
(1.00) 		1
(1.00) 		1
(1.00)
NKX2-2 6 (1%) 789 0.0282
(0.341) 		0.226
(0.792) 		0.0957
(0.584) 		0.241
(0.801) 		0.649
(1.00) 		0.925
(1.00) 		0.198
(0.739) 		1
(1.00) 		1
(1.00)
SYBU 3 (0%) 792 0.639
(1.00) 		0.518
(0.999) 		0.285
(0.844) 		0.0718
(0.541) 		0.23
(0.801) 		0.724
(1.00) 		1
(1.00) 		1
(1.00)
WDR90 9 (1%) 786 0.462
(0.955) 		0.0979
(0.589) 		0.0738
(0.541) 		1
(1.00) 		0.446
(0.955) 		0.0347
(0.376) 		0.127
(0.65) 		1
(1.00) 		1
(1.00)
TP63 10 (1%) 785 0.592
(1.00) 		0.418
(0.947) 		0.179
(0.715) 		1
(1.00) 		0.446
(0.955) 		0.471
(0.962) 		0.546
(1.00) 		1
(1.00) 		0.336
(0.877)
SLC2A3 5 (1%) 790 0.65
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.408
(0.942) 		0.316
(0.872) 		0.388
(0.92) 		0.936
(1.00) 		0.107
(0.609) 		1
(1.00)
EGR1 5 (1%) 790 0.822
(1.00) 		0.289
(0.847) 		0.351
(0.893) 		0.654
(1.00) 		0.649
(1.00) 		0.427
(0.947) 		0.47
(0.961) 		1
(1.00) 		1
(1.00)
PRB3 3 (0%) 792 0.16
(0.71) 		0.975
(1.00) 		1
(1.00) 		0.27
(0.835) 		1
(1.00) 		0.56
(1.00) 		1
(1.00) 		1
(1.00)
FBN3 18 (2%) 777 0.428
(0.947) 		0.0168
(0.256) 		0.0251
(0.322) 		0.0968
(0.588) 		0.604
(1.00) 		0.668
(1.00) 		0.0459
(0.445) 		0.106
(0.607) 		0.561
(1.00)
FLNB 10 (1%) 785 0.212
(0.775) 		0.41
(0.942) 		1
(1.00) 		0.103
(0.596) 		1
(1.00) 		0.593
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00)
SLFN11 7 (1%) 788 0.0833
(0.549) 		0.0521
(0.476) 		0.431
(0.947) 		0.706
(1.00) 		1
(1.00) 		0.965
(1.00) 		0.356
(0.897) 		1
(1.00) 		0.301
(0.864)
SEZ6L2 7 (1%) 788 0.445
(0.955) 		0.459
(0.955) 		0.25
(0.81) 		0.135
(0.657) 		0.185
(0.715) 		0.454
(0.955) 		0.754
(1.00) 		1
(1.00) 		1
(1.00)
MAX 6 (1%) 789 0.742
(1.00) 		0.262
(0.83) 		1
(1.00) 		0.241
(0.801) 		1
(1.00) 		0.491
(0.971) 		0.952
(1.00) 		1
(1.00) 		1
(1.00)
ZNF148 5 (1%) 790 0.0392
(0.412) 		0.203
(0.755) 		0.662
(1.00) 		0.654
(1.00) 		0.178
(0.715) 		0.491
(0.971) 		0.108
(0.609) 		1
(1.00)
PPL 9 (1%) 786 0.0175
(0.261) 		0.614
(1.00) 		1
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.876
(1.00) 		0.628
(1.00) 		1
(1.00) 		0.336
(0.877)
IGFN1 9 (1%) 786 0.181
(0.715) 		0.0799
(0.549) 		0.0738
(0.541) 		0.742
(1.00) 		0.287
(0.844) 		0.572
(1.00) 		0.365
(0.902) 		1
(1.00) 		0.336
(0.877)
GLYAT 5 (1%) 790 0.11
(0.609) 		0.882
(1.00) 		0.662
(1.00) 		0.408
(0.942) 		0.178
(0.715) 		0.693
(1.00) 		0.888
(1.00) 		1
(1.00) 		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 788 343 0.0 - 211.2 (17.4)
IDH1 MUTATED 410 78 0.0 - 182.3 (25.2)
IDH1 WILD-TYPE 378 265 0.1 - 211.2 (12.6)

