Correlation between gene mutation status and selected clinical features
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C17080NS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C17080NS
Overview
Introduction

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

Summary

Testing the association between mutation status of 57 genes and 13 clinical features across 663 patients, 42 significant findings detected with Q value < 0.25.

  • FAM18B2 mutation correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

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

  • KDM5C mutation correlated to 'GENDER'.

  • SETD2 mutation correlated to 'YEARS_TO_BIRTH'.

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

  • NEFH mutation correlated to 'HISTOLOGICAL_TYPE'.

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

  • MET mutation correlated to 'HISTOLOGICAL_TYPE'.

  • HNRNPM mutation correlated to 'HISTOLOGICAL_TYPE'.

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

  • TDG mutation correlated to 'HISTOLOGICAL_TYPE'.

  • MUC5B mutation correlated to 'HISTOLOGICAL_TYPE'.

  • ZNF814 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • CSGALNACT2 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • NFE2L2 mutation correlated to 'YEARS_TO_BIRTH'.

  • ATM mutation correlated to 'PATHOLOGIC_STAGE'.

  • MTOR mutation correlated to 'GENDER'.

  • EGFR mutation correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • ZNF598 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • KDM6A mutation correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

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

  • SKI mutation correlated to 'HISTOLOGICAL_TYPE'.

  • FAT1 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • CACNA1C mutation correlated to 'PATHOLOGY_M_STAGE'.

  • MLL3 mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

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

  • TTLL6 mutation correlated to 'PATHOLOGY_T_STAGE'.

