Correlation between gene mutation status and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C198865C
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/C198865C
Overview
Introduction

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

Summary

Testing the association between mutation status of 79 genes and 12 clinical features across 977 patients, 18 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'.

  • GATA3 mutation correlated to 'RADIATION_THERAPY'.

  • 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'.

  • NBPF9 mutation correlated to 'PATHOLOGY_M_STAGE'.

  • SP3 mutation correlated to 'Time to Death'.

  • TGS1 mutation correlated to 'YEARS_TO_BIRTH'.

  • LRIG2 mutation correlated to 'Time to Death'.

  • RHOA mutation correlated to 'PATHOLOGY_T_STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 79 genes and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 18 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		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 296 (30%) 681 0.207
(1.00) 		0.00283
(0.168) 		0.21
(1.00) 		0.039
(0.838) 		0.131
(1.00) 		0.111
(1.00) 		0.0642
(0.949) 		0.5
(1.00) 		1e-05
(0.00158) 		0.25
(1.00) 		1e-05
(0.00158) 		0.191
(1.00)
CDH1 107 (11%) 870 0.148
(1.00) 		0.0583
(0.937) 		0.0189
(0.527) 		1e-05
(0.00158) 		0.00372
(0.196) 		0.388
(1.00) 		0.608
(1.00) 		0.28
(1.00) 		1e-05
(0.00158) 		0.731
(1.00) 		0.348
(1.00) 		1
(1.00)
FOXA1 23 (2%) 954 1.53e-05
(0.00207) 		8.08e-05
(0.00851) 		0.336
(1.00) 		0.191
(1.00) 		0.633
(1.00) 		1
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.0117
(0.415) 		0.303
(1.00) 		0.359
(1.00) 		0.523
(1.00)
PIK3CA 316 (32%) 661 0.918
(1.00) 		0.0322
(0.777) 		0.48
(1.00) 		0.833
(1.00) 		0.929
(1.00) 		1
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.00023
(0.0182) 		0.491
(1.00) 		0.0708
(0.96) 		0.575
(1.00)
GATA3 97 (10%) 880 0.805
(1.00) 		0.0157
(0.482) 		0.0857
(0.96) 		0.199
(1.00) 		0.406
(1.00) 		0.206
(1.00) 		1
(1.00) 		2.06e-06
(0.000977) 		0.00789
(0.34) 		0.122
(1.00) 		0.308
(1.00) 		0.77
(1.00)
MLL3 70 (7%) 907 0.0138
(0.452) 		2.84e-05
(0.00337) 		0.464
(1.00) 		0.537
(1.00) 		0.116
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.357
(1.00) 		0.905
(1.00) 		0.803
(1.00) 		0.163
(1.00) 		0.505
(1.00)
SPEN 32 (3%) 945 0.315
(1.00) 		0.00103
(0.0652) 		0.525
(1.00) 		0.15
(1.00) 		0.989
(1.00) 		1
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.784
(1.00) 		0.929
(1.00) 		0.309
(1.00) 		1
(1.00)
RAB42 4 (0%) 973 1.44e-08
(1.36e-05) 		0.862
(1.00) 		0.616
(1.00) 		0.656
(1.00) 		0.841
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.281
(1.00) 		0.861
(1.00) 		0.109
(1.00) 		1
(1.00)
NBPF9 5 (1%) 972 0.509
(1.00) 		0.458
(1.00) 		0.00573
(0.286) 		0.275
(1.00) 		0.513
(1.00) 		0.00317
(0.177) 		1
(1.00) 		0.66
(1.00) 		0.752
(1.00) 		1
(1.00)
SP3 7 (1%) 970 0.000154
(0.0144) 		0.317
(1.00) 		0.0537
(0.878) 		0.577
(1.00) 		0.843
(1.00) 		0.0901
(0.96) 		1
(1.00) 		0.415
(1.00) 		0.574
(1.00) 		0.378
(1.00) 		0.752
(1.00) 		1
(1.00)
TGS1 13 (1%) 964 0.947
(1.00) 		0.00071
(0.0517) 		0.782
(1.00) 		0.859
(1.00) 		0.179
(1.00) 		1
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.352
(1.00) 		0.253
(1.00) 		1
(1.00) 		0.323
(1.00)
LRIG2 7 (1%) 970 0.000167
(0.0144) 		0.392
