Breast Invasive Carcinoma: Correlation between gene mutation status and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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, 18 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'.

  • CDKN1B mutation correlated to 'LYMPH.NODE.METASTASIS'.

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

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

  • 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, 18 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) 		0.484
(1.00) 		5.55e-05
(0.0395) 		0.0805
(1.00) 		0.283
(1.00)
DCP1B 5 (1%) 767 0.55
(1.00) 		0.025
(1.00) 		1
(1.00) 		0.335
(1.00) 		0.375
(1.00) 		0.511
(1.00) 		0.44
(1.00) 		1.04e-07
(7.51e-05)
GATA3 81 (10%) 691 0.74
(1.00) 		0.000213
(0.15) 		0.59
(1.00) 		0.139
(1.00) 		0.0975
(1.00) 		0.779
(1.00) 		0.598
(1.00) 		0.219
(1.00)
ZNF384 14 (2%) 758 0.408
(1.00) 		0.0126
(1.00) 		1
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.965
(1.00) 		1.16e-05
(0.00832) 		0.442
(1.00)
MAP3K1 57 (7%) 715 0.781
(1.00) 		0.00186
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.564
(1.00) 		0.101
(1.00) 		7.24e-07
(0.00052) 		0.676
(1.00)
CCDC144NL 8 (1%) 764 5.1e-05
(0.0364) 		0.051
(1.00) 		1
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.408
(1.00) 		0.296
(1.00) 		0.447
(1.00)
MUC12 44 (6%) 728 0.00337
(1.00) 		0.375
(1.00) 		1
(1.00) 		1
(1.00) 		0.000329
(0.233) 		0.000847
(0.595) 		0.0562
(1.00) 		0.19
(1.00)
CTU2 5 (1%) 767 0.556
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.947
(1.00) 		0.058
(1.00) 		1.52e-09
(1.09e-06)
AQP7 8 (1%) 764 0.0122
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.215
(1.00) 		1
(1.00) 		1.65e-06
(0.00118) 		0.196
(1.00) 		0.785
(1.00)
CDKN1B 7 (1%) 765 0.848
(1.00) 		0.944
(1.00) 		1
(1.00) 		1
(1.00) 		0.0221
(1.00) 		3.99e-05
(0.0285) 		0.0478
(1.00) 		0.0507
(1.00)
CASP8 10 (1%) 762 0.931
(1.00) 		0.58
(1.00) 		1
(1.00) 		0.467
(1.00) 		0.61
(1.00) 		0.898
(1.00) 		5.57e-05
(0.0396) 		0.753
(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) 		2.59e-33
(1.87e-30) 		0.585
(1.00) 		0.806
(1.00)
ZNF69 5 (1%) 767 0.156
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.335
(1.00) 		0.142
(1.00) 		0.897
(1.00) 		0.56
(1.00) 		9.9e-05
(0.0702)
HLA-DRB1 8 (1%) 764 0.568
(1.00) 		0.00708
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.166
(1.00) 		8.54e-08
(6.15e-05) 		0.695
(1.00) 		0.779
(1.00)
AFF2 15 (2%) 757 0.762
(1.00) 		0.0374
(1.00) 		1
(1.00) 		0.552
(1.00) 		0.726
(1.00) 		0.998
(1.00) 		1.99e-05
(0.0142) 		0.983
(1.00)
KRT38 4 (1%) 768 0.5
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.275
(1.00) 		1
(1.00) 		7.11e-15
(5.14e-12) 		0.0539
(1.00) 		0.991
(1.00)
KCNT2 11 (1%) 761 0.787
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.161
(1.00) 		0.967
(1.00) 		6.12e-05
(0.0435) 		0.127
(1.00)
VSTM2B 3 (0%) 769 0.5
(1.00) 		0.338
(1.00) 		1
(1.00) 		1
(1.00) 		0.245
(1.00) 		0.998
(1.00) 		1.55e-36
(1.12e-33) 		0.928
(1.00)
DSPP 26 (3%) 746 0.868
(1.00) 		0.166
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.375
(1.00) 		0.838
(1.00)
AKT1 19 (2%) 753 0.196
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.597
(1.00) 		0.0403
(1.00) 		0.902
(1.00) 		0.54
(1.00)
AOAH 19 (2%) 753 0.283
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.0353
(1.00) 		0.275
(1.00) 		0.918
(1.00) 		0.282
(1.00) 		0.186