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 = 3.8e-55 (Wilcoxon-test), Q value = 1.2e-52

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

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
IDH1 MUTATED 413 41.0 (12.4)
IDH1 WILD-TYPE 381 58.4 (14.0)

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

'IDH1 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 1.34e-97 (Fisher's exact test), Q value = 5.2e-95

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
IDH1 MUTATED 14 400
IDH1 WILD-TYPE 266 115

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

'IDH1 MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 2.67e-08 (Fisher's exact test), Q value = 2e-06

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

nPatients NO YES
ALL 232 513
IDH1 MUTATED 157 235
IDH1 WILD-TYPE 75 278

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

'IDH1 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.89e-16 (Wilcoxon-test), Q value = 2.6e-14

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

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
IDH1 MUTATED 251 87.6 (12.1)
IDH1 WILD-TYPE 262 76.9 (17.3)

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

'IDH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

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

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
IDH1 MUTATED 136 1 109 155 0 13
IDH1 WILD-TYPE 58 10 21 36 4 252

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

'TP53 MUTATION STATUS' versus 'Time to Death'

P value = 8.87e-10 (logrank test), Q value = 8e-08

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

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
TP53 MUTATED 329 114 0.0 - 211.2 (22.3)
TP53 WILD-TYPE 459 229 0.1 - 182.3 (15.0)

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 = 9.18e-19 (Wilcoxon-test), Q value = 1.4e-16

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

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
TP53 MUTATED 330 43.6 (15.2)
TP53 WILD-TYPE 464 53.5 (15.0)

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

'TP53 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 5.04e-08 (Fisher's exact test), Q value = 3.5e-06

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
TP53 MUTATED 80 250
TP53 WILD-TYPE 200 265

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

'TP53 MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 0.005 (Fisher's exact test), Q value = 0.11

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

nPatients NO YES
ALL 232 513
TP53 MUTATED 79 231
TP53 WILD-TYPE 153 282

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

'TP53 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00118 (Wilcoxon-test), Q value = 0.034

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

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
TP53 MUTATED 217 84.8 (13.9)
TP53 WILD-TYPE 296 80.1 (16.9)

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

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S12.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
TP53 MUTATED 131 2 74 45 0 78
TP53 WILD-TYPE 63 9 56 146 4 187

Figure S12.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'ATRX MUTATION STATUS' versus 'Time to Death'

P value = 5.77e-15 (logrank test), Q value = 7.4e-13

Table S13.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
ATRX MUTATED 212 55 0.0 - 211.2 (25.6)
ATRX WILD-TYPE 576 288 0.1 - 182.3 (15.2)

Figure S13.  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 = 6.85e-34 (Wilcoxon-test), Q value = 1.8e-31

Table S14.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
ATRX MUTATED 213 38.2 (12.3)
ATRX WILD-TYPE 581 53.4 (15.0)

Figure S14.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'ATRX MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 1.48e-26 (Fisher's exact test), Q value = 3.3e-24

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
ATRX MUTATED 16 197
ATRX WILD-TYPE 264 318

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

'ATRX MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000108 (Wilcoxon-test), Q value = 0.0045

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

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
ATRX MUTATED 133 86.4 (12.7)
ATRX WILD-TYPE 380 80.6 (16.6)

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

'ATRX MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S17.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
ATRX MUTATED 98 1 64 35 0 15
ATRX WILD-TYPE 96 10 66 156 4 250

Figure S17.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'CIC MUTATION STATUS' versus 'Time to Death'

P value = 1.84e-12 (logrank test), Q value = 1.8e-10

Table S18.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
CIC MUTATED 108 13 0.1 - 211.2 (24.4)
CIC WILD-TYPE 680 330 0.0 - 172.8 (16.6)

Figure S18.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CIC MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00112 (Wilcoxon-test), Q value = 0.033

Table S19.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
CIC MUTATED 109 44.7 (13.6)
CIC WILD-TYPE 685 50.1 (16.0)

Figure S19.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'CIC MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 2.84e-21 (Fisher's exact test), Q value = 4.9e-19

Table S20.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
CIC MUTATED 1 108
CIC WILD-TYPE 279 407

Figure S20.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'CIC MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 2.15e-09 (Fisher's exact test), Q value = 1.7e-07