  • AMAC1L3 mutation correlated to 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 57 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 		PATHOLOGIC
STAGE 		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
FAM18B2 35 (5%) 628 0.405
(1.00) 		0.603
(1.00) 		0.702
(1.00) 		0.876
(1.00) 		0.0139
(0.245) 		1
(1.00) 		0.855
(1.00) 		0.275
(1.00) 		1e-05
(0.000926) 		0.806
(1.00) 		0.00698
(0.181) 		1
(1.00)
TP53 35 (5%) 628 0.923
(1.00) 		0.245
(1.00) 		0.00794
(0.19) 		0.00536
(0.152) 		0.0645
(0.583) 		1
(1.00) 		0.361
(1.00) 		0.267
(1.00) 		1e-05
(0.000926) 		0.392
(1.00) 		1
(1.00) 		0.198
(0.988) 		1
(1.00)
PBRM1 138 (21%) 525 0.355
(1.00) 		0.0108
(0.233) 		0.555
(1.00) 		0.46
(1.00) 		0.042
(0.466) 		0.484
(1.00) 		0.616
(1.00) 		0.776
(1.00) 		1e-05
(0.000926) 		0.0126
(0.233) 		0.65
(1.00)
KDM6A 10 (2%) 653 0.112
(0.776) 		0.0127
(0.233) 		0.422
(1.00) 		0.922
(1.00) 		0.601
(1.00) 		0.744
(1.00) 		0.00794
(0.19) 		0.00011
(0.00741) 		1
(1.00)
VHL 195 (29%) 468 0.0162
(0.267) 		0.0638
(0.583) 		0.446
(1.00) 		0.241
(1.00) 		0.0253
(0.368) 		0.8
(1.00) 		0.245
(1.00) 		0.174
(0.921) 		1e-05
(0.000926) 		1e-05
(0.000926) 		1
(1.00)
NF2 16 (2%) 647 0.0992
(0.728) 		0.218
(1.00) 		0.0338
(0.455) 		0.121
(0.785) 		3e-05
(0.00222) 		0.0424
(0.466) 		0.795
(1.00) 		0.288
(1.00) 		0.00314
(0.0979) 		0.062
(0.582) 		0.208
(0.988)
EGFR 6 (1%) 657 0.0515
(0.516) 		0.301
(1.00) 		0.0122
(0.233) 		0.00252
(0.0889) 		0.431
(1.00) 		0.209
(0.988) 		0.67
(1.00) 		0.338
(1.00) 		1
(1.00) 		1
(1.00)
STAM 6 (1%) 657 0.702
(1.00) 		0.43
(1.00) 		0.00056
(0.0296) 		0.00202
(0.0748) 		0.0457
(0.481) 		0.101
(0.729) 		0.67
(1.00) 		0.0751
(0.656) 		1
(1.00) 		0.0369
(0.466)
MLL3 38 (6%) 625 0.935
(1.00) 		0.428
(1.00) 		0.267
(1.00) 		0.221
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.38
(1.00) 		0.314
(1.00) 		0.00065
(0.0301) 		0.611
(1.00) 		0.0102
(0.229) 		0.711
(1.00)
AHNAK2 33 (5%) 630 0.815
(1.00) 		0.221
(1.00) 		0.155
(0.893) 		0.11
(0.768) 		0.145
(0.857) 		0.564
(1.00) 		0.575
(1.00) 		0.773
(1.00) 		0.00172
(0.0729) 		0.692
(1.00) 		0.131
(0.814) 		0.00396
(0.117) 		0.648
(1.00)
KDM5C 28 (4%) 635 0.0379
(0.466) 		0.0413
(0.466) 		0.635
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.0071
(0.181) 		0.0269
(0.384) 		1
(1.00) 		0.385
(1.00)
SETD2 56 (8%) 607 0.0801
(0.674) 		0.0128
(0.233) 		0.0636
(0.583) 		0.0705
(0.63) 		0.424
(1.00) 		0.3
(1.00) 		0.558
(1.00) 		0.42
(1.00) 		0.14
(0.857) 		0.817
(1.00) 		0.497
(1.00)
NEFH 16 (2%) 647 0.311
(1.00) 		0.374
(1.00) 		0.276
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.324
(1.00) 		0.596
(1.00) 		0.92
(1.00) 		0.00317
(0.0979) 		0.28
(1.00) 		0.125
(0.793) 		1
(1.00)
MET 19 (3%) 644 0.573
(1.00) 		0.817
(1.00) 		0.463
(1.00) 		0.925
(1.00) 		0.0992
(0.728) 		1
(1.00) 		1
(1.00) 		1e-05
(0.000926) 		0.24
(1.00) 		0.775
(1.00) 		0.143
(0.857) 		1
(1.00)
HNRNPM 12 (2%) 651 0.315
(1.00) 		0.486
(1.00) 		0.459
(1.00) 		0.0601
(0.578) 		0.343
(1.00) 		0.6
(1.00) 		0.558
(1.00) 		0.644
(1.00) 		2e-05
(0.00165) 		0.269
(1.00) 		1
(1.00)
TDG 5 (1%) 658 0.245
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.116
(0.785) 		0.344
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.00184
(0.0729) 		0.477
(1.00) 		1
(1.00)
MUC5B 32 (5%) 631 0.568
(1.00) 		0.914
(1.00) 		0.442
(1.00) 		0.461
(1.00) 		0.196
(0.988) 		0.229