(1.00) 		0.908
(1.00) 		0.9
(1.00) 		0.739
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.441
(1.00) 		1
(1.00) 		1
(1.00)
RHOA 6 (1%) 971 0.765
(1.00) 		0.383
(1.00) 		0.34
(1.00) 		0.00101
(0.0652) 		0.0992
(0.97) 		1
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.389
(1.00) 		0.882
(1.00) 		1
(1.00) 		1
(1.00)
MAP3K1 71 (7%) 906 0.989
(1.00) 		0.00681
(0.307) 		0.7
(1.00) 		0.266
(1.00) 		0.96
(1.00) 		0.627
(1.00) 		1
(1.00) 		0.236
(1.00) 		0.787
(1.00) 		0.426
(1.00) 		0.885
(1.00) 		0.293
(1.00)
CBFB 22 (2%) 955 0.716
(1.00) 		0.756
(1.00) 		0.341
(1.00) 		0.261
(1.00) 		0.0807
(0.96) 		0.304
(1.00) 		0.186
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.454
(1.00) 		0.481
(1.00) 		0.544
(1.00)
PTEN 35 (4%) 942 0.76
(1.00) 		0.102
(0.986) 		0.442
(1.00) 		0.142
(1.00) 		0.532
(1.00) 		0.0932
(0.96) 		1
(1.00) 		0.271
(1.00) 		0.123
(1.00) 		0.251
(1.00) 		1
(1.00) 		1
(1.00)
RUNX1 29 (3%) 948 0.479
(1.00) 		0.808
(1.00) 		0.256
(1.00) 		0.476
(1.00) 		0.338
(1.00) 		1
(1.00) 		1
(1.00) 		0.518
(1.00) 		0.0138
(0.452) 		0.171
(1.00) 		0.334
(1.00) 		0.582
(1.00)
CDKN1B 10 (1%) 967 0.744
(1.00) 		0.594
(1.00) 		0.113
(1.00) 		0.0491
(0.853) 		0.0233
(0.598) 		0.14
(1.00) 		1
(1.00) 		0.311
(1.00) 		0.787
(1.00) 		0.0777
(0.96) 		0.755
(1.00) 		1
(1.00)
MAP2K4 32 (3%) 945 0.894
(1.00) 		0.398
(1.00) 		0.65
(1.00) 		0.358
(1.00) 		0.494
(1.00) 		0.426
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.204
(1.00) 		0.31
(1.00) 		0.674
(1.00) 		1
(1.00)
ARID1A 27 (3%) 950 0.511
(1.00) 		0.979
(1.00) 		0.518
(1.00) 		0.366
(1.00) 		0.287
(1.00) 		1
(1.00) 		1
(1.00) 		0.23
(1.00) 		0.585
(1.00) 		0.464
(1.00) 		0.2
(1.00) 		0.523
(1.00)
GPS2 10 (1%) 967 0.871
(1.00) 		0.151
(1.00) 		0.91
(1.00) 		0.26
(1.00) 		0.651
(1.00) 		1
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.472
(1.00) 		0.656
(1.00) 		0.447
(1.00) 		0.352
(1.00)
TBX3 27 (3%) 950 0.217
(1.00) 		0.0731
(0.96) 		0.738
(1.00) 		0.764
(1.00) 		0.414
(1.00) 		1
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.0451
(0.853) 		0.429
(1.00) 		0.404
(1.00) 		1
(1.00)
RB1 19 (2%) 958 0.933
(1.00) 		0.272
(1.00) 		0.463
(1.00) 		0.301
(1.00) 		0.781
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.602
(1.00) 		0.729
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.523
(1.00)
CTCF 16 (2%) 961 0.0913
(0.96) 		0.873
(1.00) 		0.257
(1.00) 		0.0798
(0.96) 		0.312
(1.00) 		1
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.584
(1.00) 		0.172
(1.00) 		0.448
(1.00) 		0.456
(1.00)
RBMX 13 (1%) 964 0.992
(1.00) 		0.368
(1.00) 		0.898
(1.00) 		0.42
(1.00) 		0.0847
(0.96) 		1
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.861
(1.00) 		0.963
(1.00) 		1
(1.00) 		1
(1.00)
HRNR 31 (3%) 946 0.0877
(0.96) 		0.245
(1.00) 		0.179
(1.00) 		0.124
(1.00) 		0.125
(1.00) 		1
(1.00) 		1
(1.00) 		0.456
(1.00) 		0.929
(1.00) 		0.599
(1.00) 		0.656
(1.00) 		0.301
(1.00)
ZMYM3 15 (2%) 962 0.436
(1.00) 		0.626
(1.00) 		0.782
(1.00) 		0.959
(1.00) 		1
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.419
(1.00) 		1
(1.00) 		0.834
(1.00) 		0.423
(1.00) 		1
(1.00)
NCOR1 40 (4%) 937 0.852
(1.00) 		0.57
(1.00) 		0.945
(1.00) 		0.718
(1.00) 		0.887
(1.00) 		1
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.651
(1.00) 		0.871
