Correlation between gene mutation status and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C17H1GGV
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C17H1GGV
Overview
Introduction

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

Summary

Testing the association between mutation status of 91 genes and 9 clinical features across 772 patients, 16 significant findings detected with Q value < 0.25.

  • PIK3R1 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • DCP1B mutation correlated to 'NEOPLASM.DISEASESTAGE'.

  • GATA3 mutation correlated to 'AGE'.

  • ZNF384 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • MAP3K1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • CCDC144NL mutation correlated to 'Time to Death'.

  • MUC12 mutation correlated to 'DISTANT.METASTASIS'.

  • CTU2 mutation correlated to 'NEOPLASM.DISEASESTAGE'.

  • AQP7 mutation correlated to 'LYMPH.NODE.METASTASIS'.

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

  • ZNF69 mutation correlated to 'NEOPLASM.DISEASESTAGE'.

  • HLA-DRB1 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • AFF2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • KRT38 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • KCNT2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • VSTM2B mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 91 genes and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 16 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER RADIATIONS
RADIATION
REGIMENINDICATION 		DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nMutated (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test t-test t-test Chi-square test
PIK3R1 21 (3%) 751 0.173
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.801
(1.00) 		1
(1.00) 		7.27e-06
(0.00517) 		0.0805
(1.00) 		0.223
(1.00)
DCP1B 5 (1%) 767 0.55
(1.00) 		0.025
(1.00) 		1
(1.00) 		0.335
(1.00) 		0.385
(1.00) 		0.176
(1.00) 		0.44
(1.00) 		2.31e-06
(0.00164)
GATA3 81 (10%) 691 0.74
(1.00) 		0.000213
(0.149) 		0.59
(1.00) 		0.139
(1.00) 		0.0673
(1.00) 		0.41
(1.00) 		0.598
(1.00) 		0.635
(1.00)
ZNF384 14 (2%) 758 0.408
(1.00) 		0.0126
(1.00) 		1
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.969
(1.00) 		1.16e-05
(0.00824) 		0.318
(1.00)
MAP3K1 57 (7%) 715 0.781
(1.00) 		0.00186
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.411
(1.00) 		0.101
(1.00) 		7.24e-07
(0.000516) 		0.539
(1.00)
CCDC144NL 8 (1%) 764 5.1e-05
(0.0361) 		0.051
(1.00) 		1
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.472
(1.00) 		0.296
(1.00) 		0.391
(1.00)
MUC12 44 (6%) 728 0.00337
(1.00) 		0.375
(1.00) 		1
(1.00) 		1
(1.00) 		0.000132
(0.0926) 		0.053
(1.00) 		0.0562
(1.00) 		0.159
(1.00)
CTU2 5 (1%) 767 0.556
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.962
(1.00) 		0.058
(1.00) 		1.18e-08
(8.42e-06)
AQP7 8 (1%) 764 0.0122
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.215
(1.00) 		1
(1.00) 		7.57e-06
(0.00537) 		0.196
(1.00) 		0.435
(1.00)
CASP8 10 (1%) 762 0.931
(1.00) 		0.58
(1.00) 		1
(1.00) 		0.467
(1.00) 		0.542
(1.00) 		0.883
(1.00) 		5.57e-05
(0.0393) 		0.877
(1.00)
ZNF69 5 (1%) 767 0.156
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.56
(1.00) 		1.45e-19
(1.04e-16)
HLA-DRB1 8 (1%) 764 0.568
(1.00) 		0.00708
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.198
(1.00) 		3.34e-08
(2.38e-05) 		0.695
(1.00) 		0.496
(1.00)
AFF2 15 (2%) 757 0.762
(1.00) 		0.0374
(1.00) 		1
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.967
(1.00) 		1.99e-05
(0.0141) 		0.794
(1.00)
KRT38 4 (1%) 768 0.5
