Correlation between gene mutation status and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1R49PBF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1R49PBF
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 10 clinical features across 949 patients, 19 significant findings detected with Q value < 0.25.

  • TP53 mutation correlated to 'HISTOLOGICAL.TYPE'.

  • CDH1 mutation correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • MLL3 mutation correlated to 'AGE'.

  • FAM86B1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • CASP8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • ASXL2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • TRPM5 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • PRICKLE3 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • WDR52 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • ERBB3 mutation correlated to 'Time to Death'.

  • PTHLH mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • HLA-DRB5 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • GYG2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • HRNR mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • DMXL2 mutation correlated to 'HISTOLOGICAL.TYPE' and 'NUMBER.OF.LYMPH.NODES'.

  • MUC5B mutation correlated to 'HISTOLOGICAL.TYPE'.

  • XBP1 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 73 genes and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 19 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES
nMutated (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test
CDH1 96 (10%) 853 0.145
(1.00) 		0.0116
(1.00) 		0.028
(1.00) 		1.3e-06
(0.000938) 		0.00747
(1.00) 		0.0048
(1.00) 		0.61
(1.00) 		1.51e-69
(1.1e-66) 		0.00907
(1.00) 		0.194
(1.00)
DMXL2 18 (2%) 931 0.727
(1.00) 		0.22
(1.00) 		0.361
(1.00) 		0.0781
(1.00) 		0.0616
(1.00) 		0.792
(1.00) 		0.159
(1.00) 		1.15e-28
(8.32e-26) 		0.304
(1.00) 		2.81e-29
(2.04e-26)
TP53 284 (30%) 665 0.116
(1.00) 		0.00502
(1.00) 		0.246
(1.00) 		0.0225
(1.00) 		0.161
(1.00) 		0.0565
(1.00) 		0.0645
(1.00) 		2.4e-12
(1.74e-09) 		0.0509
(1.00) 		0.868
(1.00)
MLL3 67 (7%) 882 0.203
(1.00) 		4.63e-05
(0.033) 		0.735
(1.00) 		0.638
(1.00) 		0.0746
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.912
(1.00) 		0.577
(1.00) 		0.992
(1.00)
FAM86B1 8 (1%) 941 0.112
(1.00) 		0.0853
(1.00) 		0.89
(1.00) 		0.908
(1.00) 		0.824
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.914
(1.00) 		0.45
(1.00) 		2.3e-07
(0.000166)
CASP8 10 (1%) 939 0.825
(1.00) 		0.574
(1.00) 		0.787
(1.00) 		0.929
(1.00) 		0.355
(1.00) 		1
(1.00) 		1
(1.00) 		0.629
(1.00) 		1
(1.00) 		1.53e-06
(0.0011)
ASXL2 16 (2%) 933 0.00686
(1.00) 		0.264
(1.00) 		0.821
(1.00) 		0.964
(1.00) 		0.138
(1.00) 		1
(1.00) 		1
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.000203
