Correlation between gene mutation status and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C17D2T4V
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/C17D2T4V
Overview
Introduction

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

Summary

Testing the association between mutation status of 151 genes and 12 clinical features across 967 patients, 24 significant findings detected with Q value < 0.25.

  • PIK3CA mutation correlated to 'HISTOLOGICAL_TYPE'.

  • TP53 mutation correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • CDH1 mutation correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • MLL3 mutation correlated to 'YEARS_TO_BIRTH'.

  • FOXA1 mutation correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • SPEN mutation correlated to 'YEARS_TO_BIRTH'.

  • RAB42 mutation correlated to 'Time to Death'.

  • TGS1 mutation correlated to 'YEARS_TO_BIRTH'.

  • EIF4A2 mutation correlated to 'PATHOLOGY_N_STAGE'.

  • NBPF9 mutation correlated to 'PATHOLOGY_M_STAGE'.

  • RHOA mutation correlated to 'PATHOLOGY_T_STAGE'.

  • LRIG2 mutation correlated to 'Time to Death'.

  • C11ORF49 mutation correlated to 'PATHOLOGY_T_STAGE'.

  • SP3 mutation correlated to 'Time to Death'.

  • JAK1 mutation correlated to 'YEARS_TO_BIRTH'.

  • TRMT2A mutation correlated to 'Time to Death'.

  • CLEC18B mutation correlated to 'Time to Death'.

  • GIPC3 mutation correlated to 'NEOPLASM_DISEASESTAGE'.