(1.00) 		0.319
(1.00) 		0.636
(1.00)
GPRIN2 11 (1%) 966 0.858
(1.00) 		0.223
(1.00) 		0.66
(1.00) 		0.936
(1.00) 		0.333
(1.00) 		1
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.162
(1.00) 		0.108
(1.00) 		0.258
(1.00) 		1
(1.00)
NF1 28 (3%) 949 0.213
(1.00) 		0.116
(1.00) 		0.2
(1.00) 		0.138
(1.00) 		0.399
(1.00) 		0.355
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.414
(1.00) 		0.129
(1.00) 		0.684
(1.00) 		1
(1.00)
TCP11 6 (1%) 971 0.0807
(0.96) 		0.832
(1.00) 		0.752
(1.00) 		0.455
(1.00) 		0.565
(1.00) 		1
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.271
(1.00) 		0.184
(1.00) 		0.678
(1.00) 		1
(1.00)
SF3B1 16 (2%) 961 0.316
(1.00) 		0.411
(1.00) 		0.486
(1.00) 		0.466
(1.00) 		0.835
(1.00) 		1
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.906
(1.00) 		0.945
(1.00) 		0.784
(1.00) 		1
(1.00)
ERBB2 20 (2%) 957 0.0476
(0.853) 		0.153
(1.00) 		0.489
(1.00) 		0.255
(1.00) 		0.0932
(0.96) 		1
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.299
(1.00) 		0.146
(1.00) 		0.456
(1.00)
CDC42EP1 5 (1%) 972 0.41
(1.00) 		0.32
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.466
(1.00) 		1
(1.00) 		1
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.378
(1.00) 		1
(1.00) 		1
(1.00)
KDM6A 15 (2%) 962 0.834
(1.00) 		0.0689
(0.96) 		0.84
(1.00) 		0.457
(1.00) 		0.0103
(0.406) 		1
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.741
(1.00) 		0.638
(1.00) 		0.864
(1.00) 		1
(1.00)
AQP12A 6 (1%) 971 0.41
(1.00) 		0.326
(1.00) 		0.836
(1.00) 		0.675
(1.00) 		0.225
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.501
(1.00) 		0.36
(1.00) 		0.677
(1.00) 		1
(1.00)
KRAS 6 (1%) 971 0.733
(1.00) 		0.125
(1.00) 		0.821
(1.00) 		0.883
(1.00) 		0.821
(1.00) 		1
(1.00) 		1
(1.00) 		0.415
(1.00) 		1
(1.00) 		0.921
(1.00) 		0.069
(0.96) 		1
(1.00)
MYB 12 (1%) 965 0.15
(1.00) 		0.177
(1.00) 		0.475
(1.00) 		0.454
(1.00) 		0.963
(1.00) 		1
(1.00) 		1
(1.00) 		0.311
(1.00) 		0.211
(1.00) 		0.281
(1.00) 		1
(1.00) 		1
(1.00)
ZNF362 5 (1%) 972 0.609
(1.00) 		0.257
(1.00) 		0.321
(1.00) 		0.376
(1.00) 		0.194
(1.00) 		1
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.751
(1.00) 		0.0604
(0.938) 		1
(1.00) 		1
(1.00)
TBL1XR1 9 (1%) 968 0.494
(1.00) 		0.264
(1.00) 		0.0633
(0.949) 		0.0463
(0.853) 		0.0334
(0.777) 		0.157
(1.00) 		1
(1.00) 		0.0696
(0.96) 		0.518
(1.00) 		0.605
(1.00) 		0.751
(1.00) 		1
(1.00)
FGFR2 11 (1%) 966 0.649
(1.00) 		0.562
(1.00) 		0.542
(1.00) 		0.0116
(0.415) 		0.708
(1.00) 		1
(1.00) 		0.0973
(0.961) 		0.525
(1.00) 		0.58
(1.00) 		0.15
(1.00) 		0.527
(1.00) 		1
(1.00)
ZBTB7C 5 (1%) 972 0.473
(1.00) 		0.536
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.169
(1.00) 		1
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.273
(1.00) 		0.175
(1.00) 		1
(1.00) 		1
(1.00)
NCDN 4 (0%) 973 0.601
(1.00) 		0.784
(1.00) 		0.547
(1.00) 		0.529
(1.00) 		0.374
(1.00) 		1
(1.00) 		1
(1.00) 		0.0872
(0.96) 		0.162
(1.00) 		0.0604
(0.938) 		0.595
(1.00) 		1
(1.00)
MUC6 14 (1%) 963 0.165
(1.00) 		0.386
(1.00) 		0.723
(1.00) 		0.773
(1.00) 		0.093
(0.96) 		0.233
(1.00) 		1
(1.00) 		1
(1.00) 		0.242
(1.00) 		0.406
(1.00) 		0.164
(1.00) 		1
(1.00)
TFE3 7 (1%) 970 0.211
(1.00) 		0.426
(1.00) 		0.853
(1.00) 		0.9
(1.00) 		0.591
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.76