(1.00) 		0.452
(1.00) 		0.242
(1.00) 		1e-05
(0.000926) 		1
(1.00) 		0.847
(1.00) 		0.401
(1.00) 		1
(1.00)
ZNF814 13 (2%) 650 0.202
(0.988) 		0.252
(1.00) 		0.133
(0.824) 		0.251
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.0414
(0.466) 		0.00046
(0.0262) 		0.332
(1.00) 		1
(1.00)
CSGALNACT2 8 (1%) 655 0.114
(0.782) 		0.498
(1.00) 		0.751
(1.00) 		0.495
(1.00) 		1
(1.00) 		0.6
(1.00) 		0.457
(1.00) 		0.00312
(0.0979) 		0.122
(0.785) 		1
(1.00)
NFE2L2 10 (2%) 653 0.944
(1.00) 		0.0118
(0.233) 		0.737
(1.00) 		0.779
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.405
(1.00) 		1
(1.00)
ATM 16 (2%) 647 0.471
(1.00) 		0.169
(0.921) 		0.00986
(0.228) 		0.0213
(0.322) 		1
(1.00) 		0.438
(1.00) 		0.435
(1.00) 		0.125
(0.793) 		0.557
(1.00) 		0.496
(1.00)
MTOR 32 (5%) 631 0.0771
(0.656) 		0.0461
(0.481) 		0.444
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.177
(0.929) 		0.0122
(0.233) 		0.0319
(0.438) 		0.0154
(0.266) 		0.875
(1.00) 		0.711
(1.00)
ZNF598 11 (2%) 652 0.419
(1.00) 		0.5
(1.00) 		0.648
(1.00) 		0.928
(1.00) 		0.0198
(0.306) 		0.101
(0.729) 		0.346
(1.00) 		0.0837
(0.689) 		1e-05
(0.000926) 		0.179
(0.934) 		0.267
(1.00) 		0.496
(1.00)
SKI 9 (1%) 654 0.592
(1.00) 		0.725
(1.00) 		0.546
(1.00) 		0.698
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.726
(1.00) 		0.00187
(0.0729) 		0.733
(1.00) 		0.265
(1.00) 		1
(1.00)
FAT1 21 (3%) 642 0.412
(1.00) 		0.4
(1.00) 		0.328
(1.00) 		0.266
(1.00) 		0.291
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.00062
(0.0301) 		0.837
(1.00) 		0.0614
(0.582) 		0.622
(1.00)
CACNA1C 17 (3%) 646 0.936
(1.00) 		0.994
(1.00) 		0.0569
(0.555) 		0.506
(1.00) 		0.0192
(0.306) 		0.00554
(0.152) 		0.799
(1.00) 		0.808
(1.00) 		0.316
(1.00) 		0.569
(1.00) 		0.591
(1.00)
TTLL6 6 (1%) 657 0.667
(1.00) 		0.121
(0.785) 		0.0407
(0.466) 		0.0129
(0.233) 		1
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.0763
(0.656) 		0.542
(1.00) 		1
(1.00)
AMAC1L3 8 (1%) 655 0.128
(0.802) 		0.3
(1.00) 		0.147
(0.866) 		0.273
(1.00) 		1
(1.00) 		1
(1.00) 		0.721
(1.00) 		0.00024
(0.0148) 		0.599
(1.00) 		1
(1.00)
PTEN 26 (4%) 637 0.714
(1.00) 		0.903
(1.00) 		0.262
(1.00) 		0.341
(1.00) 		0.162
(0.91) 		0.346
(1.00) 		0.834
(1.00) 		0.579
(1.00) 		0.0957
(0.728) 		0.884
(1.00) 		0.923
(1.00) 		0.502
(1.00) 		1
(1.00)
GPR50 5 (1%) 658 0.44
(1.00) 		0.32
(1.00) 		0.761
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.347
(1.00) 		0.606
(1.00) 		0.477
(1.00) 		1
(1.00)
STAG2 14 (2%) 649 0.996
(1.00) 		0.0158
(0.266) 		0.16
(0.909) 		0.0974
(0.728) 		1
(1.00) 		0.664
(1.00) 		0.258
(1.00) 		0.17
(0.921) 		0.493
(1.00) 		1
(1.00)
KDELR3 6 (1%) 657 0.582
(1.00) 		0.827
(1.00) 		0.275
(1.00) 		0.0427
(0.466) 		1
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.0762
(0.656) 		0.542
(1.00) 		1
(1.00)
SLC6A14 5 (1%) 658 0.793
(1.00) 		0.59
(1.00) 		0.217
(1.00) 		0.173
(0.921) 		0.0903
(0.719) 		1
(1.00) 		0.347
(1.00) 		0.249
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 12 (2%) 651 0.914
(1.00) 		0.214
(1.00) 		0.206
(0.988) 		0.202
(0.988) 		1
(1.00) 		0.202
(0.988) 		0.121
(0.785) 		0.48
(1.00) 		0.702
(1.00) 		0.496
(1.00)
EMG1 4 (1%) 659 0.204
(0.988) 		0.932
(1.00) 		0.527
(1.00) 		0.255
(1.00) 		1
(1.00) 		1
(1.00) 		0.723
(1.00) 		1
(1.00) 		1
(1.00)
RIMBP3 5 (1%) 658 0.318
(1.00) 		0.315
(1.00) 		0.625
(1.00) 		0.0906