(0.145)
TRPM5 11 (1%) 938 0.629
(1.00) 		0.747
(1.00) 		0.423
(1.00) 		0.742
(1.00) 		0.709
(1.00) 		0.695
(1.00) 		0.00421
(1.00) 		0.0113
(1.00) 		0.192
(1.00) 		4.85e-06
(0.00348)
PRICKLE3 11 (1%) 938 0.904
(1.00) 		0.303
(1.00) 		0.0621
(1.00) 		0.0207
(1.00) 		0.953
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.857
(1.00) 		0.192
(1.00) 		0.000189
(0.134)
WDR52 16 (2%) 933 0.345
(1.00) 		0.393
(1.00) 		0.679
(1.00) 		0.616
(1.00) 		0.191
(1.00) 		0.433
(1.00) 		0.142
(1.00) 		0.756
(1.00) 		1
(1.00) 		9.27e-08
(6.71e-05)
ERBB3 18 (2%) 931 2.24e-05
(0.016) 		0.089
(1.00) 		0.429
(1.00) 		0.0636
(1.00) 		0.469
(1.00) 		1
(1.00) 		1
(1.00) 		0.858
(1.00) 		0.00289
(1.00) 		0.729
(1.00)
PTHLH 7 (1%) 942 0.517
(1.00) 		0.254
(1.00) 		0.833
(1.00) 		1
(1.00) 		0.129
(1.00) 		1
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.68
(1.00) 		1.11e-41
(8.08e-39)
HLA-DRB5 6 (1%) 943 0.544
(1.00) 		0.227
(1.00) 		0.979
(1.00) 		0.669
(1.00) 		0.468
(1.00) 		1
(1.00) 		1
(1.00) 		0.944
(1.00) 		1
(1.00) 		4.02e-06
(0.00289)
GYG2 8 (1%) 941 0.597
(1.00) 		0.449
(1.00) 		0.425
(1.00) 		0.833
(1.00) 		0.789
(1.00) 		0.66
(1.00) 		1
(1.00) 		0.952
(1.00) 		0.239
(1.00) 		4.31e-06
(0.0031)
HRNR 31 (3%) 918 0.146
(1.00) 		0.268
(1.00) 		0.345
(1.00) 		0.126
(1.00) 		0.126
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.231
(1.00) 		1.15e-05
(0.00822)
MUC5B 32 (3%) 917 0.849
(1.00) 		0.821
(1.00) 		0.066
(1.00) 		0.549
(1.00) 		0.798
(1.00) 		0.407
(1.00) 		1
(1.00) 		3.53e-06
(0.00254) 		1
(1.00) 		0.935
(1.00)
XBP1 4 (0%) 945 5.47e-06
(0.00392) 		0.0268
(1.00) 		0.986
(1.00) 		0.792
(1.00) 		0.381
(1.00) 		1
(1.00) 		1
(1.00) 		0.741
(1.00) 		0.33
(1.00)
PIK3CA 304 (32%) 645 0.316
(1.00) 		0.028
(1.00) 		0.778
(1.00) 		0.827
(1.00) 		0.858
(1.00) 		0.65
(1.00) 		1
(1.00) 		0.0022
(1.00) 		0.878
(1.00) 		0.503
(1.00)
CBFB 23 (2%) 926 0.878
(1.00) 		0.947
(1.00) 		0.787
(1.00) 		0.183
(1.00) 		0.0811
(1.00) 		0.393
(1.00) 		0.199
(1.00) 		0.945
(1.00) 		1
(1.00) 		0.442
(1.00)
RUNX1 29 (3%) 920 0.833
(1.00) 		0.746
(1.00) 		0.567
(1.00) 		0.421
(1.00) 		0.368
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.00161
(1.00) 		0.68
(1.00) 		0.175
(1.00)
GATA3 95 (10%) 854 0.339
(1.00) 		0.0104
(1.00) 		0.34
(1.00) 		0.154
(1.00) 		0.45
(1.00) 		0.142
(1.00) 		1
(1.00) 		0.0423
(1.00) 		0.0748
(1.00) 		0.00116
(0.814)
FOXA1 22 (2%) 927 0.000574
(0.407) 		0.00058
(0.411) 		0.92
(1.00) 		0.311
(1.00) 		0.919
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.00883
(1.00) 		0.152
(1.00) 		0.442
(1.00)
SF3B1 16 (2%) 933 0.305
(1.00) 		0.381
(1.00) 		0.419
(1.00) 		0.636
(1.00) 		0.832
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.942
(1.00) 		1
(1.00) 		0.654
(1.00)
MAP3K1 68 (7%) 881 0.926