(1.00) 		1
(1.00) 		1
(1.00)
IRS4 11 (1%) 966 0.881
(1.00) 		0.289
(1.00) 		0.0766
(0.96) 		0.784
(1.00) 		0.0455
(0.853) 		0.173
(1.00) 		1
(1.00) 		0.477
(1.00) 		0.517
(1.00) 		0.499
(1.00) 		0.359
(1.00) 		1
(1.00)
NLGN3 11 (1%) 966 0.596
(1.00) 		0.123
(1.00) 		0.384
(1.00) 		0.179
(1.00) 		0.708
(1.00) 		1
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.749
(1.00) 		0.991
(1.00) 		0.132
(1.00) 		0.323
(1.00)
IL1RAP 9 (1%) 968 0.418
(1.00) 		0.0803
(0.96) 		0.948
(1.00) 		0.513
(1.00) 		0.46
(1.00) 		1
(1.00) 		1
(1.00) 		0.086
(0.96) 		0.874
(1.00) 		0.129
(1.00) 		0.527
(1.00) 		1
(1.00)
USP36 8 (1%) 969 0.463
(1.00) 		0.143
(1.00) 		0.0336
(0.777) 		0.128
(1.00) 		0.576
(1.00) 		1
(1.00) 		1
(1.00) 		0.415
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.478
(1.00) 		1
(1.00)
CASZ1 14 (1%) 963 0.276
(1.00) 		0.863
(1.00) 		0.83
(1.00) 		0.524
(1.00) 		0.936
(1.00) 		1
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.831
(1.00) 		0.82
(1.00) 		0.613
(1.00) 		1
(1.00)
EYS 21 (2%) 956 0.439
(1.00) 		0.0175
(0.503) 		0.751
(1.00) 		0.489
(1.00) 		0.0951
(0.961) 		1
(1.00) 		1
(1.00) 		0.492
(1.00) 		0.0957
(0.961) 		0.142
(1.00) 		0.0118
(0.415) 		1
(1.00)
KCNN3 9 (1%) 968 0.531
(1.00) 		0.718
(1.00) 		0.63
(1.00) 		0.417
(1.00) 		0.514
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.252
(1.00) 		0.822
(1.00) 		0.477
(1.00) 		0.293
(1.00)
ZFP36L1 8 (1%) 969 0.549
(1.00) 		0.403
(1.00) 		0.833
(1.00) 		0.908
(1.00) 		0.827
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.24
(1.00) 		1
(1.00)
ICOSLG 5 (1%) 972 0.746
(1.00) 		0.872
(1.00) 		0.261
(1.00) 		0.719
(1.00) 		0.605
(1.00) 		1
(1.00) 		1
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.598
(1.00) 		1
(1.00)
ACTL6B 10 (1%) 967 0.609
(1.00) 		0.115
(1.00) 		0.4
(1.00) 		0.157
(1.00) 		0.23
(1.00) 		0.157
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.662
(1.00) 		0.858
(1.00) 		0.525
(1.00) 		1
(1.00)
MYH9 18 (2%) 959 0.479
(1.00) 		0.302
(1.00) 		0.65
(1.00) 		0.915
(1.00) 		0.405
(1.00) 		1
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.215
(1.00) 		0.282
(1.00) 		0.264
(1.00) 		1
(1.00)
FBXW7 15 (2%) 962 0.576
(1.00) 		0.416
(1.00) 		0.569
(1.00) 		0.19
(1.00) 		0.696
(1.00) 		1
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.85
(1.00) 		0.282
(1.00) 		0.0504
(0.853) 		0.406
(1.00)
FRMPD2 13 (1%) 964 0.184
(1.00) 		0.647
(1.00) 		0.387
(1.00) 		0.00921
(0.38) 		0.968
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.363
(1.00) 		0.481
(1.00) 		0.352
(1.00)
ZFP36L2 7 (1%) 970 0.342
(1.00) 		0.875
(1.00) 		0.748
(1.00) 		0.899
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.0968
(0.961) 		0.229
(1.00)
TPP2 8 (1%) 969 0.673
(1.00) 		0.373
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.281
(1.00) 		1
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.429
(1.00) 		0.0402
(0.838) 		0.243
(1.00) 		1
(1.00)
C17ORF95 5 (1%) 972 0.0888
(0.96) 		0.0898
(0.96) 		0.975
(1.00) 		0.507
(1.00) 		1
(1.00) 		1
(1.00) 		0.0453
(0.853) 		0.328
(1.00) 		1
(1.00) 		0.362
(1.00) 		1
(1.00) 		1
(1.00)
RUFY1 6 (1%) 971 0.0165
(0.489) 		0.0148
(0.467) 		0.565
(1.00) 		0.236
(1.00) 		0.822
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.501
(1.00) 		0.294
(1.00) 		0.402
(1.00) 		1
(1.00)
