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 73 genes and 13 clinical features across 668 patients, 42 significant findings detected with Q value < 0.25.

  • TP53 mutation correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • PBRM1 mutation correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • BAP1 mutation correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • SETD2 mutation correlated to 'Time to Death'.

  • KDM5C mutation correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • NEFH mutation correlated to 'HISTOLOGICAL_TYPE'.

  • VHL mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • NF2 mutation correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.

  • HNRNPM mutation correlated to 'HISTOLOGICAL_TYPE'.

  • MET mutation correlated to 'HISTOLOGICAL_TYPE'.

  • MUC5B mutation correlated to 'HISTOLOGICAL_TYPE'.

  • KDM6A mutation correlated to 'RACE'.

  • TDG mutation correlated to 'HISTOLOGICAL_TYPE'.

  • NFE2L2 mutation correlated to 'YEARS_TO_BIRTH'.

  • ATM mutation correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.

  • ZNF814 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • CSGALNACT2 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • ZNF598 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • SKI mutation correlated to 'HISTOLOGICAL_TYPE'.

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

  • AHNAK2 mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • STAM mutation correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.

  • RTL1 mutation correlated to 'Time to Death' and 'NEOPLASM_DISEASESTAGE'.

  • IDUA mutation correlated to 'HISTOLOGICAL_TYPE'.