  • CD244 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 151 genes and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 24 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES 		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 Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
TP53 290 (30%) 677 0.17
(1.00) 		0.00313
(0.249) 		0.292
(1.00) 		0.0261
(0.759) 		0.171
(1.00) 		0.258
(1.00) 		0.0645
(1.00) 		1e-05
(0.00302) 		0.122
(1.00) 		0.253
(1.00) 		1e-05
(0.00302) 		0.254
(1.00)
CDH1 104 (11%) 863 0.073
(1.00) 		0.0289
(0.759) 		0.0476
(0.925) 		1e-05
(0.00302) 		0.00253
(0.249) 		0.384
(1.00) 		0.609
(1.00) 		1e-05
(0.00302) 		0.00421
(0.294) 		0.958
(1.00) 		0.43
(1.00) 		1
(1.00)
FOXA1 22 (2%) 945 0.00145
(0.164) 		0.000194
(0.0352) 		0.381
(1.00) 		0.314
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00) 		0.016
(0.708) 		0.152
(1.00) 		0.501
(1.00) 		0.528
(1.00) 		0.506
(1.00)
PIK3CA 313 (32%) 654 0.59
(1.00) 		0.0347
(0.827) 		0.315
(1.00) 		0.731
(1.00) 		0.909
(1.00) 		1
(1.00) 		1
(1.00) 		0.00036
(0.0593) 		1
(1.00) 		0.589
(1.00) 		0.0859
(1.00) 		0.575
(1.00)
MLL3 68 (7%) 899 0.228
(1.00) 		5.26e-05
(0.0136) 		0.418
(1.00) 		0.6
(1.00) 		0.116
(1.00) 		0.286
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.491
(1.00) 		0.806
(1.00) 		0.2
(1.00) 		0.505
(1.00)
SPEN 32 (3%) 935 0.233
(1.00) 		0.000962
(0.124) 		0.57
(1.00) 		0.14
(1.00) 		0.99
(1.00) 		1
(1.00) 		1
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.957
(1.00) 		0.328
(1.00) 		1
(1.00)
RAB42 4 (0%) 963 6.78e-09
(6.15e-06) 		0.866
(1.00) 		0.598
(1.00) 		0.65
(1.00) 		0.845
(1.00) 		1
(1.00) 		1
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.869
(1.00) 		0.107
(1.00) 		1
(1.00)
TGS1 13 (1%) 954 0.918
(1.00) 		0.000676
(0.0962) 		0.784
(1.00) 		0.861
(1.00) 		0.196
(1.00) 		1
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.367
(1.00) 		0.261
(1.00) 		1
(1.00) 		0.326
(1.00)
EIF4A2 9 (1%) 958 0.824
(1.00) 		0.0203
(0.728) 		0.102
(1.00) 		0.0284
(0.759) 		0.00293
(0.249) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0657
(1.00) 		0.891
(1.00) 		0.043
(0.903) 		1
(1.00)
NBPF9 5 (1%) 962 0.552
(1.00) 		0.452
(1.00) 		0.00571
(0.383) 		0.31
(1.00) 		0.585
(1.00) 		0.00281
(0.249) 		1
(1.00) 		0.751
(1.00) 		0.329
(1.00) 		1
(1.00)
RHOA 5 (1%) 962 0.84
(1.00) 		0.191
(1.00) 		0.257
(1.00) 		0.0033
(0.249) 		0.0295
(0.759) 		1
(1.00) 		1
(1.00) 		0.535
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
LRIG2 7 (1%) 960 0.000176
(0.0352) 		0.387
(1.00) 		0.894
(1.00) 		0.899
(1.00) 		0.737
(1.00) 		1
(1.00) 		1
(1.00) 		0.567
(1.00) 		0.422
(1.00) 		0.45
(1.00) 		1
(1.00) 		1
(1.00)
C11ORF49 4 (0%) 963 0.139
(1.00) 		0.0505
(0.954) 		0.269
(1.00) 		0.0018
(0.192) 		0.298
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.3
(1.00) 		0.489
(1.00) 		1
(1.00)
SP3 7 (1%) 960 0.000111
(0.0251) 		0.314
(1.00) 		0.0528
(0.986) 		0.572
(1.00) 		0.843
(1.00) 		0.0852
(1.00) 		1
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.755
(1.00) 		1
(1.00)
JAK1 11 (1%) 956 0.0138
(0.657) 		0.00313
(0.249) 		0.549
(1.00) 		0.829
(1.00) 		0.588
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.814
(1.00) 		0.524
(1.00) 		0.124
(1.00) 		0.756
(1.00) 		1
(1.00)
TRMT2A 7 (1%) 960 0.00327
(0.249) 		0.254
(1.00) 		0.989
(1.00) 		0.0656
(1.00) 		0.239
(1.00) 		1
(1.00) 		1
(1.00) 		0.814
(1.00) 		0.68
(1.00) 		0.106
(1.00) 		0.17
(1.00) 		1
(1.00)
CLEC18B 6 (1%) 961 0.00121
(0.146) 		0.999
(1.00) 		0.178
(1.00) 		0.0157
(0.708) 		0.559
(1.00) 		1
(1.00) 		1
(1.00) 		0.0415
(0.903) 		0.678
(1.00) 		0.125
(1.00) 		0.398
(1.00) 		1
(1.00)
GIPC3 4 (0%) 963 0.306
(1.00) 		0.621
(1.00) 		0.00069
(0.0962) 		0.0132
(0.657) 		0.602
(1.00) 		1
(1.00) 		1
(1.00) 		0.346
(1.00) 		0.328
(1.00) 		0.106
(1.00) 		1
(1.00) 		1
(1.00)
CD244 3 (0%) 964 0
(0) 		0.259
(1.00) 		0.918
(1.00) 		0.416
(1.00) 		1
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.56
(1.00) 		1
(1.00)
GATA3 96 (10%) 871 0.546
(1.00) 		0.00928
(0.529) 		0.205
(1.00) 		0.113
(1.00) 		0.426
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.0241
(0.754) 		0.123
(1.00) 		0.125
(1.00) 		0.332
(1.00) 		0.77
(1.00)
MAP3K1 69 (7%) 898 0.982
(1.00) 		0.00886
(0.529) 		0.565
(1.00) 		0.351
(1.00) 		0.888
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.785
(1.00) 		0.267
(1.00) 		0.94
(1.00) 		0.285
(1.00)
RUNX1 29 (3%) 938 0.531
(1.00) 		0.8
(1.00) 		0.234
(1.00) 		0.433
(1.00) 		0.355
(1.00) 		1
(1.00) 		1
(1.00) 		0.00874
(0.529) 		0.68
(1.00) 		0.162
(1.00) 		0.362
(1.00) 		0.587
(1.00)
PTEN 35 (4%) 932 0.719
(1.00) 		0.0986
(1.00) 		0.444
(1.00) 		0.138
(1.00) 		0.508
(1.00) 		0.084
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.455
(1.00) 		0.235
(1.00) 		1
(1.00) 		1
(1.00)
ARID1A 27 (3%) 940 0.568
(1.00) 		0.989
(1.00) 		0.488
(1.00) 		0.344
(1.00) 		0.271
(1.00) 		1
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.669
(1.00) 		0.482
(1.00) 		0.201
(1.00) 		0.528
(1.00)
CBFB 23 (2%) 944 0.632
(1.00) 		0.983
(1.00) 		0.349
(1.00) 		0.166
(1.00) 		0.0675
(1.00) 		0.302
(1.00) 		0.196
(1.00) 		0.682
(1.00) 		1
(1.00) 		0.408
(1.00) 		0.4
(1.00) 		0.548
(1.00)
MAP2K4 32 (3%) 935 0.81
(1.00) 		0.404
(1.00) 		0.937
(1.00) 		0.304
(1.00) 		0.456
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.204
(1.00) 		0.695
(1.00) 		0.293
(1.00) 		0.675
(1.00) 		1
(1.00)
RBMX 14 (1%) 953 0.625
(1.00) 		0.549
(1.00) 		0.808
(1.00) 		0.382
(1.00) 		0.0407
(0.903) 		1
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.768
(1.00) 		0.982
(1.00) 		0.889
(1.00) 		1
(1.00)
TBX3 27 (3%) 940 0.261
(1.00) 		0.0711
(1.00) 		0.337
(1.00) 		0.8
(1.00) 		0.424
(1.00) 		1
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.832
(1.00) 		0.413
(1.00) 		0.402
(1.00) 		1
(1.00)