Table S21.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 232 513
CIC MUTATED 60 44
CIC WILD-TYPE 172 469

Figure S21.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'RADIATION_THERAPY'

'CIC MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000469 (Wilcoxon-test), Q value = 0.015

Table S22.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
CIC MUTATED 64 88.3 (11.2)
CIC WILD-TYPE 449 81.2 (16.2)

Figure S22.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'CIC MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S23.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
CIC MUTATED 3 0 23 82 0 1
CIC WILD-TYPE 191 11 107 109 4 264

Figure S23.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'NF1 MUTATION STATUS' versus 'Time to Death'

P value = 1.07e-05 (logrank test), Q value = 5e-04

Table S24.  Gene #5: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
NF1 MUTATED 62 39 0.2 - 211.2 (12.6)
NF1 WILD-TYPE 726 304 0.0 - 182.3 (17.5)

Figure S24.  Get High-res Image Gene #5: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NF1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000558 (Wilcoxon-test), Q value = 0.018

Table S25.  Gene #5: 'NF1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
NF1 MUTATED 62 55.9 (15.2)
NF1 WILD-TYPE 732 48.8 (15.8)

Figure S25.  Get High-res Image Gene #5: 'NF1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PIK3R1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00293 (Wilcoxon-test), Q value = 0.074

Table S26.  Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
PIK3R1 MUTATED 54 55.5 (15.6)
PIK3R1 WILD-TYPE 740 48.9 (15.8)

Figure S26.  Get High-res Image Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PIK3R1 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.000307 (Fisher's exact test), Q value = 0.011

Table S27.  Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
PIK3R1 MUTATED 32 22
PIK3R1 WILD-TYPE 248 493

Figure S27.  Get High-res Image Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'PIK3R1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00448 (Fisher's exact test), Q value = 0.1

Table S28.  Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
PIK3R1 MUTATED 8 1 3 11 0 31
PIK3R1 WILD-TYPE 186 10 127 180 4 234

Figure S28.  Get High-res Image Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'NOTCH1 MUTATION STATUS' versus 'Time to Death'

P value = 0.000471 (logrank test), Q value = 0.015

Table S29.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
NOTCH1 MUTATED 40 8 0.3 - 211.2 (27.9)
NOTCH1 WILD-TYPE 748 335 0.0 - 182.3 (16.9)

Figure S29.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NOTCH1 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 1.1e-08 (Fisher's exact test), Q value = 8.4e-07

Table S30.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
NOTCH1 MUTATED 0 42
NOTCH1 WILD-TYPE 280 473

Figure S30.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'NOTCH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S31.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
NOTCH1 MUTATED 6 0 7 29 0 0
NOTCH1 WILD-TYPE 188 11 123 162 4 265

Figure S31.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'IDH2 MUTATION STATUS' versus 'Time to Death'

P value = 0.00169 (logrank test), Q value = 0.047

Table S32.  Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
IDH2 MUTATED 20 1 0.1 - 84.3 (30.4)
IDH2 WILD-TYPE 768 342 0.0 - 211.2 (17.2)

Figure S32.  Get High-res Image Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'IDH2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000505 (Wilcoxon-test), Q value = 0.016

Table S33.  Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
IDH2 MUTATED 20 37.6 (9.7)
IDH2 WILD-TYPE 774 49.6 (15.8)

Figure S33.  Get High-res Image Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'IDH2 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.000192 (Fisher's exact test), Q value = 0.0072

Table S34.  Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
IDH2 MUTATED 0 20
IDH2 WILD-TYPE 280 495

Figure S34.  Get High-res Image Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'IDH2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0013

Table S35.  Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
IDH2 MUTATED 1 0 5 14 0 0
IDH2 WILD-TYPE 193 11 125 177 4 265

Figure S35.  Get High-res Image Gene #8: 'IDH2 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'RB1 MUTATION STATUS' versus 'Time to Death'

P value = 0.0105 (logrank test), Q value = 0.19

Table S36.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
RB1 MUTATED 30 20 0.2 - 211.2 (14.2)
RB1 WILD-TYPE 758 323 0.0 - 182.3 (17.5)

Figure S36.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'RB1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000292 (Wilcoxon-test), Q value = 0.01

Table S37.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
RB1 MUTATED 30 59.9 (14.2)
RB1 WILD-TYPE 764 48.9 (15.8)