(0.719) 		1
(1.00) 		1
(1.00) 		0.347
(1.00) 		0.0829
(0.689) 		1
(1.00) 		1
(1.00)
RAI1 7 (1%) 656 0.802
(1.00) 		0.709
(1.00) 		0.257
(1.00) 		0.108
(0.759) 		1
(1.00) 		0.465
(1.00) 		0.242
(1.00) 		0.161
(0.909) 		1
(1.00) 		1
(1.00)
FAM160B2 4 (1%) 659 0.223
(1.00) 		0.731
(1.00) 		0.312
(1.00) 		0.652
(1.00) 		0.374
(1.00) 		0.612
(1.00) 		0.387
(1.00) 		1
(1.00) 		1
(1.00)
DPCR1 8 (1%) 655 0.686
(1.00) 		0.236
(1.00) 		0.222
(1.00) 		0.736
(1.00) 		0.0417
(0.466) 		0.721
(1.00) 		0.743
(1.00) 		0.649
(1.00) 		1
(1.00)
CYP4F11 5 (1%) 658 0.894
(1.00) 		0.479
(1.00) 		0.142
(0.857) 		0.0444
(0.477) 		0.506
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.343
(1.00) 		1
(1.00) 		1
(1.00)
NUDT11 5 (1%) 658 0.498
(1.00) 		0.19
(0.978) 		0.688
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.664
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PARD6B 5 (1%) 658 0.668
(1.00) 		0.0499
(0.514) 		0.427
(1.00) 		0.495
(1.00) 		1
(1.00) 		0.17
(0.921) 		0.173
(0.921) 		0.477
(1.00) 		1
(1.00)
RHEB 3 (0%) 660 0.81
(1.00) 		0.84
(1.00) 		0.69
(1.00) 		0.74
(1.00) 		0.268
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.32
(1.00) 		1
(1.00)
SLC16A1 3 (0%) 660 0.387
(1.00) 		0.194
(0.988) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.185
(0.957)
THBS1 10 (2%) 653 0.985
(1.00) 		0.154
(0.891) 		0.787
(1.00) 		1
(1.00) 		0.601
(1.00) 		0.507
(1.00) 		0.469
(1.00) 		1
(1.00) 		1
(1.00)
SH3BP2 4 (1%) 659 0.532
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.099
(0.728) 		0.405
(1.00) 		1
(1.00)
NASP 4 (1%) 659 0.202
(0.988) 		0.336
(1.00) 		0.219
(1.00) 		0.332
(1.00) 		1
(1.00) 		0.121
(0.785) 		0.0358
(0.466) 		1
(1.00) 		0.239
(1.00)
PCK1 5 (1%) 658 0.166
(0.921) 		0.447
(1.00) 		0.68
(1.00) 		0.344
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.478
(1.00) 		1
(1.00)
TPPP 3 (0%) 660 0.788
(1.00) 		0.461
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0409
(0.466) 		0.273
(1.00) 		0.0197
(0.306) 		1
(1.00)
PAM 4 (1%) 659 0.231
(1.00) 		0.949
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00) 		1
(1.00) 		0.0979
(0.728) 		0.365
(1.00) 		0.323
(1.00) 		1
(1.00)
GAPDHS 5 (1%) 658 0.3
(1.00) 		0.402
(1.00) 		0.915
(1.00) 		0.604
(1.00) 		1
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.171
(0.921) 		1
(1.00)
TMCO3 7 (1%) 656 0.464
(1.00) 		0.554
(1.00) 		0.342
(1.00) 		0.625
(1.00) 		0.429
(1.00) 		1
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.03
(0.419) 		0.289
(1.00)
RPL7A 3 (0%) 660 0.757
(1.00) 		0.204
(0.988) 		0.587
(1.00) 		1
(1.00) 		0.144
(0.857) 		0.555
(1.00) 		0.0228
(0.338) 		0.323
(1.00) 		1
(1.00)
ARHGAP35 7 (1%) 656 0.117
(0.785) 		0.854
(1.00) 		0.107
(0.759) 		0.234
(1.00) 		1
(1.00) 		0.209
(0.988) 		0.698
(1.00) 		0.849
(1.00) 		0.0407
(0.466) 		1
(1.00)
JMJD1C 10 (2%) 653 0.15
(0.878) 		0.888
(1.00) 		1
(1.00) 		0.846
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.354
(1.00) 		1
(1.00) 		0.0913
(0.719)
TRAPPC9 5 (1%) 658 0.309
(1.00) 		0.71
(1.00) 		0.762
(1.00) 		0.853
(1.00) 		1
(1.00) 		0.0508
(0.516) 		0.0539
(0.532) 		0.408
(1.00) 		1
(1.00)
MED16 4 (1%) 659 0.0352
(0.466) 		0.842
(1.00) 		0.406
(1.00) 		0.33
(1.00) 		0.0882
(0.718) 		1
(1.00) 		0.612
(1.00) 		0.098
(0.728) 		1
(1.00) 		1
(1.00)
'FAM18B2 MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 0.0139 (Fisher's exact test), Q value = 0.24