RB1 19 (2%) 948 0.517
(1.00) 		0.275
(1.00) 		0.143
(1.00) 		0.34
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.164
(1.00) 		0.7
(1.00) 		0.307
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.528
(1.00)
THEM5 11 (1%) 956 0.474
(1.00) 		0.189
(1.00) 		0.787
(1.00) 		0.0369
(0.846) 		0.369
(1.00) 		1
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.739
(1.00) 		0.618
(1.00) 		0.357
(1.00) 		0.326
(1.00)
NF1 26 (3%) 941 0.297
(1.00) 		0.126
(1.00) 		0.116
(1.00) 		0.156
(1.00) 		0.204
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.131
(1.00) 		0.157
(1.00) 		0.404
(1.00) 		1
(1.00)
ACTL6B 10 (1%) 957 0.758
(1.00) 		0.074
(1.00) 		0.387
(1.00) 		0.141
(1.00) 		0.234
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.873
(1.00) 		0.663
(1.00) 		1
(1.00)
CDKN1B 10 (1%) 957 0.725
(1.00) 		0.596
(1.00) 		0.114
(1.00) 		0.0478
(0.925) 		0.0213
(0.728) 		0.133
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.732
(1.00) 		0.0749
(1.00) 		0.754
(1.00) 		1
(1.00)
NCOR1 41 (4%) 926 0.901
(1.00) 		0.454
(1.00) 		0.971
(1.00) 		0.568
(1.00) 		0.965
(1.00) 		1
(1.00) 		1
(1.00) 		0.592
(1.00) 		0.599
(1.00) 		0.982
(1.00) 		0.294
(1.00) 		0.392
(1.00)
SF3B1 16 (2%) 951 0.335
(1.00) 		0.406
(1.00) 		0.449
(1.00) 		0.394
(1.00) 		0.816
(1.00) 		1
(1.00) 		1
(1.00) 		0.824
(1.00) 		0.788
(1.00) 		0.965
(1.00) 		0.783
(1.00) 		1
(1.00)
ZFP36L1 9 (1%) 958 0.0907
(1.00) 		0.244
(1.00) 		0.822
(1.00) 		0.785
(1.00) 		0.894
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.461
(1.00) 		0.522
(1.00) 		0.182
(1.00) 		1
(1.00)
KRAS 6 (1%) 961 0.356
(1.00) 		0.123
(1.00) 		0.811
(1.00) 		0.881
(1.00) 		0.905
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.0929
(1.00) 		1
(1.00)
AQP12A 6 (1%) 961 0.519
(1.00) 		0.326
(1.00) 		0.844
(1.00) 		0.669
(1.00) 		0.239
(1.00) 		1
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.365
(1.00) 		0.366
(1.00) 		0.67
(1.00) 		1
(1.00)
DLG1 13 (1%) 954 0.601
(1.00) 		0.515
(1.00) 		0.796
(1.00) 		0.668
(1.00) 		0.657
(1.00) 		1
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.766
(1.00) 		0.218
(1.00) 		0.581
(1.00) 		1
(1.00)
TCP11 6 (1%) 961 0.0856
(1.00) 		0.835
(1.00) 		0.739
(1.00) 		0.407
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		0.253
(1.00) 		0.678
(1.00) 		0.188
(1.00) 		0.672
(1.00) 		1
(1.00)
MYB 12 (1%) 955 0.194
(1.00) 		0.173
(1.00) 		0.478
(1.00) 		0.449
(1.00) 		0.965
(1.00) 		1
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.347
(1.00) 		0.29
(1.00) 		1
(1.00) 		1
(1.00)
RPGR 19 (2%) 948 0.981
(1.00) 		0.276
(1.00) 		0.411
(1.00) 		0.702
(1.00) 		0.0902
(1.00) 		1
(1.00) 		1
(1.00) 		0.796
(1.00) 		1
(1.00) 		0.138
(1.00) 		0.528
(1.00) 		1
(1.00)
TBL1XR1 10 (1%) 957 0.769
(1.00) 		0.237
(1.00) 		0.0783
(1.00) 		0.0764
(1.00) 		0.029
(0.759) 		0.164
(1.00) 		1
(1.00) 		0.519
(1.00) 		1
(1.00) 		0.867
(1.00) 		0.777
(1.00) 		1
(1.00)
KDM6A 16 (2%) 951 0.846
(1.00) 		0.103
(1.00) 		0.915
(1.00) 		0.503
(1.00) 		0.0599
(1.00) 		1
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.422
(1.00) 		0.741
(1.00) 		1
(1.00) 		1
(1.00)
MYH9 18 (2%) 949 0.651
(1.00) 		0.295
(1.00) 		0.641
(1.00) 		0.915
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.116
(1.00) 		0.293
(1.00) 		0.265
(1.00) 		1
(1.00)
HLA-C 9 (1%) 958 0.579
(1.00) 		0.172
(1.00) 		0.922
(1.00) 		0.224
(1.00) 		0.895
(1.00) 		1
(1.00) 		1
(1.00) 		0.87
(1.00) 		0.725
(1.00) 		0.627
(1.00) 		0.777
(1.00) 		1
(1.00)
FGFR2 11 (1%) 956 0.653
(1.00) 		0.554
(1.00) 		0.479
(1.00) 		0.0116
(0.639) 		0.674
(1.00) 		1
(1.00) 		0.0982
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.154
(1.00) 		0.664
(1.00) 		1
(1.00)
TFE3 7 (1%) 960 0.235
(1.00) 		0.429
(1.00) 		0.846
(1.00) 		0.901
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.771
(1.00) 		1
(1.00) 		1
(1.00)
ZMYM3 14 (1%) 953 0.581
(1.00) 		0.554
(1.00) 		0.578
(1.00) 		0.876
(1.00) 		0.669
(1.00) 		0.222
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.538
(1.00) 		0.287
(1.00) 		1
(1.00)
ERBB2 21 (2%) 946 0.0459
(0.923) 		0.0863
(1.00) 		0.521
(1.00) 		0.166
(1.00) 		0.078
(1.00) 		1
(1.00) 		0.18
(1.00) 		0.672
(1.00) 		0.809
(1.00) 		0.31
(1.00) 		0.16
(1.00) 		0.46
(1.00)
CTCF 17 (2%) 950 0.0807
(1.00) 		0.582
(1.00) 		0.232
(1.00) 		0.175
(1.00) 		0.646
(1.00) 		1
(1.00) 		1
(1.00) 		0.243
(1.00) 		0.421
(1.00) 		0.346
(1.00) 		0.475
(1.00) 		0.484
(1.00)
FRMPD2 11 (1%) 956 0.591
(1.00) 		0.658
(1.00) 		0.416
(1.00) 		0.0186
(0.728) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.746
(1.00) 		1
(1.00) 		0.526
(1.00) 		0.664
(1.00) 		0.326
(1.00)
GPS2 11 (1%) 956 0.403
(1.00) 		0.117
(1.00) 		0.875
(1.00) 		0.114
(1.00) 		0.61
(1.00) 		1
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.739
(1.00) 		0.492
(1.00) 		0.58
(1.00) 		0.383
(1.00)
DOCK11 20 (2%) 947 0.631
(1.00) 		0.676
(1.00) 		0.891
(1.00) 		0.948
(1.00) 		0.282
(1.00) 		1
(1.00) 		1
(1.00) 		0.069
(1.00) 		0.807
(1.00) 		0.0339
(0.818) 		0.615
(1.00) 		1
(1.00)
HRNR 31 (3%) 936 0.132
(1.00) 		0.249
(1.00) 		0.159
(1.00) 		0.122
(1.00) 		0.12
(1.00) 		1
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.234
(1.00) 		0.626
(1.00) 		0.7
(1.00) 		0.306
(1.00)
CASZ1 14 (1%) 953 0.605
(1.00) 		0.858
(1.00) 		0.834
(1.00) 		0.506
(1.00) 		0.937
(1.00) 		1
(1.00) 		1
(1.00) 		0.741
(1.00) 		0.373
(1.00) 		0.838
(1.00) 		0.61
(1.00) 		1
(1.00)
CDC42EP1 5 (1%) 962 0.406
(1.00) 		0.317
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.467
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		1
(1.00) 		1
(1.00)
C1QTNF5 7 (1%) 960 0.367
(1.00) 		0.899
(1.00) 		0.0187
(0.728) 		0.426
(1.00) 		0.678
(1.00) 		1
(1.00) 		1
(1.00) 		0.81
(1.00) 		0.68
(1.00) 		0.589
(1.00) 		1
(1.00) 		1
(1.00)
USP36 8 (1%) 959 0.537
(1.00) 		0.141
(1.00) 		0.031