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.275
(1.00) 		1
(1.00) 		1.94e-17
(1.39e-14) 		0.0539
(1.00) 		0.876
(1.00)
KCNT2 11 (1%) 761 0.787
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.0885
(1.00) 		0.885
(1.00) 		6.12e-05
(0.0432) 		0.00869
(1.00)
VSTM2B 3 (0%) 769 0.5
(1.00) 		0.338
(1.00) 		1
(1.00) 		1
(1.00) 		1.55e-36
(1.11e-33)
DSPP 26 (3%) 746 0.868
(1.00) 		0.166
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.348
(1.00) 		0.375
(1.00) 		0.946
(1.00)
AKT1 19 (2%) 753 0.196
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.75
(1.00) 		0.0969
(1.00) 		0.902
(1.00) 		0.286
(1.00)
AOAH 19 (2%) 753 0.283
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.0353
(1.00) 		0.408
(1.00) 		0.945
(1.00) 		0.282
(1.00) 		0.187
(1.00)
MAP3K4 18 (2%) 754 0.988
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.0089
(1.00) 		0.857
(1.00) 		0.912
(1.00) 		0.708
(1.00)
MEF2A 14 (2%) 758 0.788
(1.00) 		0.523
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.699
(1.00) 		0.497
(1.00) 		0.0142
(1.00) 		0.321
(1.00)
NCOA3 29 (4%) 743 0.464
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.667
(1.00) 		0.27
(1.00) 		0.148
(1.00) 		0.177
(1.00) 		0.473
(1.00)
NCOR2 29 (4%) 743 0.815
(1.00) 		0.706
(1.00) 		1
(1.00) 		1
(1.00) 		0.647
(1.00) 		0.89
(1.00) 		0.218
(1.00) 		0.902
(1.00)
NR1H2 18 (2%) 754 0.556
(1.00) 		0.712
(1.00) 		1
(1.00) 		1
(1.00) 		0.00449
(1.00) 		0.605
(1.00) 		0.954
(1.00) 		0.0184
(1.00)
PIK3CA 261 (34%) 511 0.922
(1.00) 		0.0242
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.362
(1.00) 		0.539
(1.00) 		0.339
(1.00) 		0.814
(1.00)
RBMX 13 (2%) 759 0.649
(1.00) 		0.875
(1.00) 		1
(1.00) 		0.337
(1.00) 		0.687
(1.00) 		0.886
(1.00) 		0.241
(1.00) 		0.946
(1.00)
TP53 257 (33%) 515 0.454
(1.00) 		0.0372
(1.00) 		0.0575
(1.00) 		0.432
(1.00) 		0.194
(1.00) 		0.411
(1.00) 		0.414
(1.00) 		0.949
(1.00)
TPRX1 7 (1%) 765 0.695
(1.00) 		0.123
(1.00) 		1
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.634
(1.00) 		0.205
(1.00) 		0.769
(1.00)
RUNX1 25 (3%) 747 0.449
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.353
(1.00) 		1
(1.00) 		0.961
(1.00) 		0.532
(1.00) 		0.0785
(1.00)
PTEN 29 (4%) 743 0.889
(1.00) 		0.46
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.293
(1.00) 		0.548
(1.00) 		0.221
(1.00) 		0.0193
(1.00)
TBX3 18 (2%) 754 0.185
(1.00) 		0.0155
(1.00) 		1
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.996
(1.00) 		0.472
(1.00) 		0.985
(1.00)
CBFB 16 (2%) 756 0.968
(1.00) 		0.727
(1.00) 		1
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.273
(1.00) 		0.821
(1.00) 		0.792
(1.00)
MAP2K4 32 (4%) 740 0.181
(1.00) 		0.384
(1.00) 		1
(1.00) 		0.685
(1.00) 		1
(1.00) 		0.353
(1.00) 		0.911
(1.00) 		0.975
(1.00)
CDH1 55 (7%) 717 0.419
(1.00) 		0.0873
(1.00) 		1
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.036
(1.00) 		0.129
(1.00) 		0.103
(1.00)
FOXA1 15 (2%) 757 0.0778
(1.00) 		0.0025
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.413
(1.00) 		0.876
(1.00) 		0.833
(1.00) 		0.0275
(1.00)
MLL3 56 (7%) 716 0.524
(1.00) 		0.012
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.492
(1.00) 		0.662
(1.00) 		0.918
(1.00) 		0.796
(1.00)
ATN1 17 (2%) 755 0.293
(1.00) 		0.957
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.166
(1.00) 		0.946
(1.00) 		0.609
(1.00) 		0.943
(1.00)
SF3B1 14 (2%) 758 0.291
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.369
(1.00) 		1
(1.00) 		0.87
(1.00) 		0.778
(1.00) 		0.737
(1.00)
KRTAP4-7 7 (1%) 765 0.598
(1.00) 		0.484
(1.00) 		1
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.534