  • GFM1 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • FAT1 mutation correlated to 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 73 genes and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 42 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
BAP1 49 (7%) 619 8.61e-05
(0.00681) 		0.649
(1.00) 		3e-05
(0.00316) 		8e-05
(0.00681) 		0.776
(1.00) 		0.00436
(0.129) 		0.0124
(0.262) 		0.0002
(0.0146) 		0.668
(1.00) 		0.735
(1.00)
TP53 38 (6%) 630 0.369
(1.00) 		0.202
(1.00) 		0.00318
(0.103) 		0.00325
(0.103) 		0.0911
(0.9) 		0.569
(1.00) 		0.486
(1.00) 		0.28
(1.00) 		1e-05
(0.00158) 		0.386
(1.00) 		0.974
(1.00) 		0.23
(1.00) 		1
(1.00)
PBRM1 146 (22%) 522 0.29
(1.00) 		0.00663
(0.18) 		0.764
(1.00) 		0.37
(1.00) 		0.0222
(0.376) 		0.491
(1.00) 		0.622
(1.00) 		0.981
(1.00) 		1e-05
(0.00158) 		0.00695
(0.183) 		0.267
(1.00)
KDM5C 30 (4%) 638 0.0162
(0.301) 		0.00965
(0.235) 		0.831
(1.00) 		0.816
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.00286
(0.101) 		0.0129
(0.266) 		0.868
(1.00) 		0.385
(1.00)
VHL 174 (26%) 494 0.118
(0.904) 		0.182
(1.00) 		0.358
(1.00) 		0.264
(1.00) 		0.0689
(0.777) 		0.695
(1.00) 		0.353
(1.00) 		0.795
(1.00) 		1e-05
(0.00158) 		1e-05
(0.00158) 		0.681
(1.00)
NF2 16 (2%) 652 0.109
(0.904) 		0.228
(1.00) 		0.03
(0.474) 		0.118
(0.904) 		4e-05
(0.0038) 		0.0411
(0.571) 		0.794
(1.00) 		0.00254
(0.0927) 		0.0567
(0.681) 		0.217
(1.00)
ATM 16 (2%) 652 0.962
(1.00) 		0.101
(0.9) 		0.0103
(0.246) 		0.00141
(0.0669) 		0.449
(1.00) 		0.435
(1.00) 		0.432
(1.00) 		0.122
(0.904) 		0.562
(1.00) 		0.507
(1.00)
EGFR 7 (1%) 661 0.00499
(0.139) 		0.705
(1.00) 		0.0123
(0.262) 		0.0034
(0.104) 		0.44
(1.00) 		0.263
(1.00) 		0.432
(1.00) 		0.26
(1.00) 		1
(1.00) 		1
(1.00)
AHNAK2 33 (5%) 635 0.773
(1.00) 		0.235
(1.00) 		0.171
(1.00) 		0.12
(0.904) 		0.122
(0.904) 		0.563
(1.00) 		0.574
(1.00) 		0.857
(1.00) 		0.00161
(0.0701) 		0.654
(1.00) 		0.145
(0.983) 		0.00455
(0.131) 		0.654
(1.00)
STAM 6 (1%) 662 0.714
(1.00) 		0.44
(1.00) 		0.00049
(0.0291) 		0.00168
(0.0701) 		0.047
(0.602) 		0.0997
(0.9) 		0.67
(1.00) 		0.0743
(0.811) 		1
(1.00) 		0.039
(0.57)
RTL1 7 (1%) 661 0.00825
(0.212) 		0.609
(1.00) 		0.0109
(0.25) 		0.0811
(0.855) 		1
(1.00) 		0.151
(0.989) 		0.102
(0.9) 		0.158
(1.00) 		1
(1.00) 		1
(1.00)
SETD2 58 (9%) 610 0.00934
(0.233) 		0.0309
(0.48) 		0.0552
(0.68) 		0.066
(0.763) 		0.421
(1.00) 		0.216
(1.00) 		0.312
(1.00) 		0.628
(1.00) 		0.0684
(0.777) 		0.939
(1.00) 		0.501
(1.00)
NEFH 15 (2%) 653 0.508
(1.00) 		0.419
(1.00) 		0.274
(1.00) 		0.239
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.28
(1.00) 		0.00141
(0.0669) 		0.52
(1.00) 		0.106
(0.904) 		1
(1.00)
HNRNPM 12 (2%) 656 0.322
(1.00) 		0.465
(1.00) 		0.443
(1.00) 		0.0601
(0.704) 		0.351
(1.00) 		0.601
(1.00) 		0.76
(1.00) 		0.836
(1.00) 		2e-05
(0.00237) 		0.217
(1.00) 		1
(1.00)
MET 19 (3%) 649 0.782
(1.00) 		0.845
(1.00) 		0.458
(1.00) 		0.926
(1.00) 		0.102
(0.9) 		1
(1.00) 		1
(1.00) 		1e-05
(0.00158) 		0.35
(1.00) 		0.77
(1.00) 		0.145
(0.983) 		1
(1.00)
MUC5B 30 (4%) 638 0.457
(1.00) 		0.688
(1.00) 		0.478