(0.779) 		0.134
(1.00) 		0.573
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.449
(1.00) 		0.587
(1.00) 		0.473
(1.00) 		1
(1.00)
ASB10 8 (1%) 959 0.0922
(1.00) 		0.515
(1.00) 		0.69
(1.00) 		0.762
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.0234
(0.754) 		0.264
(1.00)
DNAH12 18 (2%) 949 0.447
(1.00) 		0.682
(1.00) 		0.439
(1.00) 		0.615
(1.00) 		0.113
(1.00) 		1
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.794
(1.00) 		0.0442
(0.91) 		0.664
(1.00) 		1
(1.00)
RHBG 4 (0%) 963 0.0283
(0.759) 		0.0491
(0.936) 		0.8
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ZNF362 5 (1%) 962 0.463
(1.00) 		0.254
(1.00) 		0.329
(1.00) 		0.373
(1.00) 		0.245
(1.00) 		1
(1.00) 		1
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.0619
(1.00) 		1
(1.00) 		1
(1.00)
FXYD5 4 (0%) 963 0.788
(1.00) 		0.906
(1.00) 		0.661
(1.00) 		0.15
(1.00) 		0.842
(1.00) 		1
(1.00) 		1
(1.00) 		0.439
(1.00) 		1
(1.00) 		0.368
(1.00) 		1
(1.00) 		1
(1.00)
BCORL1 14 (1%) 953 0.216
(1.00) 		0.476
(1.00) 		0.809
(1.00) 		0.317
(1.00) 		0.122
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.703
(1.00) 		0.768
(1.00) 		0.308
(1.00) 		0.198
(1.00) 		0.383
(1.00)
PTHLH 7 (1%) 960 0.463
(1.00) 		0.319
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.137
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.68
(1.00) 		0.0619
(1.00) 		0.399
(1.00) 		1
(1.00)
PIK3R1 15 (2%) 952 0.0179
(0.728) 		0.243
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.35
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.514
(1.00) 		1
(1.00) 		0.31
(1.00) 		0.317
(1.00) 		1
(1.00)
ZNF687 11 (1%) 956 0.91
(1.00) 		0.738
(1.00) 		0.991
(1.00) 		0.935
(1.00) 		0.851
(1.00) 		1
(1.00) 		1
(1.00) 		0.901
(1.00) 		0.09
(1.00) 		0.392
(1.00) 		0.357
(1.00) 		1
(1.00)
GPRIN2 11 (1%) 956 0.998
(1.00) 		0.222
(1.00) 		0.654
(1.00) 		0.935
(1.00) 		0.366
(1.00) 		1
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.739
(1.00) 		0.113
(1.00) 		0.254
(1.00) 		1
(1.00)
ANKRD12 18 (2%) 949 0.199
(1.00) 		0.0424
(0.903) 		0.764
(1.00) 		0.716
(1.00) 		0.562
(1.00) 		1
(1.00) 		1
(1.00) 		0.459
(1.00) 		0.303
(1.00) 		0.063
(1.00) 		0.889
(1.00) 		1
(1.00)
PAX2 4 (0%) 963 0.186
(1.00) 		0.144
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.842
(1.00) 		1
(1.00) 		1
(1.00) 		0.712
(1.00) 		0.585
(1.00) 		0.212
(1.00) 		1
(1.00) 		1
(1.00)
KCNN3 9 (1%) 958 0.404
(1.00) 		0.725
(1.00) 		0.637
(1.00) 		0.412
(1.00) 		0.511
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.809
(1.00) 		0.477
(1.00) 		0.296
(1.00)
ICOSLG 5 (1%) 962 0.781
(1.00) 		0.864
(1.00) 		0.267
(1.00) 		0.715
(1.00) 		0.605
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.632
(1.00) 		0.626
(1.00) 		0.591
(1.00) 		1
(1.00)
MR1 7 (1%) 960 0.669
(1.00) 		0.715
(1.00) 		0.191
(1.00) 		0.0734
(1.00) 		0.246
(1.00) 		1
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.68
(1.00) 		0.0619
(1.00) 		0.74
(1.00) 		1
(1.00)
ZBTB7C 5 (1%) 962 0.47
(1.00) 		0.534
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.169
(1.00) 		1
(1.00) 		1
(1.00) 		0.254
(1.00) 		0.329
(1.00) 		0.17
(1.00) 		1
(1.00) 		1
(1.00)
CABYR 6 (1%) 961 0.487
(1.00) 		0.572
(1.00) 		0.615
(1.00) 		1
(1.00) 		0.736
(1.00) 		1
(1.00) 		1
(1.00) 		0.78
(1.00) 		0.365
(1.00) 		0.924
(1.00) 		0.346
(1.00) 		1
(1.00)
AKT2 5 (1%) 962 0.621
(1.00) 		0.846
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.518
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.329
(1.00) 		0.514
(1.00) 		0.317
(1.00) 		1
(1.00)
TARBP2 6 (1%) 961 0.479
(1.00) 		0.46
(1.00) 		0.696
(1.00) 		1
(1.00) 		0.288
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.905
(1.00) 		1
(1.00) 		1
(1.00)
RIBC1 4 (0%) 963 0.809
(1.00) 		0.891
(1.00) 		0.489
(1.00) 		0.524
(1.00) 		0.224
(1.00) 		1
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.328
(1.00) 		0.23
(1.00) 		1
(1.00)
PSIP1 8 (1%) 959 0.12
(1.00) 		0.267
(1.00) 		0.243
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.503
(1.00) 		0.449
(1.00) 		0.673
(1.00) 		0.304
(1.00) 		1
(1.00)
CEP57 6 (1%) 961 0.195
(1.00) 		0.445
(1.00) 		0.556
(1.00) 		0.772
(1.00) 		0.352
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.638
(1.00) 		0.672
(1.00) 		1
(1.00)
ANKRD20A4 7 (1%) 960 0.57
(1.00) 		0.473
(1.00) 		0.369
(1.00) 		0.229
(1.00) 		0.234
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.0626
(1.00) 		1
(1.00) 		1
(1.00)
HIST1H3B 11 (1%) 956 0.885
(1.00) 		0.0128
(0.657) 		0.369
(1.00) 		0.547
(1.00) 		0.816
(1.00) 		1
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.739
(1.00) 		0.186
(1.00) 		0.8
(1.00) 		1
(1.00)
MED23 14 (1%) 953 0.343
(1.00) 		0.0359
(0.845) 		0.238
(1.00) 		0.335
(1.00) 		0.773
(1.00) 		1
(1.00) 		1
(1.00) 		0.638
(1.00) 		0.25
(1.00) 		0.361
(1.00) 		0.321
(1.00) 		1
(1.00)
MUC6 14 (1%) 953 0.372
(1.00) 		0.39
(1.00) 		0.738
(1.00) 		0.772
(1.00) 		0.103
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.0929
(1.00) 		0.768
(1.00) 		0.418
(1.00) 		0.165
(1.00) 		1
(1.00)
ANGPT4 9 (1%) 958 0.213
(1.00) 		0.489
(1.00) 		0.545
(1.00) 		0.0212
(0.728) 		0.729
(1.00) 		1
(1.00) 		1
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.522
(1.00) 		0.13
(1.00) 		1
(1.00)
PCNXL2 21 (2%) 946 0.169
(1.00) 		0.0297
(0.759) 		0.408
(1.00) 		0.541
(1.00) 		0.868
(1.00) 		1
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.809
(1.00) 		0.939
(1.00) 		0.812
(1.00) 		1
(1.00)
SLC35B2 7 (1%) 960 0.982
(1.00) 		0.865
(1.00) 		0.959
(1.00) 		0.802
(1.00) 		0.297
(1.00) 		1
(1.00) 		1
(1.00) 		0.4
(1.00) 		0.422
(1.00) 		0.992
(1.00) 		0.473
(1.00) 		1
(1.00)
MKL1 5 (1%) 962 0.812
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.605
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.329
(1.00) 		0.0222
(0.747) 		1
(1.00)
PRICKLE3 11 (1%) 956 0.957
(1.00) 		0.291
