Correlation between gene mutation status and selected clinical features
Overview
Introduction

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

Summary

Testing the association between mutation status of 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.

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)
Made with Nozzle