(1.00) 		0.58
(1.00) 		0.115
(0.904) 		0.51
(1.00) 		0.844
(1.00) 		0.44
(1.00) 		1e-05
(0.00158) 		0.989
(1.00) 		0.784
(1.00) 		0.386
(1.00) 		1
(1.00)
KDM6A 11 (2%) 657 0.578
(1.00) 		0.0559
(0.68) 		0.371
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.0158
(0.301) 		0.00036
(0.0244) 		1
(1.00)
TDG 5 (1%) 663 0.237
(1.00) 		0.459
(1.00) 		1
(1.00) 		0.116
(0.904) 		0.351
(1.00) 		1
(1.00) 		0.665
(1.00) 		0.0017
(0.0701) 		0.477
(1.00) 		1
(1.00)
NFE2L2 10 (1%) 658 0.897
(1.00) 		0.0111
(0.25) 		0.764
(1.00) 		0.781
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.462
(1.00) 		0.408
(1.00) 		1
(1.00)
ZNF814 13 (2%) 655 0.211
(1.00) 		0.242
(1.00) 		0.147
(0.986) 		0.264
(1.00) 		0.438
(1.00) 		1
(1.00) 		0.0421
(0.571) 		0.00045
(0.0285) 		0.339
(1.00) 		1
(1.00)
CSGALNACT2 8 (1%) 660 0.103
(0.9) 		0.486
(1.00) 		0.751
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.601
(1.00) 		0.456
(1.00) 		0.00297
(0.101) 		0.133
(0.951) 		1
(1.00)
ZNF598 11 (2%) 657 0.741
(1.00) 		0.479
(1.00) 		0.603
(1.00) 		0.867
(1.00) 		0.0204
(0.352) 		0.0997
(0.9) 		0.347
(1.00) 		0.361
(1.00) 		2e-05
(0.00237) 		0.217
(1.00) 		0.507
(1.00)
SKI 9 (1%) 659 0.579
(1.00) 		0.743
(1.00) 		0.63
(1.00) 		0.697
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.726
(1.00) 		0.00187
(0.071) 		0.769
(1.00) 		0.268
(1.00) 		1
(1.00)
IDUA 5 (1%) 663 0.691
(1.00) 		0.213
(1.00) 		0.841
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.665
(1.00) 		0.00184
(0.071) 		0.173
(1.00) 		1
(1.00)
GFM1 3 (0%) 665 0.706
(1.00) 		0.0295
(0.474) 		0.689
(1.00) 		0.742
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.00082
(0.0458) 		1
(1.00) 		1
(1.00)
FAT1 22 (3%) 646 0.552
(1.00) 		0.231
(1.00) 		0.264
(1.00) 		0.294
(1.00) 		0.295
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.00138
(0.0669) 		0.897
(1.00) 		0.0917
(0.9) 		0.624
(1.00)
PTEN 28 (4%) 640 0.651
(1.00) 		0.665
(1.00) 		0.274
(1.00) 		0.475
(1.00) 		0.166
(1.00) 		0.23
(1.00) 		0.685
(1.00) 		0.28
(1.00) 		0.12
(0.904) 		1
(1.00) 		0.841
(1.00) 		0.549
(1.00) 		1
(1.00)
DNMT3A 10 (1%) 658 0.129
(0.93) 		0.956
(1.00) 		0.329
(1.00) 		0.351
(1.00) 		0.513
(1.00) 		0.601
(1.00) 		0.323
(1.00) 		0.463
(1.00) 		0.408
(1.00) 		0.431
(1.00)
CDK12 9 (1%) 659 0.912
(1.00) 		0.0421
(0.571) 		0.681
(1.00) 		0.696
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.501
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 14 (2%) 654 0.83
(1.00) 		0.493
(1.00) 		0.589
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.412
(1.00) 		0.0875
(0.9) 		0.392
(1.00) 		0.536
(1.00) 		0.573
(1.00)
KIAA1751 8 (1%) 660 0.967
(1.00) 		0.101
(0.9) 		0.611
(1.00) 		0.81
(1.00) 		0.514
(1.00) 		0.601
(1.00) 		0.722
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.645
(1.00) 		1
(1.00)
MTOR 32 (5%) 636 0.0725
(0.8) 		0.0415
(0.571) 		0.326
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.174
(1.00) 		0.0118
(0.261) 		0.0136
(0.276) 		0.0198
(0.352) 		0.773
(1.00) 		0.711
(1.00)
RIMBP3 5 (1%) 663 0.332
(1.00) 		0.308
(1.00) 		0.628
(1.00) 		0.0896
(0.9) 		1
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.0802