(1.00) 		0.0322
(0.789) 		0.0209
(0.728) 		0.953
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.536
(1.00) 		0.191
(1.00) 		0.176
(1.00) 		0.398
(1.00) 		1
(1.00)
CCDC82 6 (1%) 961 0.0865
(1.00) 		0.273
(1.00) 		0.93
(1.00) 		0.881
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.189
(1.00) 		0.106
(1.00) 		0.0614
(1.00) 		1
(1.00)
CXCR3 6 (1%) 961 0.0719
(1.00) 		0.653
(1.00) 		0.201
(1.00) 		0.048
(0.925) 		0.165
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.0895
(1.00) 		1
(1.00) 		0.54
(1.00) 		0.397
(1.00) 		1
(1.00)
TPP2 8 (1%) 959 0.558
(1.00) 		0.368
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.28
(1.00) 		1
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.114
(1.00) 		0.0418
(0.903) 		0.238
(1.00) 		1
(1.00)
C15ORF39 9 (1%) 958 0.437
(1.00) 		0.755
(1.00) 		0.924
(1.00) 		1
(1.00) 		0.177
(1.00) 		1
(1.00) 		1
(1.00) 		0.353
(1.00) 		0.461
(1.00) 		0.289
(1.00) 		0.609
(1.00) 		1
(1.00)
CASP8 12 (1%) 955 0.592
(1.00) 		0.42
(1.00) 		0.396
(1.00) 		0.846
(1.00) 		0.181
(1.00) 		1
(1.00) 		1
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.0269
(0.759) 		0.435
(1.00) 		1
(1.00)
TNRC6B 17 (2%) 950 0.85
(1.00) 		0.48
(1.00) 		0.704
(1.00) 		0.967
(1.00) 		0.315
(1.00) 		1
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.287
(1.00) 		0.623
(1.00) 		0.887
(1.00) 		0.436
(1.00)
OXCT2 4 (0%) 963 0.106
(1.00) 		0.437
(1.00) 		0.393
(1.00) 		0.0773
(1.00) 		0.687
(1.00) 		1
(1.00) 		1
(1.00) 		0.709
(1.00) 		1
(1.00) 		0.371
(1.00) 		1
(1.00) 		1
(1.00)
IRS4 11 (1%) 956 0.753
(1.00) 		0.292
(1.00) 		0.0753
(1.00) 		0.784
(1.00) 		0.0433
(0.903) 		0.164
(1.00) 		1
(1.00) 		0.536
(1.00) 		0.524
(1.00) 		0.486
(1.00) 		0.359
(1.00) 		1
(1.00)
MLL4 13 (1%) 954 0.032
(0.789) 		0.196
(1.00) 		0.932
(1.00) 		0.238
(1.00) 		0.732
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.287
(1.00) 		0.36
(1.00) 		1
(1.00)
ATHL1 10 (1%) 957 0.928
(1.00) 		0.24
(1.00) 		0.784
(1.00) 		0.67
(1.00) 		0.894
(1.00) 		1
(1.00) 		1
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.687
(1.00) 		1
(1.00)
LILRA6 6 (1%) 961 0.4
(1.00) 		0.658
(1.00) 		0.522
(1.00) 		0.772
(1.00) 		0.353
(1.00) 		1
(1.00) 		1
(1.00) 		0.626
(1.00) 		0.365
(1.00) 		0.638
(1.00) 		0.673
(1.00) 		1
(1.00)
SDC1 3 (0%) 964 0.319
(1.00) 		0.268
(1.00) 		0.117
(1.00) 		0.3
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MLH1 6 (1%) 961 0.623
(1.00) 		0.671
(1.00) 		0.931
(1.00) 		0.774
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.764
(1.00) 		0.476
(1.00) 		1
(1.00)
NUP93 4 (0%) 963 0.884
(1.00) 		0.845
(1.00) 		0.472
(1.00) 		0.648
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00) 		0.0134
(0.657) 		0.585
(1.00) 		0.994
(1.00) 		0.59
(1.00) 		1
(1.00)
ALDH1L1 8 (1%) 959 0.762
(1.00) 		0.343
(1.00) 		0.216
(1.00) 		0.108
(1.00) 		0.628
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.449
(1.00) 		0.935
(1.00) 		1
(1.00) 		1
(1.00)
TMEM120B 5 (1%) 962 0.487
(1.00) 		0.566
(1.00) 		0.468
(1.00) 		0.588
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.94
(1.00) 		0.174
(1.00) 		1
(1.00)
CCDC78 5 (1%) 962 0.0257
(0.759) 		0.708
(1.00) 		0.859
(1.00) 		0.439
(1.00) 		0.843
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.536
(1.00) 		0.395
(1.00) 		1
(1.00)
GAL3ST1 5 (1%) 962 0.991
(1.00) 		0.985
(1.00) 		0.491
(1.00) 		0.504
(1.00) 		0.692
(1.00) 		1
(1.00) 		1
(1.00) 		0.538
(1.00) 		0.329
(1.00) 		0.446
(1.00) 		0.171
(1.00) 		1
(1.00)
FAM20C 4 (0%) 963 0.325
(1.00) 		0.66
(1.00) 		0.658
(1.00) 		0.649
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.585
(1.00) 		0.729
(1.00) 		0.0129
(0.657) 		1
(1.00)
RCC1 3 (0%) 964 0.466
(1.00) 		0.378
(1.00) 		0.16
(1.00) 		0.149
(1.00) 		0.602
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.205
(1.00) 		0.106
(1.00) 		1
(1.00) 		1
(1.00)
CHD4 19 (2%) 948 0.809
(1.00) 		0.701
(1.00) 		0.21
(1.00) 		0.0201
(0.728) 		0.00657
(0.425) 		1
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.078
(1.00) 		0.962
(1.00) 		0.15
(1.00) 		1
(1.00)
STAG2 13 (1%) 954 0.0166
(0.708) 		0.0296
(0.759) 		0.568
(1.00) 		0.95
(1.00) 		0.922
(1.00) 		0.193
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.539
(1.00) 		0.671
(1.00) 		1
(1.00) 		1
(1.00)
HIST1H2BC 6 (1%) 961 0.372
(1.00) 		0.881
(1.00) 		0.586
(1.00) 		0.67
(1.00) 		0.822
(1.00) 		1
(1.00) 		1
(1.00) 		0.781
(1.00) 		0.678
(1.00) 		0.281
(1.00) 		0.736
(1.00) 		0.197
(1.00)
BPHL 5 (1%) 962 0.658
(1.00) 		0.547
(1.00) 		0.0788
(1.00) 		0.311
(1.00) 		0.691
(1.00) 		1
(1.00) 		1
(1.00) 		0.754
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.4
(1.00) 		1
(1.00)
ATP2A1 11 (1%) 956 0.0248
(0.759) 		0.0939
(1.00) 		0.551
(1.00) 		0.785
(1.00) 		0.102
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.0259
(0.759) 		1
(1.00) 		0.57
(1.00) 		0.844
(1.00) 		1
(1.00)
LRRC37A3 9 (1%) 958 0.292
(1.00) 		0.73
(1.00) 		0.454
(1.00) 		0.209
(1.00) 		0.215
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.0685
(1.00) 		0.755
(1.00) 		0.231
(1.00)
EPDR1 5 (1%) 962 0.488
(1.00) 		0.408
(1.00) 		0.419
(1.00) 		0.373
(1.00) 		0.215
(1.00) 		1
(1.00) 		1
(1.00) 		0.539
(1.00) 		0.632
(1.00) 		0.584
(1.00) 		0.316
(1.00) 		1
(1.00)
EXOC4 8 (1%) 959 0.0662
(1.00) 		0.14
(1.00) 		0.119
(1.00) 		0.763
(1.00) 		0.0233
(0.754) 		1
(1.00) 		1
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.299
(1.00) 		1
(1.00)
SARM1 6 (1%) 961 0.392
(1.00) 		0.0266
(0.759) 		0.38
(1.00) 		0.207
(1.00) 		0.871
(1.00) 		1
(1.00) 		1
(1.00) 		0.78
(1.00) 		0.678
(1.00) 		0.0619
(1.00) 		0.672
(1.00) 		1
(1.00)
ACTG1 8 (1%) 959 0.349
(1.00) 		0.24
(1.00) 		0.289
(1.00) 		0.835
(1.00) 		0.445
(1.00) 		1
(1.00) 		1
(1.00) 		0.561
(1.00) 		0.449
(1.00) 		0.417
(1.00) 		0.422
(1.00) 		1
(1.00)
ANXA11 3 (0%) 964 0.546
(1.00) 		0.698