(1.00) 		0.00552
(1.00) 		0.717
(1.00) 		0.455
(1.00) 		0.912
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.782
(1.00) 		0.0178
(1.00)
MAP2K4 32 (3%) 917 0.715
(1.00) 		0.393
(1.00) 		0.946
(1.00) 		0.297
(1.00) 		0.475
(1.00) 		0.586
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.696
(1.00) 		0.556
(1.00)
PTEN 35 (4%) 914 0.971
(1.00) 		0.107
(1.00) 		0.0608
(1.00) 		0.252
(1.00) 		0.527
(1.00) 		0.0569
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.261
(1.00) 		0.439
(1.00)
TBX3 26 (3%) 923 0.332
(1.00) 		0.0302
(1.00) 		0.6
(1.00) 		0.859
(1.00) 		0.601
(1.00) 		0.85
(1.00) 		1
(1.00) 		0.276
(1.00) 		1
(1.00) 		0.497
(1.00)
RB1 19 (2%) 930 0.6
(1.00) 		0.155
(1.00) 		0.459
(1.00) 		0.342
(1.00) 		0.769
(1.00) 		0.401
(1.00) 		0.167
(1.00) 		0.891
(1.00) 		0.306
(1.00) 		0.473
(1.00)
NCOR1 41 (4%) 908 0.656
(1.00) 		0.363
(1.00) 		0.939
(1.00) 		0.557
(1.00) 		0.948
(1.00) 		0.31
(1.00) 		1
(1.00) 		0.659
(1.00) 		0.599
(1.00) 		0.46
(1.00)
CTCF 17 (2%) 932 0.118
(1.00) 		0.623
(1.00) 		0.532
(1.00) 		0.184
(1.00) 		0.622
(1.00) 		1
(1.00) 		1
(1.00) 		0.494
(1.00) 		0.421
(1.00) 		0.0335
(1.00)
GPS2 11 (1%) 938 0.457
(1.00) 		0.136
(1.00) 		0.993
(1.00) 		0.108
(1.00) 		0.592
(1.00) 		1
(1.00) 		1
(1.00) 		0.62
(1.00) 		0.739
(1.00) 		0.56
(1.00)
THEM5 11 (1%) 938 0.534
(1.00) 		0.202
(1.00) 		0.643
(1.00) 		0.0375
(1.00) 		0.386
(1.00) 		1
(1.00) 		1
(1.00) 		0.00766
(1.00) 		0.739
(1.00) 		0.367
(1.00)
RPGR 17 (2%) 932 0.484
(1.00) 		0.28
(1.00) 		0.903
(1.00) 		0.817
(1.00) 		0.203
(1.00) 		0.587
(1.00) 		1
(1.00) 		0.986
(1.00) 		0.79
(1.00) 		0.00065
(0.459)
DNAH12 17 (2%) 932 0.671
(1.00) 		0.531
(1.00) 		0.916
(1.00) 		0.716
(1.00) 		0.18
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.592
(1.00) 		0.287
(1.00)
CDKN1B 9 (1%) 940 0.987
(1.00) 		0.932
(1.00) 		0.183
(1.00) 		0.0339
(1.00) 		0.0138
(1.00) 		0.0681
(1.00) 		1
(1.00) 		0.982
(1.00) 		1
(1.00) 		0.114
(1.00)
ZFP36L1 9 (1%) 940 0.386
(1.00) 		0.381
(1.00) 		0.953
(1.00) 		0.787
(1.00) 		0.895
(1.00) 		1
(1.00) 		1
(1.00) 		0.972
(1.00) 		0.46
(1.00) 		0.0542
(1.00)
ASB10 8 (1%) 941 0.0813
(1.00) 		0.506
(1.00) 		0.929
(1.00) 		0.763
(1.00) 		0.174
(1.00) 		1
(1.00) 		1
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.38
(1.00)
HIST1H3B 10 (1%) 939 0.846
(1.00) 		0.0535
(1.00) 		0.531
(1.00) 		0.559
(1.00) 		0.622
(1.00) 		1
(1.00) 		1
(1.00) 		0.956
(1.00) 		0.487
(1.00) 		0.465
(1.00)
PIK3R1 15 (2%) 934 0.0101
(1.00) 		0.302
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.305
(1.00) 		1
(1.00) 		0.909
(1.00) 		1
(1.00) 		0.00748
(1.00)
MYH9 19 (2%) 930 0.601
(1.00) 		0.422
(1.00) 		0.73
(1.00) 		0.841
(1.00) 		0.307
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.0786
(1.00) 		0.00061
(0.431)