(0.855) 		1
(1.00) 		1
(1.00)
GPR50 5 (1%) 663 0.454
(1.00) 		0.311
(1.00) 		0.764
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.604
(1.00) 		0.474
(1.00) 		1
(1.00)
CCDC120 4 (1%) 664 0.19
(1.00) 		0.751
(1.00) 		0.114
(0.904) 		0.149
(0.986) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.19
(1.00)
SLC6A14 5 (1%) 663 0.728
(1.00) 		0.599
(1.00) 		0.218
(1.00) 		0.172
(1.00) 		0.093
(0.9) 		1
(1.00) 		0.345
(1.00) 		0.247
(1.00) 		1
(1.00) 		1
(1.00)
CYP4F11 5 (1%) 663 0.828
(1.00) 		0.495
(1.00) 		0.141
(0.983) 		0.0453
(0.598) 		0.513
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.342
(1.00) 		1
(1.00) 		1
(1.00)
STAG2 14 (2%) 654 0.962
(1.00) 		0.0145
(0.282) 		0.161
(1.00) 		0.0918
(0.9) 		1
(1.00) 		0.662
(1.00) 		0.256
(1.00) 		0.165
(1.00) 		0.495
(1.00) 		1
(1.00)
ARID1A 19 (3%) 649 0.749
(1.00) 		0.776
(1.00) 		0.351
(1.00) 		0.67
(1.00) 		0.108
(0.904) 		0.713
(1.00) 		0.47
(1.00) 		0.587
(1.00) 		0.113
(0.904) 		0.0143
(0.282) 		0.243
(1.00)
DPCR1 8 (1%) 660 0.607
(1.00) 		0.226
(1.00) 		0.203
(1.00) 		0.674
(1.00) 		0.0407
(0.571) 		0.722
(1.00) 		0.74
(1.00) 		0.647
(1.00) 		1
(1.00)
GUSB 4 (1%) 664 0.593
(1.00) 		0.0578
(0.686) 		0.223
(1.00) 		0.332
(1.00) 		1
(1.00) 		1
(1.00) 		0.721
(1.00) 		1
(1.00) 		1
(1.00)
MED16 4 (1%) 664 0.035
(0.519) 		0.828
(1.00) 		0.41
(1.00) 		0.328
(1.00) 		0.0913
(0.9) 		1
(1.00) 		0.61
(1.00) 		0.0958
(0.9) 		1
(1.00) 		1
(1.00)
PTCH1 8 (1%) 660 0.0464
(0.602) 		0.295
(1.00) 		0.259
(1.00) 		0.077
(0.83) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.63
(1.00) 		0.642
(1.00) 		1
(1.00)
RLIM 9 (1%) 659 0.595
(1.00) 		0.129
(0.93) 		0.73
(1.00) 		0.764
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.249
(1.00) 		0.676
(1.00) 		1
(1.00)
SLC23A1 7 (1%) 661 0.342
(1.00) 		0.308
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.206
(1.00) 		0.239
(1.00) 		1
(1.00) 		0.269
(1.00) 		1
(1.00)
RHEB 4 (1%) 664 0.835
(1.00) 		0.297
(1.00) 		0.877
(1.00) 		0.827
(1.00) 		0.371
(1.00) 		0.119
(0.904) 		1
(1.00) 		0.403
(1.00) 		1
(1.00)
SLC4A8 6 (1%) 662 0.48
(1.00) 		0.382
(1.00) 		0.556
(1.00) 		0.665
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.103
(0.9) 		1
(1.00) 		1
(1.00)
RUFY3 7 (1%) 661 0.647
(1.00) 		0.564
(1.00) 		0.947
(1.00) 		0.888
(1.00) 		1
(1.00) 		0.539
(1.00) 		0.432
(1.00) 		0.312
(1.00) 		0.595
(1.00) 		0.345
(1.00)
PCK1 6 (1%) 662 0.196
(1.00) 		0.426
(1.00) 		0.265
(1.00) 		0.148
(0.986) 		1
(1.00) 		0.601
(1.00) 		1
(1.00) 		1
(1.00) 		0.535
(1.00) 		1
(1.00)
TXNIP 8 (1%) 660 0.472
(1.00) 		0.61
(1.00) 		0.143
(0.983) 		0.3
(1.00) 		0.0201
(0.352) 		0.32
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.345
(1.00)
RNF128 5 (1%) 663 0.595
(1.00) 		0.913
(1.00) 		0.469
(1.00) 		0.143
(0.983) 		1
(1.00) 		0.665
(1.00) 		0.171
(1.00) 		0.174
(1.00) 		0.245
(1.00)
ZFYVE26 9 (1%) 659 0.485
(1.00) 		0.269
(1.00) 		0.678
(1.00) 		0.698
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.879
(1.00) 		1
(1.00) 		1
(1.00)
FAM160B2 4 (1%) 664 0.223
(1.00) 		0.746
(1.00) 		0.313
(1.00) 		0.658
(1.00) 		0.371