MED23 14 (1%) 963 0.32
(1.00) 		0.0356
(0.803) 		0.256
(1.00) 		0.298
(1.00) 		0.775
(1.00) 		1
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.654
(1.00) 		0.349
(1.00) 		0.326
(1.00) 		1
(1.00)
PAX2 4 (0%) 973 0.132
(1.00) 		0.146
(1.00) 		0.857
(1.00) 		1
(1.00) 		0.842
(1.00) 		1
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.719
(1.00) 		0.208
(1.00) 		1
(1.00) 		1
(1.00)
MED12 21 (2%) 956 0.883
(1.00) 		0.431
(1.00) 		0.738
(1.00) 		0.546
(1.00) 		0.444
(1.00) 		1
(1.00) 		1
(1.00) 		0.133
(1.00) 		0.687
(1.00) 		0.273
(1.00) 		0.0798
(0.96) 		1
(1.00)
CHD4 19 (2%) 958 0.871
(1.00) 		0.706
(1.00) 		0.22
(1.00) 		0.0229
(0.598) 		0.00677
(0.307) 		1
(1.00) 		1
(1.00) 		0.0905
(0.96) 		0.202
(1.00) 		0.98
(1.00) 		0.115
(1.00) 		1
(1.00)
PFKP 6 (1%) 971 0.519
(1.00) 		0.227
(1.00) 		0.513
(1.00) 		0.574
(1.00) 		0.565
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.784
(1.00) 		0.0213
(0.576) 		0.738
(1.00) 		1
(1.00)
RHBG 4 (0%) 973 0.0304
(0.76) 		0.0495
(0.853) 		0.823
(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)
PSIP1 8 (1%) 969 0.136
(1.00) 		0.268
(1.00) 		0.227
(1.00) 		0.248
(1.00) 		0.927
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.514
(1.00) 		0.662
(1.00) 		0.302
(1.00) 		1
(1.00)
RIBC1 4 (0%) 973 0.775
(1.00) 		0.885
(1.00) 		0.494
(1.00) 		0.524
(1.00) 		0.225
(1.00) 		1
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.719
(1.00) 		0.232
(1.00) 		1
(1.00)
PLK2 9 (1%) 968 0.648
(1.00) 		0.154
(1.00) 		0.536
(1.00) 		0.582
(1.00) 		0.538
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.394
(1.00) 		0.677
(1.00) 		0.613
(1.00) 		1
(1.00)
ANKRD20A4 7 (1%) 970 0.481
(1.00) 		0.473
(1.00) 		0.365
(1.00) 		0.234
(1.00) 		0.238
(1.00) 		1
(1.00) 		1
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.065
(0.949) 		1
(1.00) 		1
(1.00)
PHACTR1 7 (1%) 970 0.0454
(0.853) 		0.33
(1.00) 		0.338
(1.00) 		0.254
(1.00) 		0.549
(1.00) 		0.124
(1.00) 		1
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.915
(1.00) 		0.477
(1.00) 		1
(1.00)
DLG1 13 (1%) 964 0.536
(1.00) 		0.521
(1.00) 		0.774
(1.00) 		0.699
(1.00) 		0.626
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0529
(0.878) 		0.21
(1.00) 		0.582
(1.00) 		1
(1.00)
GPRASP2 10 (1%) 967 0.858
(1.00) 		0.184
(1.00) 		0.651
(1.00) 		0.384
(1.00) 		0.654
(1.00) 		0.157
(1.00) 		1
(1.00) 		0.739
(1.00) 		0.786
(1.00) 		0.928
(1.00) 		0.48
(1.00) 		1
(1.00)
CCDC82 6 (1%) 971 0.0931
(0.96) 		0.275
(1.00) 		0.909
(1.00) 		0.884
(1.00) 		0.563
(1.00) 		1
(1.00) 		1
(1.00) 		0.0872
(0.96) 		1
(1.00) 		0.104
(0.997) 		0.0621
(0.949) 		1
(1.00)
CCDC27 7 (1%) 970 0.632
(1.00) 		0.243
(1.00) 		0.888
(1.00) 		0.9
(1.00) 		0.506
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.0383
(0.838) 		0.93
(1.00) 		0.0407
(0.838) 		1
(1.00)
MAMLD1 10 (1%) 967 0.488
(1.00) 		0.114
(1.00) 		0.444
(1.00) 		0.763
(1.00) 		0.24
(1.00) 		1
(1.00) 		1
(1.00) 		0.0488
(0.853) 		0.889
(1.00) 		0.4
(1.00) 		1
(1.00) 		1
(1.00)
OR8D1 5 (1%) 972 0.308
(1.00) 		0.49
(1.00) 		0.841
(1.00) 		0.439
(1.00) 		0.873
(1.00) 		1
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.75
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.159
(1.00)
'PIK3CA MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00023 (Fisher's exact test), Q value = 0.018