(1.00) 		0.458
(1.00) 		0.0459
(1.00)
ZFP36L1 10 (1%) 762 0.981
(1.00) 		0.0124
(1.00) 		1
(1.00) 		0.0719
(1.00) 		1
(1.00) 		0.972
(1.00) 		0.41
(1.00) 		0.786
(1.00)
NCOR1 31 (4%) 741 0.878
(1.00) 		0.937
(1.00) 		1
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.788
(1.00) 		0.462
(1.00) 		0.831
(1.00)
KRAS 6 (1%) 766 0.639
(1.00) 		0.0718
(1.00) 		1
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.308
(1.00) 		0.761
(1.00)
PHLDA1 9 (1%) 763 0.789
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.46
(1.00) 		1
(1.00) 		0.372
(1.00) 		0.000817
(0.573) 		0.0236
(1.00)
VEZF1 8 (1%) 764 0.581
(1.00) 		0.0875
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.542
(1.00) 		0.985
(1.00) 		0.0425
(1.00) 		0.804
(1.00)
ERBB2 12 (2%) 760 0.139
(1.00) 		0.543
(1.00) 		0.118
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.522
(1.00) 		0.777
(1.00)
CTCF 18 (2%) 754 0.117
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.92
(1.00) 		0.0498
(1.00) 		0.712
(1.00)
KRTAP9-9 6 (1%) 766 0.596
(1.00) 		0.409
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.443
(1.00) 		0.977
(1.00) 		0.293
(1.00) 		0.865
(1.00)
BCL6B 8 (1%) 764 0.607
(1.00) 		0.751
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.0547
(1.00) 		0.809
(1.00) 		0.805
(1.00) 		0.935
(1.00)
RB1 14 (2%) 758 0.881
(1.00) 		0.12
(1.00) 		0.137
(1.00) 		0.131
(1.00) 		0.687
(1.00) 		0.015
(1.00) 		0.459
(1.00) 		0.0169
(1.00)
HIST1H3B 7 (1%) 765 0.395
(1.00) 		0.286
(1.00) 		1
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.366
(1.00) 		0.452
(1.00) 		0.364
(1.00)
MYB 11 (1%) 761 0.176
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.487
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.0364
(1.00) 		0.517
(1.00)
E2F4 4 (1%) 768 0.367
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.959
(1.00) 		0.993
(1.00)
MUC20 10 (1%) 762 0.421
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.585
(1.00) 		0.495
(1.00) 		0.533
(1.00) 		0.892
(1.00)
AKD1 19 (2%) 753 0.808
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.408
(1.00) 		0.395
(1.00) 		0.437
(1.00) 		0.67
(1.00)
CDKN1B 7 (1%) 765 0.848
(1.00) 		0.944
(1.00) 		1
(1.00) 		1
(1.00) 		0.0535
(1.00) 		0.0128
(1.00) 		0.0478
(1.00) 		0.0311
(1.00)
KRTAP4-5 4 (1%) 768 0.596
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.275
(1.00) 		0.322
(1.00) 		0.954
(1.00) 		0.466
(1.00) 		0.873
(1.00)
RPGR 14 (2%) 758 0.869
(1.00) 		0.457
(1.00) 		1
(1.00) 		1
(1.00) 		0.212
(1.00) 		0.964
(1.00) 		0.856
(1.00) 		0.673
(1.00)
HLA-A 4 (1%) 768 0.211
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.585
(1.00) 		0.912
(1.00)
FGFR2 7 (1%) 765 0.000457
(0.321) 		0.752
(1.00) 		1
(1.00) 		0.684
(1.00) 		0.163
(1.00) 		0.737
(1.00) 		0.0471
(1.00) 		0.618
(1.00)
TBL1XR1 9 (1%) 763 0.565
(1.00) 		0.0224
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.146
(1.00) 		0.278
(1.00) 		0.454
(1.00) 		0.283
(1.00)
PRRX1 6 (1%) 766 0.487
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.769
(1.00) 		0.722
(1.00) 		0.988
(1.00)
GNRH2 3 (0%) 769 0.91
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.253
(1.00) 		0.233
(1.00) 		0.434
(1.00) 		0.999
(1.00)
DENND4B 8 (1%) 764 0.546
(1.00) 		0.738
(1.00) 		1
(1.00) 		1
(1.00) 		0.542
(1.00) 		0.996
(1.00) 		0.806
(1.00) 		0.902
(1.00)
CCDC66 9 (1%) 763 0.695
(1.00) 		0.751
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.585
(1.00) 		0.636
(1.00) 		0.772
(1.00) 		0.58
(1.00)
HNF1A 9 (1%) 763 0.538
(1.00) 		0.204
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.0691