(1.00) 		0.61
(1.00) 		0.384
(1.00) 		1
(1.00) 		1
(1.00)
FAM47A 6 (1%) 662 0.023
(0.376) 		0.349
(1.00) 		0.599
(1.00) 		0.569
(1.00) 		0.461
(1.00) 		0.0198
(0.352) 		0.655
(1.00) 		1
(1.00) 		1
(1.00)
ATP1A1 10 (1%) 658 0.232
(1.00) 		0.365
(1.00) 		0.292
(1.00) 		0.779
(1.00) 		0.0921
(0.9) 		0.507
(1.00) 		0.464
(1.00) 		0.406
(1.00) 		1
(1.00)
SH3BP2 4 (1%) 664 0.533
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.0958
(0.9) 		0.404
(1.00) 		1
(1.00)
FAM200A 5 (1%) 663 0.67
(1.00) 		0.603
(1.00) 		0.84
(1.00) 		0.604
(1.00) 		1
(1.00) 		1
(1.00) 		0.0495
(0.626) 		0.465
(1.00) 		1
(1.00) 		1
(1.00)
NASP 4 (1%) 664 0.106
(0.904) 		0.343
(1.00) 		0.22
(1.00) 		0.33
(1.00) 		1
(1.00) 		0.119
(0.904) 		0.0347
(0.519) 		1
(1.00) 		0.245
(1.00)
RPL7A 3 (0%) 665 0.753
(1.00) 		0.2
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.143
(0.983) 		0.555
(1.00) 		0.0227
(0.376) 		0.319
(1.00) 		1
(1.00)
UIMC1 5 (1%) 663 0.0555
(0.68) 		0.532
(1.00) 		0.295
(1.00) 		0.0448
(0.598) 		1
(1.00) 		0.539
(1.00) 		0.665
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TCEB1 3 (0%) 665 0.325
(1.00) 		0.199
(1.00) 		0.815
(1.00) 		0.43
(1.00) 		1
(1.00) 		1
(1.00) 		0.683
(1.00) 		0.319
(1.00) 		0.19
(1.00)
SFMBT1 3 (0%) 665 0.115
(0.904) 		0.322
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.272
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SLC16A1 3 (0%) 665 0.416
(1.00) 		0.2
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.19
(1.00)
PAM 4 (1%) 664 0.223
(1.00) 		0.961
(1.00) 		0.778
(1.00) 		1
(1.00) 		0.351
(1.00) 		1
(1.00) 		1
(1.00) 		0.0948
(0.9) 		0.399
(1.00) 		0.321
(1.00) 		1
(1.00)
TMCO3 7 (1%) 661 0.523
(1.00) 		0.565
(1.00) 		0.34
(1.00) 		0.626
(1.00) 		0.439
(1.00) 		1
(1.00) 		0.239
(1.00) 		1
(1.00) 		0.0315
(0.482) 		0.297
(1.00)
CCDC82 6 (1%) 662 0.356
(1.00) 		0.514
(1.00) 		0.878
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.188
(1.00) 		0.254
(1.00) 		1
(1.00) 		1
(1.00)
NFAT5 8 (1%) 660 0.772
(1.00) 		0.744
(1.00) 		0.348
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.722
(1.00) 		0.743
(1.00) 		0.643
(1.00) 		1
(1.00)
HNF1B 3 (0%) 665 0.109
(0.904) 		0.765
(1.00) 		0.123
(0.904) 		0.184
(1.00) 		0.266
(1.00) 		0.272
(1.00) 		0.4
(1.00) 		1
(1.00)
OR2L8 7 (1%) 661 0.214
(1.00) 		0.567
(1.00) 		0.568
(1.00) 		0.494
(1.00) 		0.151
(0.989) 		0.239
(1.00) 		0.124
(0.906) 		1
(1.00) 		1
(1.00)
ZC3H18 6 (1%) 662 0.137
(0.969) 		0.777
(1.00) 		1
(1.00) 		0.763
(1.00) 		1
(1.00) 		0.418
(1.00) 		0.821
(1.00) 		0.54
(1.00) 		1
(1.00)
GAPDHS 5 (1%) 663 0.307
(1.00) 		0.396
(1.00) 		0.919
(1.00) 		0.604
(1.00) 		1
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.174
(1.00) 		1
(1.00)
GPR137 4 (1%) 664 0.756
(1.00) 		0.388
(1.00) 		0.877
(1.00) 		0.824
(1.00) 		0.461
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
RRP12 9 (1%) 659 0.792
(1.00) 		0.116
(0.904) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0696
(0.777) 		0.574
(1.00) 		1
(1.00) 		0.345
(1.00)
'TP53 MUTATION STATUS' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00318 (Fisher's exact test), Q value = 0.1