COL6A5 23 (2%) 926 0.353
(1.00) 		0.4
(1.00) 		0.997
(1.00) 		0.899
(1.00) 		0.973
(1.00) 		1
(1.00) 		1
(1.00) 		0.232
(1.00) 		0.642
(1.00) 		0.685
(1.00)
TBL1XR1 10 (1%) 939 0.883
(1.00) 		0.218
(1.00) 		0.379
(1.00) 		0.0879
(1.00) 		0.0291
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.309
(1.00)
ARID1A 27 (3%) 922 0.514
(1.00) 		0.896
(1.00) 		0.589
(1.00) 		0.355
(1.00) 		0.269
(1.00) 		1
(1.00) 		1
(1.00) 		0.706
(1.00) 		0.667
(1.00) 		0.938
(1.00)
AQP12A 6 (1%) 943 0.511
(1.00) 		0.401
(1.00) 		0.999
(1.00) 		0.669
(1.00) 		0.241
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.889
(1.00) 		0.364
(1.00) 		0.925
(1.00)
EPDR1 5 (1%) 944 0.509
(1.00) 		0.463
(1.00) 		0.8
(1.00) 		0.374
(1.00) 		0.245
(1.00) 		1
(1.00) 		1
(1.00) 		0.883
(1.00) 		0.631
(1.00) 		0.76
(1.00)
ERBB2 21 (2%) 928 0.204
(1.00) 		0.117
(1.00) 		0.784
(1.00) 		0.186
(1.00) 		0.0841
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.664
(1.00) 		0.465
(1.00) 		0.53
(1.00)
MYB 12 (1%) 937 0.173
(1.00) 		0.135
(1.00) 		0.776
(1.00) 		0.41
(1.00) 		0.965
(1.00) 		0.501
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.344
(1.00) 		0.0115
(1.00)
TMEM151B 6 (1%) 943 0.557
(1.00) 		0.659
(1.00) 		0.61
(1.00) 		0.328
(1.00) 		0.564
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.19
(1.00) 		0.000693
(0.489)
GALNTL6 5 (1%) 944 0.465
(1.00) 		0.189
(1.00) 		0.999
(1.00) 		1
(1.00) 		0.606
(1.00) 		1
(1.00) 		1
(1.00) 		0.941
(1.00) 		0.149
(1.00) 		0.251
(1.00)
AKD1 18 (2%) 931 0.709
(1.00) 		0.16
(1.00) 		0.736
(1.00) 		0.792
(1.00) 		0.593
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.748
(1.00) 		0.304
(1.00) 		0.154
(1.00)
AARS 9 (1%) 940 0.592
(1.00) 		0.299
(1.00) 		0.983
(1.00) 		0.129
(1.00) 		0.731
(1.00) 		0.668
(1.00) 		1
(1.00) 		0.972
(1.00) 		0.724
(1.00) 		0.298
(1.00)
HLA-C 9 (1%) 940 0.607
(1.00) 		0.166
(1.00) 		0.957
(1.00) 		0.224
(1.00) 		0.895
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.982
(1.00) 		0.724
(1.00) 		0.256
(1.00)
GPRIN2 11 (1%) 938 0.936
(1.00) 		0.304
(1.00) 		0.933
(1.00) 		0.935
(1.00) 		0.333
(1.00) 		0.695
(1.00) 		1
(1.00) 		0.337
(1.00) 		0.739
(1.00) 		0.194
(1.00)
ANKRD12 17 (2%) 932 0.285
(1.00) 		0.178
(1.00) 		0.963
(1.00) 		0.586
(1.00) 		0.647
(1.00) 		0.36
(1.00) 		1
(1.00) 		0.809
(1.00) 		0.421
(1.00) 		0.000375
(0.266)
FBXW7 15 (2%) 934 0.717
(1.00) 		0.407
(1.00) 		0.707
(1.00) 		0.193
(1.00) 		0.639
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.00166
(1.00)
CDC42EP1 4 (0%) 945 0.394
(1.00) 		0.576
(1.00) 		0.00437
(1.00) 		1
(1.00) 		0.44
(1.00) 		1
(1.00) 		1
(1.00) 		0.966
(1.00) 		1
(1.00) 		0.31
(1.00)
FHOD3 13 (1%) 936 0.143
(1.00) 		0.0782
(1.00) 		0.997
(1.00) 		0.493
(1.00) 		0.78
(1.00) 		0.729
(1.00) 		0.117
(1.00) 		0.806