Figure S37.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RB1 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 4.04e-07 (Fisher's exact test), Q value = 2.7e-05

Table S38.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
RB1 MUTATED 24 6
RB1 WILD-TYPE 256 509

Figure S38.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'RB1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S39.  Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
RB1 MUTATED 5 2 0 1 0 22
RB1 WILD-TYPE 189 9 130 190 4 243

Figure S39.  Get High-res Image Gene #11: 'RB1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'FUBP1 MUTATION STATUS' versus 'Time to Death'

P value = 0.000234 (logrank test), Q value = 0.0086

Table S40.  Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
FUBP1 MUTATED 46 6 0.1 - 211.2 (21.8)
FUBP1 WILD-TYPE 742 337 0.0 - 182.3 (17.2)

Figure S40.  Get High-res Image Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'FUBP1 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 1.03e-09 (Fisher's exact test), Q value = 8.8e-08

Table S41.  Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
FUBP1 MUTATED 0 47
FUBP1 WILD-TYPE 280 468

Figure S41.  Get High-res Image Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'FUBP1 MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 0.00374 (Fisher's exact test), Q value = 0.091

Table S42.  Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 232 513
FUBP1 MUTATED 23 21
FUBP1 WILD-TYPE 209 492

Figure S42.  Get High-res Image Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'RADIATION_THERAPY'

'FUBP1 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0102 (Wilcoxon-test), Q value = 0.18

Table S43.  Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
FUBP1 MUTATED 29 89.0 (12.1)
FUBP1 WILD-TYPE 484 81.7 (16.0)

Figure S43.  Get High-res Image Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'FUBP1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S44.  Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
FUBP1 MUTATED 2 0 9 36 0 0
FUBP1 WILD-TYPE 192 11 121 155 4 265

Figure S44.  Get High-res Image Gene #12: 'FUBP1 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'PTEN MUTATION STATUS' versus 'Time to Death'

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

Table S45.  Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
PTEN MUTATED 109 80 0.1 - 211.2 (12.6)
PTEN WILD-TYPE 679 263 0.0 - 182.3 (18.5)

Figure S45.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTEN MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 1.74e-14 (Wilcoxon-test), Q value = 2.1e-12

Table S46.  Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
PTEN MUTATED 110 60.2 (12.9)
PTEN WILD-TYPE 684 47.6 (15.6)

Figure S46.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PTEN MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 4.34e-23 (Fisher's exact test), Q value = 8.4e-21

Table S47.  Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
PTEN MUTATED 86 24
PTEN WILD-TYPE 194 491

Figure S47.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'PTEN MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0017 (Wilcoxon-test), Q value = 0.047

Table S48.  Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
PTEN MUTATED 77 76.9 (18.3)
PTEN WILD-TYPE 436 83.1 (15.2)

Figure S48.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'PTEN MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S49.  Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
PTEN MUTATED 17 1 4 3 2 83
PTEN WILD-TYPE 177 10 126 188 2 182

Figure S49.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'ARID1A MUTATION STATUS' versus 'Time to Death'

P value = 0.00409 (logrank test), Q value = 0.098

Table S50.  Gene #16: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
ARID1A MUTATED 22 4 6.7 - 211.2 (24.0)
ARID1A WILD-TYPE 766 339 0.0 - 182.3 (17.2)

Figure S50.  Get High-res Image Gene #16: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ARID1A MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.0108 (Fisher's exact test), Q value = 0.19

Table S51.  Gene #16: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
ARID1A MUTATED 2 20
ARID1A WILD-TYPE 278 495

Figure S51.  Get High-res Image Gene #16: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'ARID1A MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00538 (Fisher's exact test), Q value = 0.11

Table S52.  Gene #16: 'ARID1A MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
ARID1A MUTATED 4 1 7 9 0 1
ARID1A WILD-TYPE 190 10 123 182 4 264

Figure S52.  Get High-res Image Gene #16: 'ARID1A MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'NIPBL MUTATION STATUS' versus 'Time to Death'

P value = 0.00485 (logrank test), Q value = 0.11

Table S53.  Gene #17: 'NIPBL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
NIPBL MUTATED 20 4 0.2 - 211.2 (22.5)
NIPBL WILD-TYPE 768 339 0.0 - 182.3 (17.2)

Figure S53.  Get High-res Image Gene #17: 'NIPBL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NUDT11 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.0101 (Fisher's exact test), Q value = 0.18