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.6
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.488
(1.00) 		1
(1.00)
OR8D1 5 (1%) 962 0.322
(1.00) 		0.494
(1.00) 		0.485
(1.00) 		0.436
(1.00) 		0.873
(1.00) 		1
(1.00) 		1
(1.00) 		0.751
(1.00) 		0.632
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.16
(1.00)
GYLTL1B 4 (0%) 963 0.454
(1.00) 		0.362
(1.00) 		0.385
(1.00) 		0.32
(1.00) 		0.692
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.368
(1.00) 		1
(1.00) 		1
(1.00)
ANGPTL6 3 (0%) 964 0.603
(1.00) 		0.307
(1.00) 		0.409
(1.00) 		0.292
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0868
(1.00) 		1
(1.00) 		1
(1.00)
PFKP 7 (1%) 960 0.763
(1.00) 		0.461
(1.00) 		0.652
(1.00) 		0.718
(1.00) 		0.588
(1.00) 		1
(1.00) 		1
(1.00) 		0.684
(1.00) 		0.203
(1.00) 		0.0979
(1.00) 		0.755
(1.00) 		1
(1.00)
SPTAN1 11 (1%) 956 0.0465
(0.925) 		0.174
(1.00) 		0.462
(1.00) 		0.881
(1.00) 		0.472
(1.00) 		1
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.314
(1.00) 		0.339
(1.00) 		0.0168
(0.708) 		1
(1.00)
LIFR 9 (1%) 958 0.776
(1.00) 		0.0587
(1.00) 		0.6
(1.00) 		0.269
(1.00) 		0.852
(1.00) 		1
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.725
(1.00) 		0.773
(1.00) 		0.665
(1.00) 		1
(1.00)
TTPAL 4 (0%) 963 0.52
(1.00) 		0.834
(1.00) 		0.179
(1.00) 		0.794
(1.00) 		0.222
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.106
(1.00) 		1
(1.00) 		1
(1.00)
HCFC2 10 (1%) 957 0.688
(1.00) 		0.0674
(1.00) 		0.993
(1.00) 		0.594
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.297
(1.00) 		0.577
(1.00) 		0.132
(1.00) 		1
(1.00)
OR6C76 7 (1%) 960 0.361
(1.00) 		0.0806
(1.00) 		0.283
(1.00) 		0.717
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.0636
(1.00) 		0.811
(1.00) 		0.422
(1.00) 		0.0745
(1.00) 		0.299
(1.00) 		0.231
(1.00)
ACOT2 5 (1%) 962 0.351
(1.00) 		0.631
(1.00) 		0.212
(1.00) 		0.374
(1.00) 		0.461
(1.00) 		1
(1.00) 		1
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.317
(1.00) 		1
(1.00)
KIAA0430 15 (2%) 952 0.045
(0.916) 		0.246
(1.00) 		0.779
(1.00) 		0.72
(1.00) 		0.549
(1.00) 		1
(1.00) 		1
(1.00) 		0.135
(1.00) 		0.254
(1.00) 		0.0792
(1.00) 		0.507
(1.00) 		1
(1.00)
SEC14L5 7 (1%) 960 0.831
(1.00) 		0.785
(1.00) 		0.289
(1.00) 		0.773
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00) 		0.683
(1.00) 		0.203
(1.00) 		0.929
(1.00) 		0.424
(1.00) 		1
(1.00)
GTF2IRD2 8 (1%) 959 0.0969
(1.00) 		0.021
(0.728) 		0.749
(1.00) 		0.533
(1.00) 		0.729
(1.00) 		1
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.449
(1.00) 		0.555
(1.00) 		1
(1.00) 		1
(1.00)
FGFR3 4 (0%) 963 0.768
(1.00) 		0.259
(1.00) 		0.588
(1.00) 		0.793
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.024
(0.754) 		1
(1.00) 		0.536
(1.00) 		0.488
(1.00) 		1
(1.00)
FBXW7 15 (2%) 952 0.664
(1.00) 		0.419
(1.00) 		0.586
(1.00) 		0.187
(1.00) 		0.68
(1.00) 		1
(1.00) 		1
(1.00) 		0.805
(1.00) 		1
(1.00) 		0.293
(1.00) 		0.0427
(0.903) 		0.41
(1.00)
SHANK2 15 (2%) 952 0.253
(1.00) 		0.0968
(1.00) 		0.303
(1.00) 		0.191
(1.00) 		0.522
(1.00) 		1
(1.00) 		1
(1.00) 		0.376
(1.00) 		0.573
(1.00) 		0.316
(1.00) 		0.162
(1.00) 		0.41
(1.00)
CCNL2 7 (1%) 960 0.29
(1.00) 		0.852
(1.00) 		0.874
(1.00) 		0.513
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		0.812
(1.00) 		0.68
(1.00) 		0.0619
(1.00) 		1
(1.00) 		1
(1.00)
RUFY1 6 (1%) 961 0.0207
(0.728) 		0.0145
(0.674) 		0.569
(1.00) 		0.233
(1.00) 		0.906
(1.00) 		1
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.189
(1.00) 		0.287
(1.00) 		0.396
(1.00) 		1
(1.00)
HPS3 9 (1%) 958 0.618
(1.00) 		0.589
(1.00) 		0.783
(1.00) 		0.68
(1.00) 		0.356
(1.00) 		1
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.295
(1.00) 		0.948
(1.00) 		1
(1.00) 		1
(1.00)
OR2T35 4 (0%) 963 0.735
(1.00) 		0.519
(1.00) 		0.213
(1.00) 		0.793
(1.00) 		0.319
(1.00) 		1
(1.00) 		1
(1.00) 		0.71
(1.00) 		0.585
(1.00) 		0.807
(1.00) 		1
(1.00) 		1
(1.00)
PPIL2 6 (1%) 961 0.385
(1.00) 		0.989
(1.00) 		0.941
(1.00) 		0.18
(1.00) 		0.822
(1.00) 		1
(1.00) 		1
(1.00) 		0.00935
(0.529) 		0.678
(1.00) 		0.671
(1.00) 		0.0425
(0.903) 		1
(1.00)
NPAS4 9 (1%) 958 0.891
(1.00) 		0.953
(1.00) 		0.316
(1.00) 		0.367
(1.00) 		0.415
(1.00) 		1
(1.00) 		1
(1.00) 		0.351
(1.00) 		0.295
(1.00) 		0.32
(1.00) 		0.0692
(1.00) 		1
(1.00)
SHISA4 5 (1%) 962 0.438
(1.00) 		0.942
(1.00) 		0.771
(1.00) 		0.503
(1.00) 		0.52
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.632
(1.00) 		0.804
(1.00) 		1
(1.00) 		1
(1.00)
MLL 17 (2%) 950 0.69
(1.00) 		0.879
(1.00) 		0.819
(1.00) 		0.432
(1.00) 		0.213
(1.00) 		1
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.79
(1.00) 		0.217
(1.00) 		0.492
(1.00) 		1
(1.00)
ACVR1B 7 (1%) 960 0.486
(1.00) 		0.278
(1.00) 		0.185
(1.00) 		0.642
(1.00) 		0.56
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.683
(1.00) 		1
(1.00) 		0.0367
(0.846) 		1
(1.00) 		1
(1.00)
GPR158 3 (0%) 964 0.47
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.732
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.486
(1.00) 		1
(1.00)
ARHGEF15 9 (1%) 958 0.432
(1.00) 		0.346
(1.00) 		0.675
(1.00) 		0.208
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.476
(1.00) 		1
(1.00)
ZNF397 7 (1%) 960 0.262
(1.00) 		0.169
(1.00) 		0.857
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.327
(1.00) 		1
(1.00) 		1
(1.00)
COL9A2 3 (0%) 964 0.711
(1.00) 		0.411
(1.00) 		0.92
(1.00) 		0.732
(1.00) 		0.487
(1.00) 		1
(1.00) 		1
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.531
(1.00) 		1
(1.00) 		1
(1.00)
TXNDC2 4 (0%) 963 0.7
(1.00) 		0.475
(1.00) 		0.342
(1.00) 		0.0778
(1.00) 		0.764
(1.00) 		1
(1.00) 		1
(1.00) 		0.709
(1.00) 		1
(1.00) 		0.00396
(0.287) 		1
(1.00)
'PIK3CA MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00036 (Fisher's exact test), Q value = 0.059