(1.00) 		0.538
(1.00) 		0.0533
(1.00)
SHISA4 5 (1%) 944 0.471
(1.00) 		0.872
(1.00) 		0.994
(1.00) 		0.505
(1.00) 		0.521
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.631
(1.00) 		0.151
(1.00)
KCNN3 9 (1%) 940 0.164
(1.00) 		0.549
(1.00) 		0.81
(1.00) 		0.417
(1.00) 		0.513
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.0688
(1.00)
FGFR2 10 (1%) 939 0.163
(1.00) 		0.386
(1.00) 		0.561
(1.00) 		0.0149
(1.00) 		0.697
(1.00) 		0.441
(1.00) 		0.0913
(1.00) 		0.85
(1.00) 		1
(1.00) 		0.00186
(1.00)
ICOSLG 6 (1%) 943 0.473
(1.00) 		0.126
(1.00) 		0.625
(1.00) 		0.88
(1.00) 		0.738
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.944
(1.00) 		1
(1.00) 		0.735
(1.00)
PPEF1 11 (1%) 938 0.0382
(1.00) 		0.489
(1.00) 		0.997
(1.00) 		1
(1.00) 		0.371
(1.00) 		1
(1.00) 		1
(1.00) 		0.934
(1.00) 		0.525
(1.00) 		0.0776
(1.00)
MAP4K1 10 (1%) 939 0.449
(1.00) 		0.943
(1.00) 		0.93
(1.00) 		0.529
(1.00) 		0.341
(1.00) 		1
(1.00) 		1
(1.00) 		0.956
(1.00) 		0.732
(1.00) 		0.526
(1.00)
ZNF41 11 (1%) 938 0.483
(1.00) 		0.839
(1.00) 		0.933
(1.00) 		0.667
(1.00) 		0.571
(1.00) 		0.488
(1.00) 		1
(1.00) 		0.978
(1.00) 		0.739
(1.00) 		0.393
(1.00)
FBXO17 5 (1%) 944 0.00264
(1.00) 		0.636
(1.00) 		0.981
(1.00) 		0.505
(1.00) 		0.163
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.997
(1.00) 		1
(1.00) 		0.611
(1.00)
STAG2 13 (1%) 936 0.0165
(1.00) 		0.042
(1.00) 		0.831
(1.00) 		0.951
(1.00) 		0.922
(1.00) 		0.254
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.538
(1.00) 		0.735
(1.00)
CEP57 4 (0%) 945 0.23
(1.00) 		0.207
(1.00) 		0.951
(1.00) 		0.523
(1.00) 		0.139
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.966
(1.00) 		0.584
(1.00) 		0.88
(1.00)
SPRR2B 3 (0%) 946 0.715
(1.00) 		0.369
(1.00) 		0.998
(1.00) 		0.731
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.984
(1.00) 		1
(1.00) 		0.0115
(1.00)
ZFP36L2 7 (1%) 942 0.428
(1.00) 		0.929
(1.00) 		0.984
(1.00) 		0.901
(1.00) 		0.928
(1.00) 		1
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.112
(1.00) 		0.00669
(1.00)
ZBTB7C 5 (1%) 944 0.541
(1.00) 		0.687
(1.00) 		0.958
(1.00) 		1
(1.00) 		0.168
(1.00) 		1
(1.00) 		1
(1.00) 		0.486
(1.00) 		0.329
(1.00) 		0.946
(1.00)
FXYD5 4 (0%) 945 0.767
(1.00) 		0.931
(1.00) 		0.872
(1.00) 		0.149
(1.00) 		0.842
(1.00) 		1
(1.00) 		1
(1.00) 		0.741
(1.00) 		1
(1.00) 		0.0115
(1.00)
ATXN2 15 (2%) 934 0.614
(1.00) 		0.121
(1.00) 		0.965
(1.00) 		0.573
(1.00) 		0.692
(1.00) 		1
(1.00) 		1
(1.00) 		0.983
(1.00) 		0.573
(1.00) 		0.553
(1.00)
CCL13 4 (0%) 945 0.351
(1.00) 		0.161
(1.00) 		0.979
(1.00) 		0.65
(1.00) 		0.842
(1.00) 		1
(1.00) 		1
(1.00) 		0.741
(1.00) 		0.584
(1.00) 		0.0115
(1.00)
'TP53 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.4e-12 (Chi-square test), Q value = 1.7e-09