(1.00) 		0.978
(1.00) 		0.636
(1.00) 		0.959
(1.00)
RAI1 7 (1%) 765 0.679
(1.00) 		0.919
(1.00) 		1
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.0482
(1.00) 		0.584
(1.00)
GPS2 6 (1%) 766 0.22
(1.00) 		0.965
(1.00) 		1
(1.00) 		0.651
(1.00) 		0.638
(1.00)
PCMTD1 3 (0%) 769 0.524
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.996
(1.00) 		0.0156
(1.00) 		0.912
(1.00)
SLC25A5 3 (0%) 769 0.522
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.253
(1.00) 		0.91
(1.00) 		0.932
(1.00) 		0.999
(1.00)
STXBP2 9 (1%) 763 0.251
(1.00) 		0.0463
(1.00) 		1
(1.00) 		0.702
(1.00) 		1
(1.00) 		0.996
(1.00) 		0.935
(1.00) 		0.72
(1.00)
FAM21A 7 (1%) 765 0.785
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.2
(1.00) 		1
(1.00) 		0.971
(1.00) 		0.165
(1.00) 		0.939
(1.00)
ZNF587 9 (1%) 763 0.0994
(1.00) 		0.229
(1.00) 		1
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.987
(1.00) 		0.774
(1.00) 		0.731
(1.00)
POLR2J3 3 (0%) 769 0.889
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.999
(1.00) 		0.148
(1.00) 		0.983
(1.00)
AXL 6 (1%) 766 0.438
(1.00) 		0.733
(1.00) 		1
(1.00) 		0.347
(1.00) 		0.443
(1.00) 		0.621
(1.00) 		0.447
(1.00) 		0.564
(1.00)
MUC21 6 (1%) 766 0.413
(1.00) 		0.462
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.999
(1.00) 		0.00268
(1.00) 		0.429
(1.00)
MED23 13 (2%) 759 0.426
(1.00) 		0.0131
(1.00) 		1
(1.00) 		0.109
(1.00) 		1
(1.00) 		0.835
(1.00) 		0.168
(1.00) 		0.188
(1.00)
HS6ST1 5 (1%) 767 0.688
(1.00) 		0.685
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.0133
(1.00) 		0.98
(1.00)
RALY 6 (1%) 766 0.728
(1.00) 		0.523
(1.00) 		1
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.902
(1.00) 		0.437
(1.00) 		0.734
(1.00)
UBC 8 (1%) 764 0.216
(1.00) 		0.672
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.927
(1.00) 		0.844
(1.00) 		0.98
(1.00)
TLR4 11 (1%) 761 0.41
(1.00) 		0.457
(1.00) 		1
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.651
(1.00) 		0.656
(1.00) 		0.926
(1.00)
ODF1 5 (1%) 767 0.722
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.0808
(1.00) 		0.731
(1.00) 		0.966
(1.00) 		0.549
(1.00)
PABPC3 8 (1%) 764 0.302
(1.00) 		0.94
(1.00) 		0.0803
(1.00) 		1
(1.00) 		1
(1.00) 		0.993
(1.00) 		0.164
(1.00) 		0.809
(1.00)
NEK5 9 (1%) 763 0.899
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.46
(1.00) 		1
(1.00) 		0.14
(1.00) 		0.832
(1.00) 		0.0973
(1.00)
ASPHD1 3 (0%) 769 0.0442
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.727
(1.00) 		0.946
(1.00)
FAM47B 7 (1%) 765 0.434
(1.00) 		0.729
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.385
(1.00) 		0.3
(1.00) 		0.418
(1.00) 		0.591
(1.00)
PCDH19 14 (2%) 758 0.517
(1.00) 		0.876
(1.00) 		1
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.819
(1.00) 		0.482
(1.00) 		0.334
(1.00)
ZIC3 4 (1%) 768 0.625
(1.00) 		0.869
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.766
(1.00) 		0.999
(1.00)
FAM21C 6 (1%) 766 0.768
(1.00) 		0.684
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.385
(1.00) 		0.953
(1.00) 		0.058
(1.00) 		0.931
(1.00)
SELPLG 7 (1%) 765 0.662
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.198
(1.00) 		0.448
(1.00) 		0.000817
(0.573) 		0.761
(1.00)
SLC30A10 5 (1%) 767 0.449
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.229
(1.00) 		0.421
(1.00) 		0.959
(1.00)
RGS7 8 (1%) 764 0.365
(1.00) 		1
(1.00) 		1
(1.00) 		0.215
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.594
(1.00) 		0.837
(1.00)
'PIK3R1 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 7.27e-06 (Chi-square test), Q value = 0.0052