(1.00)
MAP3K4 18 (2%) 754 0.988
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.00144
(1.00) 		0.854
(1.00) 		0.912
(1.00) 		0.807
(1.00)
MEF2A 14 (2%) 758 0.788
(1.00) 		0.523
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.719
(1.00) 		0.758
(1.00) 		0.0142
(1.00) 		0.433
(1.00)
NCOA3 29 (4%) 743 0.464
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.667
(1.00) 		0.141
(1.00) 		0.219
(1.00) 		0.177
(1.00) 		0.475
(1.00)
NCOR2 29 (4%) 743 0.815
(1.00) 		0.706
(1.00) 		1
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.931
(1.00) 		0.218
(1.00) 		0.956
(1.00)
NR1H2 18 (2%) 754 0.556
(1.00) 		0.712
(1.00) 		1
(1.00) 		1
(1.00) 		0.0028
(1.00) 		0.639
(1.00) 		0.954
(1.00) 		0.0161
(1.00)
PIK3CA 261 (34%) 511 0.922
(1.00) 		0.0242
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.357
(1.00) 		0.435
(1.00) 		0.339
(1.00) 		0.474
(1.00)
RBMX 13 (2%) 759 0.649
(1.00) 		0.875
(1.00) 		1
(1.00) 		0.337
(1.00) 		1
(1.00) 		0.95
(1.00) 		0.241
(1.00) 		0.972
(1.00)
TP53 257 (33%) 515 0.454
(1.00) 		0.0372
(1.00) 		0.0575
(1.00) 		0.432
(1.00) 		0.0546
(1.00) 		0.39
(1.00) 		0.414
(1.00) 		0.739
(1.00)
TPRX1 7 (1%) 765 0.695
(1.00) 		0.123
(1.00) 		1
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.976
(1.00) 		0.205
(1.00) 		0.803
(1.00)
RUNX1 25 (3%) 747 0.449
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.353
(1.00) 		1
(1.00) 		0.885
(1.00) 		0.532
(1.00) 		0.102
(1.00)
PTEN 29 (4%) 743 0.889
(1.00) 		0.46
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.0616
(1.00) 		0.385
(1.00) 		0.221
(1.00) 		0.0204
(1.00)
TBX3 18 (2%) 754 0.185
(1.00) 		0.0155
(1.00) 		1
(1.00) 		1
(1.00) 		0.57
(1.00) 		0.989
(1.00) 		0.472
(1.00) 		0.672
(1.00)
CBFB 16 (2%) 756 0.968
(1.00) 		0.727
(1.00) 		1
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.471
(1.00) 		0.821
(1.00) 		0.916
(1.00)
MAP2K4 32 (4%) 740 0.181
(1.00) 		0.384
(1.00) 		1
(1.00) 		0.685
(1.00) 		0.647
(1.00) 		0.331
(1.00) 		0.911
(1.00) 		0.986
(1.00)
CDH1 55 (7%) 717 0.419
(1.00) 		0.0873
(1.00) 		1
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.0256
(1.00) 		0.129
(1.00) 		0.133
(1.00)
FOXA1 15 (2%) 757 0.0778
(1.00) 		0.0025
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.484
(1.00) 		0.99
(1.00) 		0.833
(1.00) 		0.0945
(1.00)
MLL3 56 (7%) 716 0.524
(1.00) 		0.012
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.418
(1.00) 		0.317
(1.00) 		0.918
(1.00) 		0.86
(1.00)
ATN1 17 (2%) 755 0.293
(1.00) 		0.957
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.104
(1.00) 		0.988
(1.00) 		0.609
(1.00) 		0.833
(1.00)
SF3B1 14 (2%) 758 0.291
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.719
(1.00) 		0.982
(1.00) 		0.778
(1.00) 		0.295
(1.00)
KRTAP4-7 7 (1%) 765 0.598
(1.00) 		0.484
(1.00) 		1
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.558
(1.00) 		0.458
(1.00) 		0.0516
(1.00)
ZFP36L1 10 (1%) 762 0.981
(1.00) 		0.0124
(1.00) 		1
(1.00) 		0.0719
(1.00) 		0.222
(1.00) 		0.943
(1.00) 		0.41
(1.00) 		0.668
(1.00)
NCOR1 31 (4%) 741 0.878
(1.00) 		0.937
(1.00) 		1
(1.00) 		1
(1.00) 		0.348
(1.00) 		0.822
(1.00) 		0.462
(1.00) 		0.879
(1.00)
KRAS 6 (1%) 766 0.639
(1.00) 		0.0718
(1.00) 		1
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.948
(1.00) 		0.308
(1.00) 		0.701
(1.00)
PHLDA1 9 (1%) 763 0.789
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.198
(1.00) 		0.909
(1.00) 		0.000817