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 327 79 165 86
TP53 MUTATED 12 11 7 8
TP53 WILD-TYPE 315 68 158 78

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'TP53 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00325 (Fisher's exact test), Q value = 0.1

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 340 97 221 10
TP53 MUTATED 12 12 12 2
TP53 WILD-TYPE 328 85 209 8

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
TP53 MUTATED 22 12 4
TP53 WILD-TYPE 44 429 157

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'PBRM1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00663 (Wilcoxon-test), Q value = 0.18

Table S4.  Gene #2: 'PBRM1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 665 59.5 (12.6)
PBRM1 MUTATED 146 62.1 (10.9)
PBRM1 WILD-TYPE 519 58.7 (13.0)

Figure S4.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PBRM1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S5.  Gene #2: 'PBRM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
PBRM1 MUTATED 1 139 6
PBRM1 WILD-TYPE 65 302 155

Figure S5.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'PBRM1 MUTATION STATUS' versus 'RACE'

P value = 0.00695 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #2: 'PBRM1 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 65 569
PBRM1 MUTATED 0 1 5 136
PBRM1 WILD-TYPE 2 10 60 433

Figure S6.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'BAP1 MUTATION STATUS' versus 'Time to Death'

P value = 8.61e-05 (logrank test), Q value = 0.0068

Table S7.  Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 661 175 0.1 - 194.8 (34.3)
BAP1 MUTATED 49 25 0.1 - 93.3 (27.6)
BAP1 WILD-TYPE 612 150 0.1 - 194.8 (35.1)

Figure S7.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'BAP1 MUTATION STATUS' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0032

Table S8.  Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 327 79 165 86
BAP1 MUTATED 9 8 19 13
BAP1 WILD-TYPE 318 71 146 73

Figure S8.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'BAP1 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0068

Table S9.  Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 340 97 221 10
BAP1 MUTATED 10 12 27 0
BAP1 WILD-TYPE 330 85 194 10

Figure S9.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'BAP1 MUTATION STATUS' versus 'PATHOLOGY_M_STAGE'

P value = 0.00436 (Fisher's exact test), Q value = 0.13

Table S10.  Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 468 78
BAP1 MUTATED 34 14
BAP1 WILD-TYPE 434 64

Figure S10.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'BAP1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 2e-04 (Fisher's exact test), Q value = 0.015

Table S11.  Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
BAP1 MUTATED 0 44 5
BAP1 WILD-TYPE 66 397 156

Figure S11.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'SETD2 MUTATION STATUS' versus 'Time to Death'

P value = 0.00934 (logrank test), Q value = 0.23

Table S12.  Gene #5: 'SETD2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 661 175 0.1 - 194.8 (34.3)
SETD2 MUTATED 58 24 0.5 - 152.0 (33.0)
SETD2 WILD-TYPE 603 151 0.1 - 194.8 (34.3)

Figure S12.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'KDM5C MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00965 (Wilcoxon-test), Q value = 0.23

Table S13.  Gene #6: 'KDM5C MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 665 59.5 (12.6)
KDM5C MUTATED 30 65.4 (12.3)
KDM5C WILD-TYPE 635 59.2 (12.6)