Table S1.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 272 35 6
FAM18B2 MUTATED 4 3 1
FAM18B2 WILD-TYPE 268 32 5

Figure S1.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'FAM18B2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00093

Table S2.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
FAM18B2 MUTATED 0 0 35
FAM18B2 WILD-TYPE 66 436 126

Figure S2.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'FAM18B2 MUTATION STATUS' versus 'RACE'

P value = 0.00698 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 10 66 565
FAM18B2 MUTATED 1 0 8 22
FAM18B2 WILD-TYPE 1 10 58 543

Figure S3.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'TP53 MUTATION STATUS' versus 'PATHOLOGIC_STAGE'

P value = 0.00794 (Fisher's exact test), Q value = 0.19

Table S4.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 325 76 163 88
TP53 MUTATED 12 10 6 7
TP53 WILD-TYPE 313 66 157 81

Figure S4.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'TP53 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00536 (Fisher's exact test), Q value = 0.15

Table S5.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 337 95 221 10
TP53 MUTATED 12 11 10 2
TP53 WILD-TYPE 325 84 211 8

Figure S5.  Get High-res Image Gene #2: '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 = 0.00093

Table S6.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
TP53 MUTATED 22 9 4
TP53 WILD-TYPE 44 427 157

Figure S6.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'KDM5C MUTATION STATUS' versus 'GENDER'

P value = 0.0071 (Fisher's exact test), Q value = 0.18

Table S7.  Gene #4: 'KDM5C MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 229 434
KDM5C MUTATED 3 25
KDM5C WILD-TYPE 226 409

Figure S7.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'SETD2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0128 (Wilcoxon-test), Q value = 0.23

Table S8.  Gene #5: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 660 59.5 (12.6)
SETD2 MUTATED 56 63.3 (10.8)
SETD2 WILD-TYPE 604 59.2 (12.7)

Figure S8.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PBRM1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0108 (Wilcoxon-test), Q value = 0.23

Table S9.  Gene #6: 'PBRM1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 660 59.5 (12.6)
PBRM1 MUTATED 138 62.1 (10.9)
PBRM1 WILD-TYPE 522 58.9 (13.0)

Figure S9.  Get High-res Image Gene #6: '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 = 0.00093

Table S10.  Gene #6: 'PBRM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
PBRM1 MUTATED 1 131 6
PBRM1 WILD-TYPE 65 305 155

Figure S10.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'PBRM1 MUTATION STATUS' versus 'RACE'

P value = 0.0126 (Fisher's exact test), Q value = 0.23

Table S11.  Gene #6: 'PBRM1 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 10 66 565
PBRM1 MUTATED 0 1 5 128
PBRM1 WILD-TYPE 2 9 61 437

Figure S11.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'NEFH MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00317 (Fisher's exact test), Q value = 0.098

Table S12.  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 66 436 161
NEFH MUTATED 0 6 10
NEFH WILD-TYPE 66 430 151