Table S1.  Gene #8: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 703 154 5 28 14 43
TP53 MUTATED 1 251 8 3 5 1 14
TP53 WILD-TYPE 0 452 146 2 23 13 29

Figure S1.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'CDH1 MUTATION STATUS' versus 'PATHOLOGY.T.STAGE'

P value = 1.3e-06 (Fisher's exact test), Q value = 0.00094

Table S2.  Gene #11: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 252 549 111 35
CDH1 MUTATED 15 50 29 2
CDH1 WILD-TYPE 237 499 82 33

Figure S2.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'CDH1 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.51e-69 (Chi-square test), Q value = 1.1e-66

Table S3.  Gene #11: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 703 154 5 28 14 43
CDH1 MUTATED 0 14 78 1 3 0 0
CDH1 WILD-TYPE 1 689 76 4 25 14 43

Figure S3.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'MLL3 MUTATION STATUS' versus 'AGE'

P value = 4.63e-05 (t-test), Q value = 0.033

Table S4.  Gene #13: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 936 58.7 (13.1)
MLL3 MUTATED 67 65.3 (13.0)
MLL3 WILD-TYPE 869 58.2 (13.0)

Figure S4.  Get High-res Image Gene #13: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'FAM86B1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.3e-07 (t-test), Q value = 0.00017

Table S5.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
FAM86B1 MUTATED 8 0.5 (0.5)
FAM86B1 WILD-TYPE 788 2.4 (4.6)

Figure S5.  Get High-res Image Gene #25: 'FAM86B1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'CASP8 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.53e-06 (t-test), Q value = 0.0011

Table S6.  Gene #28: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
CASP8 MUTATED 9 0.3 (0.7)
CASP8 WILD-TYPE 787 2.4 (4.6)

Figure S6.  Get High-res Image Gene #28: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'ASXL2 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000203 (t-test), Q value = 0.14

Table S7.  Gene #31: 'ASXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
ASXL2 MUTATED 11 0.7 (1.0)
ASXL2 WILD-TYPE 785 2.4 (4.6)

Figure S7.  Get High-res Image Gene #31: 'ASXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'TRPM5 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.85e-06 (t-test), Q value = 0.0035

Table S8.  Gene #43: 'TRPM5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
TRPM5 MUTATED 9 0.4 (0.7)
TRPM5 WILD-TYPE 787 2.4 (4.6)