Table S54.  Gene #19: 'NUDT11 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
NUDT11 MUTATED 0 11
NUDT11 WILD-TYPE 280 504

Figure S54.  Get High-res Image Gene #19: 'NUDT11 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'PLCG1 MUTATION STATUS' versus 'Time to Death'

P value = 0.00257 (logrank test), Q value = 0.066

Table S55.  Gene #22: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
PLCG1 MUTATED 11 9 6.7 - 39.0 (14.8)
PLCG1 WILD-TYPE 777 334 0.0 - 211.2 (17.5)

Figure S55.  Get High-res Image Gene #22: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PLCG1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0117 (Wilcoxon-test), Q value = 0.2

Table S56.  Gene #22: 'PLCG1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
PLCG1 MUTATED 11 60.5 (9.6)
PLCG1 WILD-TYPE 783 49.2 (15.8)

Figure S56.  Get High-res Image Gene #22: 'PLCG1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PDGFRA MUTATION STATUS' versus 'Time to Death'

P value = 0.00428 (logrank test), Q value = 0.099

Table S57.  Gene #25: 'PDGFRA MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
PDGFRA MUTATED 20 15 0.5 - 211.2 (9.7)
PDGFRA WILD-TYPE 768 328 0.0 - 182.3 (17.6)

Figure S57.  Get High-res Image Gene #25: 'PDGFRA MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'STAG2 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.00213 (Fisher's exact test), Q value = 0.057

Table S58.  Gene #26: 'STAG2 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
STAG2 MUTATED 12 4
STAG2 WILD-TYPE 268 511

Figure S58.  Get High-res Image Gene #26: 'STAG2 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'REN MUTATION STATUS' versus 'Time to Death'

P value = 0.000159 (logrank test), Q value = 0.0061

Table S59.  Gene #30: 'REN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
REN MUTATED 7 6 1.0 - 34.5 (8.0)
REN WILD-TYPE 781 337 0.0 - 211.2 (17.5)

Figure S59.  Get High-res Image Gene #30: 'REN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'HTRA2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00731 (Wilcoxon-test), Q value = 0.15

Table S60.  Gene #32: 'HTRA2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
HTRA2 MUTATED 5 31.2 (9.7)
HTRA2 WILD-TYPE 789 49.5 (15.8)

Figure S60.  Get High-res Image Gene #32: 'HTRA2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'BRAF MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00312 (Fisher's exact test), Q value = 0.077

Table S61.  Gene #34: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
BRAF MUTATED 5 2 0 0 0 4
BRAF WILD-TYPE 189 9 130 191 4 261

Figure S61.  Get High-res Image Gene #34: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'MX2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0145 (Wilcoxon-test), Q value = 0.24

Table S62.  Gene #41: 'MX2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
MX2 MUTATED 9 62.4 (11.9)
MX2 WILD-TYPE 785 49.2 (15.8)

Figure S62.  Get High-res Image Gene #41: 'MX2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'EGFR MUTATION STATUS' versus 'Time to Death'

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

Table S63.  Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
EGFR MUTATED 108 80 0.2 - 211.2 (13.6)
EGFR WILD-TYPE 680 263 0.0 - 182.3 (18.6)

Figure S63.  Get High-res Image Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'EGFR MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 1.9e-14 (Wilcoxon-test), Q value = 2.1e-12

Table S64.  Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
EGFR MUTATED 108 59.7 (10.9)
EGFR WILD-TYPE 686 47.7 (15.9)

Figure S64.  Get High-res Image Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'EGFR MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 2.5e-13 (Fisher's exact test), Q value = 2.6e-11

Table S65.  Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
EGFR MUTATED 73 35
EGFR WILD-TYPE 207 480

Figure S65.  Get High-res Image Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'EGFR MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 0.0017 (Fisher's exact test), Q value = 0.047

Table S66.  Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 232 513
EGFR MUTATED 18 83
EGFR WILD-TYPE 214 430

Figure S66.  Get High-res Image Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'RADIATION_THERAPY'

'EGFR MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.1e-05 (Wilcoxon-test), Q value = 0.00095

Table S67.  Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
EGFR MUTATED 76 75.5 (16.8)
EGFR WILD-TYPE 437 83.3 (15.4)