Figure S12.  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 = 0.00093

Table S13.  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 66 436 161
VHL MUTATED 1 192 2
VHL WILD-TYPE 65 244 159

Figure S13.  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 = 0.00093

Table S14.  Gene #8: 'VHL MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 10 66 565
VHL MUTATED 0 2 2 189
VHL WILD-TYPE 2 8 64 376

Figure S14.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'MET MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00093

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

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
MET MUTATED 0 4 15
MET WILD-TYPE 66 432 146

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

'HNRNPM MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S16.  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 66 436 161
HNRNPM MUTATED 1 1 10
HNRNPM WILD-TYPE 65 435 151

Figure S16.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'NF2 MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

Table S17.  Gene #11: 'NF2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 272 35 6
NF2 MUTATED 1 6 0
NF2 WILD-TYPE 271 29 6

Figure S17.  Get High-res Image Gene #11: 'NF2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'NF2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00314 (Fisher's exact test), Q value = 0.098

Table S18.  Gene #11: 'NF2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
NF2 MUTATED 0 6 10
NF2 WILD-TYPE 66 430 151

Figure S18.  Get High-res Image Gene #11: 'NF2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'TDG MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00184 (Fisher's exact test), Q value = 0.073

Table S19.  Gene #12: 'TDG MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
TDG MUTATED 0 0 5
TDG WILD-TYPE 66 436 156

Figure S19.  Get High-res Image Gene #12: 'TDG MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'MUC5B MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00093

Table S20.  Gene #13: 'MUC5B MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
MUC5B MUTATED 12 6 14
MUC5B WILD-TYPE 54 430 147

Figure S20.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'ZNF814 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00046 (Fisher's exact test), Q value = 0.026

Table S21.  Gene #14: 'ZNF814 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
ZNF814 MUTATED 3 2 8
ZNF814 WILD-TYPE 63 434 153

Figure S21.  Get High-res Image Gene #14: 'ZNF814 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'CSGALNACT2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00312 (Fisher's exact test), Q value = 0.098

Table S22.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
CSGALNACT2 MUTATED 2 1 5
CSGALNACT2 WILD-TYPE 64 435 156

Figure S22.  Get High-res Image Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'NFE2L2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0118 (Wilcoxon-test), Q value = 0.23

Table S23.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 660 59.5 (12.6)
NFE2L2 MUTATED 10 68.9 (7.0)
NFE2L2 WILD-TYPE 650 59.4 (12.6)

Figure S23.  Get High-res Image Gene #18: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'ATM MUTATION STATUS' versus 'PATHOLOGIC_STAGE'

P value = 0.00986 (Fisher's exact test), Q value = 0.23

Table S24.  Gene #20: 'ATM MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 325 76 163 88
ATM MUTATED 6 6 1 3
ATM WILD-TYPE 319 70 162 85

Figure S24.  Get High-res Image Gene #20: 'ATM MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'MTOR MUTATION STATUS' versus 'GENDER'

P value = 0.0122 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #21: 'MTOR MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 229 434
MTOR MUTATED 18 14
MTOR WILD-TYPE 211 420

Figure S25.  Get High-res Image Gene #21: 'MTOR MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'EGFR MUTATION STATUS' versus 'PATHOLOGIC_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.23

Table S26.  Gene #22: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 325 76 163 88
EGFR MUTATED 0 0 4 2
EGFR WILD-TYPE 325 76 159 86

Figure S26.  Get High-res Image Gene #22: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'EGFR MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00252 (Fisher's exact test), Q value = 0.089

Table S27.  Gene #22: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 337 95 221 10
EGFR MUTATED 0 0 5 1
EGFR WILD-TYPE 337 95 216 9

Figure S27.  Get High-res Image Gene #22: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'ZNF598 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00093

Table S28.  Gene #29: 'ZNF598 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
ZNF598 MUTATED 1 0 10
ZNF598 WILD-TYPE 65 436 151

Figure S28.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'KDM6A MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.0127 (Wilcoxon-test), Q value = 0.23