Table S1.  Gene #1: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: '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 1 712 171 5 6 26 14 41
PIK3CA MUTATED 0 216 74 0 0 12 0 14
PIK3CA WILD-TYPE 1 496 97 5 6 14 14 27

Figure S1.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00283 (Wilcoxon-test), Q value = 0.17

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

nPatients Mean (Std.Dev)
ALL 964 58.7 (13.1)
TP53 MUTATED 291 56.9 (12.3)
TP53 WILD-TYPE 673 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 = 0.0016

Table S3.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #9: '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 1 712 171 5 6 26 14 41
TP53 MUTATED 1 261 9 3 4 6 1 10
TP53 WILD-TYPE 0 451 162 2 2 20 13 31

Figure S3.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'RACE'

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

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 57 121 705
TP53 MUTATED 1 29 56 189
TP53 WILD-TYPE 0 28 65 516

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

'GATA3 MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 2.06e-06 (Fisher's exact test), Q value = 0.00098

Table S5.  Gene #3: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 377 472
GATA3 MUTATED 59 27
GATA3 WILD-TYPE 318 445

Figure S5.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'RADIATION_THERAPY'

'CDH1 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

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

Table S6.  Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 258 563 119 35
CDH1 MUTATED 16 56 33 2
CDH1 WILD-TYPE 242 507 86 33

Figure S6.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'CDH1 MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 0.00372 (Fisher's exact test), Q value = 0.2