Figure S67.  Get High-res Image Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'EGFR MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S68.  Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
EGFR MUTATED 20 1 7 8 0 72
EGFR WILD-TYPE 174 10 123 183 4 193

Figure S68.  Get High-res Image Gene #49: 'EGFR MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'WRN MUTATION STATUS' versus 'ETHNICITY'

P value = 0.00202 (Fisher's exact test), Q value = 0.055

Table S69.  Gene #57: 'WRN MUTATION STATUS' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 35 671
WRN MUTATED 3 3
WRN WILD-TYPE 32 668

Figure S69.  Get High-res Image Gene #57: 'WRN MUTATION STATUS' versus Clinical Feature #9: 'ETHNICITY'

'ZNF41 MUTATION STATUS' versus 'GENDER'

P value = 0.0107 (Fisher's exact test), Q value = 0.19

Table S70.  Gene #61: 'ZNF41 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 331 464
ZNF41 MUTATED 7 1
ZNF41 WILD-TYPE 324 463

Figure S70.  Get High-res Image Gene #61: 'ZNF41 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

'ATF7IP2 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00992 (Wilcoxon-test), Q value = 0.18

Table S71.  Gene #67: 'ATF7IP2 MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
ATF7IP2 MUTATED 7 70.0 (10.0)
ATF7IP2 WILD-TYPE 506 82.3 (15.9)

Figure S71.  Get High-res Image Gene #67: 'ATF7IP2 MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'ZBTB20 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.00113 (Fisher's exact test), Q value = 0.033

Table S72.  Gene #69: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
ZBTB20 MUTATED 1 21
ZBTB20 WILD-TYPE 279 494

Figure S72.  Get High-res Image Gene #69: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'ZBTB20 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00747 (Fisher's exact test), Q value = 0.15

Table S73.  Gene #69: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
ZBTB20 MUTATED 5 0 4 12 0 1
ZBTB20 WILD-TYPE 189 11 126 179 4 264

Figure S73.  Get High-res Image Gene #69: 'ZBTB20 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'PDHA1 MUTATION STATUS' versus 'GENDER'

P value = 0.00507 (Fisher's exact test), Q value = 0.11

Table S74.  Gene #72: 'PDHA1 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 331 464
PDHA1 MUTATED 6 0
PDHA1 WILD-TYPE 325 464

Figure S74.  Get High-res Image Gene #72: 'PDHA1 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

'FAM123C MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00254 (Wilcoxon-test), Q value = 0.066

Table S75.  Gene #74: 'FAM123C MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
FAM123C MUTATED 11 63.2 (13.2)
FAM123C WILD-TYPE 783 49.2 (15.8)

Figure S75.  Get High-res Image Gene #74: 'FAM123C MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'DNMT3A MUTATION STATUS' versus 'Time to Death'

P value = 0.00429 (logrank test), Q value = 0.099

Table S76.  Gene #78: 'DNMT3A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
DNMT3A MUTATED 11 0 13.3 - 211.2 (20.2)
DNMT3A WILD-TYPE 777 343 0.0 - 182.3 (17.3)

Figure S76.  Get High-res Image Gene #78: 'DNMT3A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DNMT3A MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.0101 (Fisher's exact test), Q value = 0.18

Table S77.  Gene #78: 'DNMT3A MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
DNMT3A MUTATED 0 11
DNMT3A WILD-TYPE 280 504

Figure S77.  Get High-res Image Gene #78: 'DNMT3A MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'QKI MUTATION STATUS' versus 'Time to Death'

P value = 0.00714 (logrank test), Q value = 0.14

Table S78.  Gene #90: 'QKI MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
QKI MUTATED 6 6 10.4 - 36.8 (15.8)
QKI WILD-TYPE 782 337 0.0 - 211.2 (17.4)

Figure S78.  Get High-res Image Gene #90: 'QKI MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SMARCA4 MUTATION STATUS' versus 'Time to Death'

P value = 0.000115 (logrank test), Q value = 0.0047

Table S79.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
SMARCA4 MUTATED 27 2 0.2 - 211.2 (28.1)
SMARCA4 WILD-TYPE 761 341 0.0 - 182.3 (17.0)

Figure S79.  Get High-res Image Gene #99: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SMARCA4 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.000137 (Fisher's exact test), Q value = 0.0054