Figure S13.  Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'KDM5C MUTATION STATUS' versus 'GENDER'

P value = 0.00286 (Fisher's exact test), Q value = 0.1

Table S14.  Gene #6: 'KDM5C MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 229 439
KDM5C MUTATED 3 27
KDM5C WILD-TYPE 226 412

Figure S14.  Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'NEFH MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00141 (Fisher's exact test), Q value = 0.067

Table S15.  Gene #7: 'NEFH MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
NEFH MUTATED 0 5 10
NEFH WILD-TYPE 66 436 151

Figure S15.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'VHL MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S16.  Gene #8: 'VHL MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
VHL MUTATED 1 171 2
VHL WILD-TYPE 65 270 159

Figure S16.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'VHL MUTATION STATUS' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S17.  Gene #8: 'VHL MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 65 569
VHL MUTATED 0 2 2 167
VHL WILD-TYPE 2 9 63 402

Figure S17.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'NF2 MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0038

Table S18.  Gene #9: 'NF2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 272 36 6
NF2 MUTATED 1 6 0
NF2 WILD-TYPE 271 30 6

Figure S18.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'NF2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00254 (Fisher's exact test), Q value = 0.093

Table S19.  Gene #9: 'NF2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
NF2 MUTATED 0 6 10
NF2 WILD-TYPE 66 435 151

Figure S19.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'HNRNPM MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0024

Table S20.  Gene #10: 'HNRNPM MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
HNRNPM MUTATED 1 1 10
HNRNPM WILD-TYPE 65 440 151

Figure S20.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'MET MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S21.  Gene #11: 'MET MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
MET MUTATED 0 4 15
MET WILD-TYPE 66 437 146

Figure S21.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'MUC5B MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S22.  Gene #12: 'MUC5B MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
MUC5B MUTATED 11 5 14
MUC5B WILD-TYPE 55 436 147

Figure S22.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'KDM6A MUTATION STATUS' versus 'RACE'

P value = 0.00036 (Fisher's exact test), Q value = 0.024

Table S23.  Gene #13: 'KDM6A MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 65 569
KDM6A MUTATED 1 0 4 3
KDM6A WILD-TYPE 1 11 61 566

Figure S23.  Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'TDG MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.0017 (Fisher's exact test), Q value = 0.07

Table S24.  Gene #14: 'TDG MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
TDG MUTATED 0 0 5
TDG WILD-TYPE 66 441 156

Figure S24.  Get High-res Image Gene #14: 'TDG MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'NFE2L2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0111 (Wilcoxon-test), Q value = 0.25

Table S25.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 665 59.5 (12.6)
NFE2L2 MUTATED 10 68.9 (7.0)
NFE2L2 WILD-TYPE 655 59.3 (12.7)

Figure S25.  Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'ATM MUTATION STATUS' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0103 (Fisher's exact test), Q value = 0.25

Table S26.  Gene #16: 'ATM MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 327 79 165 86
ATM MUTATED 6 6 1 3
ATM WILD-TYPE 321 73 164 83

Figure S26.  Get High-res Image Gene #16: 'ATM MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'ATM MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00141 (Fisher's exact test), Q value = 0.067

Table S27.  Gene #16: 'ATM MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 340 97 221 10
ATM MUTATED 6 6 2 2
ATM WILD-TYPE 334 91 219 8

Figure S27.  Get High-res Image Gene #16: 'ATM MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'ZNF814 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00045 (Fisher's exact test), Q value = 0.028

Table S28.  Gene #17: 'ZNF814 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
ZNF814 MUTATED 3 2 8
ZNF814 WILD-TYPE 63 439 153

Figure S28.  Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'CSGALNACT2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00297 (Fisher's exact test), Q value = 0.1

Table S29.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
CSGALNACT2 MUTATED 2 1 5
CSGALNACT2 WILD-TYPE 64 440 156

Figure S29.  Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'ZNF598 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0024