Figure S8.  Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'PRICKLE3 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000189 (t-test), Q value = 0.13

Table S9.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
PRICKLE3 MUTATED 7 0.4 (0.8)
PRICKLE3 WILD-TYPE 789 2.4 (4.6)

Figure S9.  Get High-res Image Gene #46: 'PRICKLE3 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'WDR52 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 9.27e-08 (t-test), Q value = 6.7e-05

Table S10.  Gene #47: 'WDR52 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
WDR52 MUTATED 12 0.3 (0.8)
WDR52 WILD-TYPE 784 2.4 (4.6)

Figure S10.  Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'ERBB3 MUTATION STATUS' versus 'Time to Death'

P value = 2.24e-05 (logrank test), Q value = 0.016

Table S11.  Gene #49: 'ERBB3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 928 110 0.0 - 234.3 (21.6)
ERBB3 MUTATED 15 7 0.3 - 97.5 (18.8)
ERBB3 WILD-TYPE 913 103 0.0 - 234.3 (21.6)

Figure S11.  Get High-res Image Gene #49: 'ERBB3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTHLH MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.11e-41 (t-test), Q value = 8.1e-39

Table S12.  Gene #51: 'PTHLH MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
PTHLH MUTATED 4 0.0 (0.0)
PTHLH WILD-TYPE 792 2.4 (4.6)

Figure S12.  Get High-res Image Gene #51: 'PTHLH MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'HLA-DRB5 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.02e-06 (t-test), Q value = 0.0029

Table S13.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
HLA-DRB5 MUTATED 5 0.2 (0.4)
HLA-DRB5 WILD-TYPE 791 2.4 (4.6)

Figure S13.  Get High-res Image Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'GYG2 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.31e-06 (t-test), Q value = 0.0031

Table S14.  Gene #57: 'GYG2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
GYG2 MUTATED 6 0.3 (0.5)
GYG2 WILD-TYPE 790 2.4 (4.6)

Figure S14.  Get High-res Image Gene #57: 'GYG2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'HRNR MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.15e-05 (t-test), Q value = 0.0082

Table S15.  Gene #62: 'HRNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
HRNR MUTATED 29 1.0 (1.2)
HRNR WILD-TYPE 767 2.4 (4.7)

Figure S15.  Get High-res Image Gene #62: 'HRNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'DMXL2 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.15e-28 (Chi-square test), Q value = 8.3e-26

Table S16.  Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 703 154 5 28 14 43
DMXL2 MUTATED 1 9 3 3 1 0 1
DMXL2 WILD-TYPE 0 694 151 2 27 14 42

Figure S16.  Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DMXL2 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.81e-29 (t-test), Q value = 2e-26

Table S17.  Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 796 2.3 (4.6)
DMXL2 MUTATED 13 0.1 (0.3)
DMXL2 WILD-TYPE 783 2.4 (4.6)

Figure S17.  Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'MUC5B MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.53e-06 (Chi-square test), Q value = 0.0025

Table S18.  Gene #69: 'MUC5B MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 703 154 5 28 14 43
MUC5B MUTATED 1 23 5 0 1 2 0
MUC5B WILD-TYPE 0 680 149 5 27 12 43

Figure S18.  Get High-res Image Gene #69: 'MUC5B MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'XBP1 MUTATION STATUS' versus 'Time to Death'

P value = 5.47e-06 (logrank test), Q value = 0.0039

Table S19.  Gene #70: 'XBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 928 110 0.0 - 234.3 (21.6)
XBP1 MUTATED 4 2 0.1 - 51.2 (1.7)
XBP1 WILD-TYPE 924 108 0.0 - 234.3 (21.6)

Figure S19.  Get High-res Image Gene #70: 'XBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Clinical data file = BRCA-TP.merged_data.txt

  • Number of patients = 949

  • Number of significantly mutated genes = 73

  • Number of selected clinical features = 10

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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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