Table S29.  Gene #30: 'KDM6A MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 660 59.5 (12.6)
KDM6A MUTATED 8 70.6 (10.1)
KDM6A WILD-TYPE 652 59.4 (12.6)

Figure S29.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'KDM6A MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00794 (Fisher's exact test), Q value = 0.19

Table S30.  Gene #30: 'KDM6A MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
KDM6A MUTATED 0 3 7
KDM6A WILD-TYPE 66 433 154

Figure S30.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'KDM6A MUTATION STATUS' versus 'RACE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0074

Table S31.  Gene #30: 'KDM6A MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 10 66 565
KDM6A MUTATED 1 0 4 2
KDM6A WILD-TYPE 1 10 62 563

Figure S31.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'STAM MUTATION STATUS' versus 'PATHOLOGIC_STAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.03

Table S32.  Gene #33: 'STAM MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 325 76 163 88
STAM MUTATED 0 3 0 3
STAM WILD-TYPE 325 73 163 85

Figure S32.  Get High-res Image Gene #33: 'STAM MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'STAM MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00202 (Fisher's exact test), Q value = 0.075

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

nPatients T1 T2 T3 T4
ALL 337 95 221 10
STAM MUTATED 0 3 2 1
STAM WILD-TYPE 337 92 219 9

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

'SKI MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00187 (Fisher's exact test), Q value = 0.073

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

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
SKI MUTATED 2 1 6
SKI WILD-TYPE 64 435 155

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

'FAT1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00062 (Fisher's exact test), Q value = 0.03

Table S35.  Gene #42: 'FAT1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
FAT1 MUTATED 1 7 13
FAT1 WILD-TYPE 65 429 148

Figure S35.  Get High-res Image Gene #42: 'FAT1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'CACNA1C MUTATION STATUS' versus 'PATHOLOGY_M_STAGE'

P value = 0.00554 (Fisher's exact test), Q value = 0.15

Table S36.  Gene #43: 'CACNA1C MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 463 78
CACNA1C MUTATED 7 6
CACNA1C WILD-TYPE 456 72

Figure S36.  Get High-res Image Gene #43: 'CACNA1C MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'MLL3 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00065 (Fisher's exact test), Q value = 0.03

Table S37.  Gene #46: 'MLL3 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
MLL3 MUTATED 9 15 14
MLL3 WILD-TYPE 57 421 147

Figure S37.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'MLL3 MUTATION STATUS' versus 'RACE'

P value = 0.0102 (Fisher's exact test), Q value = 0.23

Table S38.  Gene #46: 'MLL3 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 10 66 565
MLL3 MUTATED 0 1 10 26
MLL3 WILD-TYPE 2 9 56 539

Figure S38.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'AHNAK2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00172 (Fisher's exact test), Q value = 0.073

Table S39.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
AHNAK2 MUTATED 10 16 7
AHNAK2 WILD-TYPE 56 420 154

Figure S39.  Get High-res Image Gene #52: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'AHNAK2 MUTATION STATUS' versus 'RACE'

P value = 0.00396 (Fisher's exact test), Q value = 0.12

Table S40.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 10 66 565
AHNAK2 MUTATED 1 2 6 22
AHNAK2 WILD-TYPE 1 8 60 543

Figure S40.  Get High-res Image Gene #52: 'AHNAK2 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'TTLL6 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.0129 (Fisher's exact test), Q value = 0.23

Table S41.  Gene #54: 'TTLL6 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 337 95 221 10
TTLL6 MUTATED 1 4 1 0
TTLL6 WILD-TYPE 336 91 220 10

Figure S41.  Get High-res Image Gene #54: 'TTLL6 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'AMAC1L3 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00024 (Fisher's exact test), Q value = 0.015

Table S42.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 161
AMAC1L3 MUTATED 5 1 2
AMAC1L3 WILD-TYPE 61 435 159

Figure S42.  Get High-res Image Gene #55: 'AMAC1L3 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/20230417/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/19775252/KIPAN-TP.merged_data.txt

  • Number of patients = 663

  • Number of significantly mutated genes = 57

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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