Table S30.  Gene #25: 'ZNF598 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
ZNF598 MUTATED 1 0 10
ZNF598 WILD-TYPE 65 441 151

Figure S30.  Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'SKI MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00187 (Fisher's exact test), Q value = 0.071

Table S31.  Gene #31: 'SKI MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
SKI MUTATED 2 1 6
SKI WILD-TYPE 64 440 155

Figure S31.  Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'EGFR MUTATION STATUS' versus 'Time to Death'

P value = 0.00499 (logrank test), Q value = 0.14

Table S32.  Gene #33: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 661 175 0.1 - 194.8 (34.3)
EGFR MUTATED 7 5 2.3 - 61.3 (34.0)
EGFR WILD-TYPE 654 170 0.1 - 194.8 (34.3)

Figure S32.  Get High-res Image Gene #33: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'EGFR MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.0034 (Fisher's exact test), Q value = 0.1

Table S33.  Gene #33: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 340 97 221 10
EGFR MUTATED 0 1 5 1
EGFR WILD-TYPE 340 96 216 9

Figure S33.  Get High-res Image Gene #33: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'AHNAK2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00161 (Fisher's exact test), Q value = 0.07

Table S34.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
AHNAK2 MUTATED 10 16 7
AHNAK2 WILD-TYPE 56 425 154

Figure S34.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'AHNAK2 MUTATION STATUS' versus 'RACE'

P value = 0.00455 (Fisher's exact test), Q value = 0.13

Table S35.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 65 569
AHNAK2 MUTATED 1 2 6 22
AHNAK2 WILD-TYPE 1 9 59 547

Figure S35.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'STAM MUTATION STATUS' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00049 (Fisher's exact test), Q value = 0.029

Table S36.  Gene #41: 'STAM MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 327 79 165 86
STAM MUTATED 0 3 0 3
STAM WILD-TYPE 327 76 165 83

Figure S36.  Get High-res Image Gene #41: 'STAM MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'STAM MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00168 (Fisher's exact test), Q value = 0.07

Table S37.  Gene #41: 'STAM MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 340 97 221 10
STAM MUTATED 0 3 2 1
STAM WILD-TYPE 340 94 219 9

Figure S37.  Get High-res Image Gene #41: 'STAM MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'RTL1 MUTATION STATUS' versus 'Time to Death'

P value = 0.00825 (logrank test), Q value = 0.21

Table S38.  Gene #54: 'RTL1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 661 175 0.1 - 194.8 (34.3)
RTL1 MUTATED 7 5 8.1 - 115.0 (21.6)
RTL1 WILD-TYPE 654 170 0.1 - 194.8 (34.3)

Figure S38.  Get High-res Image Gene #54: 'RTL1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'RTL1 MUTATION STATUS' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0109 (Fisher's exact test), Q value = 0.25

Table S39.  Gene #54: 'RTL1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 327 79 165 86
RTL1 MUTATED 0 2 3 2
RTL1 WILD-TYPE 327 77 162 84

Figure S39.  Get High-res Image Gene #54: 'RTL1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'IDUA MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00184 (Fisher's exact test), Q value = 0.071

Table S40.  Gene #67: 'IDUA MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
IDUA MUTATED 0 0 5
IDUA WILD-TYPE 66 441 156

Figure S40.  Get High-res Image Gene #67: 'IDUA MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'GFM1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00082 (Fisher's exact test), Q value = 0.046

Table S41.  Gene #71: 'GFM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
GFM1 MUTATED 3 0 0
GFM1 WILD-TYPE 63 441 161

Figure S41.  Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'FAT1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00138 (Fisher's exact test), Q value = 0.067

Table S42.  Gene #72: 'FAT1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 441 161
FAT1 MUTATED 1 8 13
FAT1 WILD-TYPE 65 433 148

Figure S42.  Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

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/KIPAN-TP/15639742/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/15081103/KIPAN-TP.merged_data.txt

  • Number of patients = 668

  • Number of significantly mutated genes = 73

  • Number of selected clinical features = 13

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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