Table S1.  Gene #1: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 164 5 1 27 14 44
PIK3CA MUTATED 0 216 71 0 0 13 0 13
PIK3CA WILD-TYPE 1 494 93 5 1 14 14 31

Figure S1.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00313 (Wilcoxon-test), Q value = 0.25

Table S2.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 954 58.7 (13.1)
TP53 MUTATED 285 56.9 (12.2)
TP53 WILD-TYPE 669 59.5 (13.4)

Figure S2.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S3.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 164 5 1 27 14 44
TP53 MUTATED 1 256 9 3 1 5 1 13
TP53 WILD-TYPE 0 454 155 2 0 22 13 31

Figure S3.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S4.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 57 116 698
TP53 MUTATED 1 29 50 189
TP53 WILD-TYPE 0 28 66 509

Figure S4.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'

'CDH1 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S5.  Gene #3: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 257 559 114 35
CDH1 MUTATED 16 55 31 2
CDH1 WILD-TYPE 241 504 83 33

Figure S5.  Get High-res Image Gene #3: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'CDH1 MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 0.00253 (Fisher's exact test), Q value = 0.25

Table S6.  Gene #3: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 461 319 106 66
CDH1 MUTATED 57 25 7 15
CDH1 WILD-TYPE 404 294 99 51

Figure S6.  Get High-res Image Gene #3: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'CDH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S7.  Gene #3: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 164 5 1 27 14 44
CDH1 MUTATED 0 14 85 1 0 3 0 1
CDH1 WILD-TYPE 1 696 79 4 1 24 14 43

Figure S7.  Get High-res Image Gene #3: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'MLL3 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 5.26e-05 (Wilcoxon-test), Q value = 0.014

Table S8.  Gene #10: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 954 58.7 (13.1)
MLL3 MUTATED 68 65.1 (13.1)
MLL3 WILD-TYPE 886 58.2 (13.0)

Figure S8.  Get High-res Image Gene #10: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'FOXA1 MUTATION STATUS' versus 'Time to Death'