Table S1.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B NX
ALL 207 10 72 1 77 100 24 2 16 42 44 10 23 2 8
PIK3R1 MUTATED 5 0 1 1 3 1 0 0 1 1 1 0 0 0 0
PIK3R1 WILD-TYPE 202 10 71 0 74 99 24 2 15 41 43 10 23 2 8

Figure S1.  Get High-res Image Gene #2: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'DCP1B MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.31e-06 (Chi-square test), Q value = 0.0016

Table S2.  Gene #5: 'DCP1B MUTATION STATUS' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 60 41 2 3 223 140 100 20 28 9 11
DCP1B MUTATED 1 0 0 1 0 2 1 0 0 0 0
DCP1B WILD-TYPE 59 41 2 2 223 138 99 20 28 9 11

Figure S2.  Get High-res Image Gene #5: 'DCP1B MUTATION STATUS' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

'GATA3 MUTATION STATUS' versus 'AGE'

P value = 0.000213 (t-test), Q value = 0.15

Table S3.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 772 58.0 (13.1)
GATA3 MUTATED 81 52.8 (13.0)
GATA3 WILD-TYPE 691 58.6 (13.0)

Figure S3.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'ZNF384 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-05 (t-test), Q value = 0.0082

Table S4.  Gene #16: 'ZNF384 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
ZNF384 MUTATED 14 0.6 (0.9)
ZNF384 WILD-TYPE 621 2.2 (4.1)

Figure S4.  Get High-res Image Gene #16: 'ZNF384 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

'MAP3K1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.24e-07 (t-test), Q value = 0.00052

Table S5.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
MAP3K1 MUTATED 45 0.9 (1.3)
MAP3K1 WILD-TYPE 590 2.2 (4.1)

Figure S5.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

'CCDC144NL MUTATION STATUS' versus 'Time to Death'

P value = 5.1e-05 (logrank test), Q value = 0.036

Table S6.  Gene #28: 'CCDC144NL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 715 91 0.0 - 223.4 (18.4)
CCDC144NL MUTATED 6 1 1.6 - 15.0 (7.5)
CCDC144NL WILD-TYPE 709 90 0.0 - 223.4 (18.9)

Figure S6.  Get High-res Image Gene #28: 'CCDC144NL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'MUC12 MUTATION STATUS' versus 'DISTANT.METASTASIS'

P value = 0.000132 (Fisher's exact test), Q value = 0.093

Table S7.  Gene #29: 'MUC12 MUTATION STATUS' versus Clinical Feature #5: 'DISTANT.METASTASIS'

nPatients CM0 (I+) M0 M1 MX
ALL 2 579 9 48
MUC12 MUTATED 0 26 1 11
MUC12 WILD-TYPE 2 553 8 37

Figure S7.  Get High-res Image Gene #29: 'MUC12 MUTATION STATUS' versus Clinical Feature #5: 'DISTANT.METASTASIS'