Table S7.  Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 462 325 107 68
CDH1 MUTATED 56 27 8 16
CDH1 WILD-TYPE 406 298 99 52

Figure S7.  Get High-res Image Gene #5: '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 = 0.0016

Table S8.  Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: '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 1 712 171 5 6 26 14 41
CDH1 MUTATED 0 13 89 1 0 3 0 1
CDH1 WILD-TYPE 1 699 82 4 6 23 14 40

Figure S8.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'MLL3 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 2.84e-05 (Wilcoxon-test), Q value = 0.0034

Table S9.  Gene #9: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 964 58.7 (13.1)
MLL3 MUTATED 70 65.2 (13.0)
MLL3 WILD-TYPE 894 58.2 (13.0)

Figure S9.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'FOXA1 MUTATION STATUS' versus 'Time to Death'

P value = 1.53e-05 (logrank test), Q value = 0.0021

Table S10.  Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 962 137 0.0 - 282.9 (30.2)
FOXA1 MUTATED 21 7 1.0 - 118.6 (20.4)
FOXA1 WILD-TYPE 941 130 0.0 - 282.9 (31.0)

Figure S10.  Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'FOXA1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 8.08e-05 (Wilcoxon-test), Q value = 0.0085

Table S11.  Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 964 58.7 (13.1)
FOXA1 MUTATED 23 70.6 (13.3)
FOXA1 WILD-TYPE 941 58.5 (13.0)

Figure S11.  Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'SPEN MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00103 (Wilcoxon-test), Q value = 0.065

Table S12.  Gene #23: 'SPEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 964 58.7 (13.1)
SPEN MUTATED 32 66.4 (13.6)
SPEN WILD-TYPE 932 58.5 (13.1)

Figure S12.  Get High-res Image Gene #23: 'SPEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RAB42 MUTATION STATUS' versus 'Time to Death'

P value = 1.44e-08 (logrank test), Q value = 1.4e-05

Table S13.  Gene #28: 'RAB42 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 962 137 0.0 - 282.9 (30.2)
RAB42 MUTATED 4 2 9.6 - 24.8 (16.7)
RAB42 WILD-TYPE 958 135 0.0 - 282.9 (30.4)

Figure S13.  Get High-res Image Gene #28: 'RAB42 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NBPF9 MUTATION STATUS' versus 'PATHOLOGY_M_STAGE'

P value = 0.00317 (Fisher's exact test), Q value = 0.18

Table S14.  Gene #33: 'NBPF9 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 841 16
NBPF9 MUTATED 3 2
NBPF9 WILD-TYPE 838 14

Figure S14.  Get High-res Image Gene #33: 'NBPF9 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'SP3 MUTATION STATUS' versus 'Time to Death'

P value = 0.000154 (logrank test), Q value = 0.014

Table S15.  Gene #37: 'SP3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 962 137 0.0 - 282.9 (30.2)
SP3 MUTATED 6 3 5.7 - 84.6 (19.4)
SP3 WILD-TYPE 956 134 0.0 - 282.9 (30.4)

Figure S15.  Get High-res Image Gene #37: 'SP3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'TGS1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00071 (Wilcoxon-test), Q value = 0.052

Table S16.  Gene #42: 'TGS1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 964 58.7 (13.1)
TGS1 MUTATED 13 71.5 (10.8)
TGS1 WILD-TYPE 951 58.6 (13.1)

Figure S16.  Get High-res Image Gene #42: 'TGS1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'LRIG2 MUTATION STATUS' versus 'Time to Death'

P value = 0.000167 (logrank test), Q value = 0.014

Table S17.  Gene #68: 'LRIG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 962 137 0.0 - 282.9 (30.2)
LRIG2 MUTATED 7 3 5.2 - 63.1 (16.6)
LRIG2 WILD-TYPE 955 134 0.0 - 282.9 (30.4)

Figure S17.  Get High-res Image Gene #68: 'LRIG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'RHOA MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00101 (Fisher's exact test), Q value = 0.065

Table S18.  Gene #77: 'RHOA MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 258 563 119 35
RHOA MUTATED 0 1 4 1
RHOA WILD-TYPE 258 562 115 34

Figure S18.  Get High-res Image Gene #77: 'RHOA MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

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/20231617/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt

  • Number of patients = 977

  • Number of significantly mutated genes = 79

  • 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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