P value = 0.00145 (logrank test), Q value = 0.16

Table S9.  Gene #11: 'FOXA1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 120 0.0 - 234.3 (25.8)
FOXA1 MUTATED 21 5 1.0 - 84.2 (20.1)
FOXA1 WILD-TYPE 929 115 0.0 - 234.3 (25.9)

Figure S9.  Get High-res Image Gene #11: 'FOXA1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'FOXA1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000194 (Wilcoxon-test), Q value = 0.035

Table S10.  Gene #11: 'FOXA1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 954 58.7 (13.1)
FOXA1 MUTATED 22 70.2 (13.5)
FOXA1 WILD-TYPE 932 58.4 (13.0)

Figure S10.  Get High-res Image Gene #11: 'FOXA1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'SPEN MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000962 (Wilcoxon-test), Q value = 0.12

Table S11.  Gene #19: 'SPEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 954 58.7 (13.1)
SPEN MUTATED 32 66.4 (13.6)
SPEN WILD-TYPE 922 58.4 (13.0)

Figure S11.  Get High-res Image Gene #19: 'SPEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RAB42 MUTATION STATUS' versus 'Time to Death'

P value = 6.78e-09 (logrank test), Q value = 6.1e-06

Table S12.  Gene #35: 'RAB42 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 120 0.0 - 234.3 (25.8)
RAB42 MUTATED 4 2 9.6 - 24.8 (16.7)
RAB42 WILD-TYPE 946 118 0.0 - 234.3 (25.9)

Figure S12.  Get High-res Image Gene #35: 'RAB42 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'TGS1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000676 (Wilcoxon-test), Q value = 0.096

Table S13.  Gene #47: 'TGS1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 954 58.7 (13.1)
TGS1 MUTATED 13 71.5 (10.8)
TGS1 WILD-TYPE 941 58.5 (13.0)

Figure S13.  Get High-res Image Gene #47: 'TGS1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'EIF4A2 MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 0.00293 (Fisher's exact test), Q value = 0.25

Table S14.  Gene #50: 'EIF4A2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 461 319 106 66
EIF4A2 MUTATED 3 1 0 4
EIF4A2 WILD-TYPE 458 318 106 62

Figure S14.  Get High-res Image Gene #50: 'EIF4A2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'NBPF9 MUTATION STATUS' versus 'PATHOLOGY_M_STAGE'

P value = 0.00281 (Fisher's exact test), Q value = 0.25

Table S15.  Gene #80: 'NBPF9 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 837 15
NBPF9 MUTATED 3 2
NBPF9 WILD-TYPE 834 13

Figure S15.  Get High-res Image Gene #80: 'NBPF9 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'RHOA MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.0033 (Fisher's exact test), Q value = 0.25

Table S16.  Gene #91: 'RHOA MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 257 559 114 35
RHOA MUTATED 0 1 3 1
RHOA WILD-TYPE 257 558 111 34

Figure S16.  Get High-res Image Gene #91: 'RHOA MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'LRIG2 MUTATION STATUS' versus 'Time to Death'

P value = 0.000176 (logrank test), Q value = 0.035

Table S17.  Gene #99: 'LRIG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 120 0.0 - 234.3 (25.8)
LRIG2 MUTATED 7 3 5.2 - 63.1 (16.6)
LRIG2 WILD-TYPE 943 117 0.0 - 234.3 (25.8)

Figure S17.  Get High-res Image Gene #99: 'LRIG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'C11ORF49 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.0018 (Fisher's exact test), Q value = 0.19

Table S18.  Gene #112: 'C11ORF49 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 257 559 114 35
C11ORF49 MUTATED 2 0 0 2
C11ORF49 WILD-TYPE 255 559 114 33

Figure S18.  Get High-res Image Gene #112: 'C11ORF49 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'SP3 MUTATION STATUS' versus 'Time to Death'

P value = 0.000111 (logrank test), Q value = 0.025

Table S19.  Gene #114: 'SP3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 120 0.0 - 234.3 (25.8)
SP3 MUTATED 6 3 1.6 - 84.6 (15.8)
SP3 WILD-TYPE 944 117 0.0 - 234.3 (25.9)

Figure S19.  Get High-res Image Gene #114: 'SP3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'JAK1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00313 (Wilcoxon-test), Q value = 0.25

Table S20.  Gene #130: 'JAK1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 954 58.7 (13.1)
JAK1 MUTATED 11 70.4 (11.5)
JAK1 WILD-TYPE 943 58.6 (13.1)

Figure S20.  Get High-res Image Gene #130: 'JAK1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TRMT2A MUTATION STATUS' versus 'Time to Death'

P value = 0.00327 (logrank test), Q value = 0.25

Table S21.  Gene #134: 'TRMT2A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 120 0.0 - 234.3 (25.8)
TRMT2A MUTATED 6 2 1.0 - 55.9 (18.3)
TRMT2A WILD-TYPE 944 118 0.0 - 234.3 (25.8)

Figure S21.  Get High-res Image Gene #134: 'TRMT2A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CLEC18B MUTATION STATUS' versus 'Time to Death'

P value = 0.00121 (logrank test), Q value = 0.15

Table S22.  Gene #136: 'CLEC18B MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 120 0.0 - 234.3 (25.8)
CLEC18B MUTATED 5 3 12.4 - 72.1 (31.8)
CLEC18B WILD-TYPE 945 117 0.0 - 234.3 (25.7)

Figure S22.  Get High-res Image Gene #136: 'CLEC18B MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'GIPC3 MUTATION STATUS' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00069 (Fisher's exact test), Q value = 0.096

Table S23.  Gene #138: 'GIPC3 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 87 70 8 3 329 221 2 133 26 55 15 1 12
GIPC3 MUTATED 0 1 1 0 0 0 0 0 1 0 0 0 1
GIPC3 WILD-TYPE 87 69 7 3 329 221 2 133 25 55 15 1 11

Figure S23.  Get High-res Image Gene #138: 'GIPC3 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'CD244 MUTATION STATUS' versus 'Time to Death'

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

Table S24.  Gene #151: 'CD244 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 120 0.0 - 234.3 (25.8)
CD244 MUTATED 3 2 5.7 - 14.9 (10.0)
CD244 WILD-TYPE 947 118 0.0 - 234.3 (25.8)

Figure S24.  Get High-res Image Gene #151: 'CD244 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

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/BRCA-TP/15165591/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/15076769/BRCA-TP.merged_data.txt

  • Number of patients = 967

  • Number of significantly mutated genes = 151

  • Number of selected clinical features = 12

  • 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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