'CTU2 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.18e-08 (Chi-square test), Q value = 8.4e-06

Table S8.  Gene #40: 'CTU2 MUTATION STATUS' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 60 41 2 3 223 140 100 20 28 9 11
CTU2 MUTATED 0 2 0 1 1 0 0 1 0 0 0
CTU2 WILD-TYPE 60 39 2 2 222 140 100 19 28 9 11

Figure S8.  Get High-res Image Gene #40: 'CTU2 MUTATION STATUS' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

'AQP7 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 7.57e-06 (Chi-square test), Q value = 0.0054

Table S9.  Gene #43: 'AQP7 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B NX
ALL 207 10 72 1 77 100 24 2 16 42 44 10 23 2 8
AQP7 MUTATED 1 0 0 0 2 1 0 0 0 1 1 0 0 1 0
AQP7 WILD-TYPE 206 10 72 1 75 99 24 2 16 41 43 10 23 1 8

Figure S9.  Get High-res Image Gene #43: 'AQP7 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

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

P value = 5.57e-05 (t-test), Q value = 0.039

Table S10.  Gene #51: 'CASP8 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
CASP8 MUTATED 8 0.4 (0.7)
CASP8 WILD-TYPE 627 2.2 (4.0)

Figure S10.  Get High-res Image Gene #51: 'CASP8 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

'ZNF69 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.45e-19 (Chi-square test), Q value = 1e-16

Table S11.  Gene #56: 'ZNF69 MUTATION STATUS' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 60 41 2 3 223 140 100 20 28 9 11
ZNF69 MUTATED 0 0 1 0 0 1 0 0 1 0 0
ZNF69 WILD-TYPE 60 41 1 3 223 139 100 20 27 9 11

Figure S11.  Get High-res Image Gene #56: 'ZNF69 MUTATION STATUS' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

'HLA-DRB1 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 3.34e-08 (Chi-square test), Q value = 2.4e-05

Table S12.  Gene #58: 'HLA-DRB1 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B NX
ALL 207 10 72 1 77 100 24 2 16 42 44 10 23 2 8
HLA-DRB1 MUTATED 1 0 0 0 0 3 2 0 0 0 0 0 0 1 0
HLA-DRB1 WILD-TYPE 206 10 72 1 77 97 22 2 16 42 44 10 23 1 8

Figure S12.  Get High-res Image Gene #58: 'HLA-DRB1 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'AFF2 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.99e-05 (t-test), Q value = 0.014

Table S13.  Gene #61: 'AFF2 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
AFF2 MUTATED 11 0.5 (0.8)
AFF2 WILD-TYPE 624 2.2 (4.0)

Figure S13.  Get High-res Image Gene #61: 'AFF2 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

'KRT38 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 1.94e-17 (Chi-square test), Q value = 1.4e-14

Table S14.  Gene #74: 'KRT38 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B NX
ALL 207 10 72 1 77 100 24 2 16 42 44 10 23 2 8
KRT38 MUTATED 0 0 0 0 0 2 0 1 0 0 0 0 0 0 0
KRT38 WILD-TYPE 207 10 72 1 77 98 24 1 16 42 44 10 23 2 8

Figure S14.  Get High-res Image Gene #74: 'KRT38 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'KCNT2 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.12e-05 (t-test), Q value = 0.043

Table S15.  Gene #81: 'KCNT2 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
KCNT2 MUTATED 9 0.7 (0.7)
KCNT2 WILD-TYPE 626 2.2 (4.0)

Figure S15.  Get High-res Image Gene #81: 'KCNT2 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

'VSTM2B MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.55e-36 (t-test), Q value = 1.1e-33

Table S16.  Gene #88: 'VSTM2B MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
VSTM2B MUTATED 3 0.0 (0.0)
VSTM2B WILD-TYPE 632 2.2 (4.0)

Figure S16.  Get High-res Image Gene #88: 'VSTM2B MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

  • Mutation data file = BRCA-TP.mutsig.cluster.txt

  • Clinical data file = BRCA-TP.clin.merged.picked.txt

  • Number of patients = 772

  • Number of significantly mutated genes = 91

  • Number of selected clinical features = 9

  • 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

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

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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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