Table S80.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
SMARCA4 MUTATED 1 26
SMARCA4 WILD-TYPE 279 489

Figure S80.  Get High-res Image Gene #99: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'SMARCA4 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00603 (Fisher's exact test), Q value = 0.13

Table S81.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 11 130 191 4 265
SMARCA4 MUTATED 11 0 5 10 0 1
SMARCA4 WILD-TYPE 183 11 125 181 4 264

Figure S81.  Get High-res Image Gene #99: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'GRHL3 MUTATION STATUS' versus 'GENDER'

P value = 0.000859 (Fisher's exact test), Q value = 0.026

Table S82.  Gene #108: 'GRHL3 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 331 464
GRHL3 MUTATED 8 0
GRHL3 WILD-TYPE 323 464

Figure S82.  Get High-res Image Gene #108: 'GRHL3 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

'TNFRSF9 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00962 (Wilcoxon-test), Q value = 0.18

Table S83.  Gene #118: 'TNFRSF9 MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 513 82.1 (15.9)
TNFRSF9 MUTATED 3 56.7 (5.8)
TNFRSF9 WILD-TYPE 510 82.3 (15.8)

Figure S83.  Get High-res Image Gene #118: 'TNFRSF9 MUTATION STATUS' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'PASD1 MUTATION STATUS' versus 'GENDER'

P value = 0.0107 (Fisher's exact test), Q value = 0.19

Table S84.  Gene #134: 'PASD1 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 331 464
PASD1 MUTATED 7 1
PASD1 WILD-TYPE 324 463

Figure S84.  Get High-res Image Gene #134: 'PASD1 MUTATION STATUS' versus Clinical Feature #4: 'GENDER'

'IL4R MUTATION STATUS' versus 'Time to Death'

P value = 6.81e-05 (logrank test), Q value = 0.0029

Table S85.  Gene #137: 'IL4R MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
IL4R MUTATED 10 8 1.4 - 24.2 (9.5)
IL4R WILD-TYPE 778 335 0.0 - 211.2 (17.5)

Figure S85.  Get High-res Image Gene #137: 'IL4R MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'IL4R MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000403 (Wilcoxon-test), Q value = 0.014

Table S86.  Gene #137: 'IL4R MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
IL4R MUTATED 10 67.5 (10.3)
IL4R WILD-TYPE 784 49.1 (15.8)

Figure S86.  Get High-res Image Gene #137: 'IL4R MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'IL4R MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.0048 (Fisher's exact test), Q value = 0.11

Table S87.  Gene #137: 'IL4R MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
IL4R MUTATED 8 2
IL4R WILD-TYPE 272 513

Figure S87.  Get High-res Image Gene #137: 'IL4R MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'GABRA6 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.00414 (Fisher's exact test), Q value = 0.098

Table S88.  Gene #141: 'GABRA6 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
GABRA6 MUTATED 11 4
GABRA6 WILD-TYPE 269 511

Figure S88.  Get High-res Image Gene #141: 'GABRA6 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'AK7 MUTATION STATUS' versus 'Time to Death'

P value = 0.00746 (logrank test), Q value = 0.15

Table S89.  Gene #157: 'AK7 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 788 343 0.0 - 211.2 (17.4)
AK7 MUTATED 8 6 2.5 - 42.7 (9.7)
AK7 WILD-TYPE 780 337 0.0 - 211.2 (17.5)

Figure S89.  Get High-res Image Gene #157: 'AK7 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DSP MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00655 (Wilcoxon-test), Q value = 0.13

Table S90.  Gene #159: 'DSP MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 794 49.3 (15.8)
DSP MUTATED 20 58.5 (13.7)
DSP WILD-TYPE 774 49.1 (15.8)

Figure S90.  Get High-res Image Gene #159: 'DSP MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PAN3 MUTATION STATUS' versus 'TUMOR_TISSUE_SITE'

P value = 0.00906 (Fisher's exact test), Q value = 0.17

Table S91.  Gene #168: 'PAN3 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 280 515
PAN3 MUTATED 6 1
PAN3 WILD-TYPE 274 514

Figure S91.  Get High-res Image Gene #168: 'PAN3 MUTATION STATUS' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

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/22818077/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBMLGG-TP/22506567/GBMLGG-TP.merged_data.txt

  • Number of patients = 795

  • Number of significantly mutated genes = 171

  • 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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