(0.576) 		0.248
(1.00)
VEZF1 8 (1%) 764 0.581
(1.00) 		0.0875
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.529
(1.00) 		0.995
(1.00) 		0.0425
(1.00) 		0.943
(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) 		0.977
(1.00) 		0.522
(1.00) 		0.931
(1.00)
CTCF 18 (2%) 754 0.117
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00) 		0.57
(1.00) 		0.991
(1.00) 		0.0498
(1.00) 		0.361
(1.00)
KRTAP9-9 6 (1%) 766 0.596
(1.00) 		0.409
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.431
(1.00) 		0.979
(1.00) 		0.293
(1.00) 		0.929
(1.00)
BCL6B 8 (1%) 764 0.607
(1.00) 		0.751
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.0407
(1.00) 		0.823
(1.00) 		0.805
(1.00) 		0.938
(1.00)
RB1 14 (2%) 758 0.881
(1.00) 		0.12
(1.00) 		0.137
(1.00) 		0.131
(1.00) 		0.719
(1.00) 		0.0718
(1.00) 		0.459
(1.00) 		0.00167
(1.00)
HIST1H3B 7 (1%) 765 0.395
(1.00) 		0.286
(1.00) 		1
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.874
(1.00) 		0.452
(1.00) 		0.803
(1.00)
MYB 11 (1%) 761 0.176
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.487
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.0364
(1.00) 		0.757
(1.00)
E2F4 4 (1%) 768 0.367
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.988
(1.00) 		0.982
(1.00)
MUC20 10 (1%) 762 0.421
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.61
(1.00) 		0.812
(1.00) 		0.533
(1.00) 		0.969
(1.00)
AKD1 19 (2%) 753 0.808
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.275
(1.00) 		0.372
(1.00) 		0.437
(1.00) 		0.705
(1.00)
KRTAP4-5 4 (1%) 768 0.596
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.275
(1.00) 		0.313
(1.00) 		0.972
(1.00) 		0.466
(1.00) 		0.905
(1.00)
RPGR 14 (2%) 758 0.869
(1.00) 		0.457
(1.00) 		1
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.879
(1.00) 		0.856
(1.00) 		0.892
(1.00)
FGFR2 7 (1%) 765 0.000457
(0.323) 		0.752
(1.00) 		1
(1.00) 		0.684
(1.00) 		0.134
(1.00) 		0.789
(1.00) 		0.0471
(1.00) 		0.755
(1.00)
TBL1XR1 9 (1%) 763 0.565
(1.00) 		0.0224
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.198
(1.00) 		0.413
(1.00) 		0.454
(1.00) 		0.445
(1.00)
PRRX1 6 (1%) 766 0.487
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.778
(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) 		0.245
(1.00) 		0.204
(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) 		0.529
(1.00) 		0.998
(1.00) 		0.806
(1.00) 		0.925
(1.00)
CCDC66 9 (1%) 763 0.695
(1.00) 		0.751
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.571
(1.00) 		0.809
(1.00) 		0.772
(1.00) 		0.749
(1.00)
HNF1A 9 (1%) 763 0.538
(1.00) 		0.204
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.0652
(1.00) 		0.99
(1.00) 		0.636
(1.00) 		0.98
(1.00)
RAI1 7 (1%) 765 0.679
(1.00) 		0.919
(1.00) 		1
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.963
(1.00) 		0.0482
(1.00) 		0.378
(1.00)
GPS2 6 (1%) 766 0.22
(1.00) 		0.965
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.358
(1.00) 		0.638
(1.00) 		0.109
(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) 		0.977
(1.00)
SLC25A5 3 (0%) 769 0.522
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.245
(1.00) 		0.948
(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) 		0.995
(1.00) 		0.935
(1.00) 		0.698
(1.00)
FAM21A 7 (1%) 765 0.785
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.2
(1.00) 		1
(1.00) 		0.979
(1.00) 		0.165
(1.00) 		0.817
(1.00)
ZNF587 9 (1%) 763 0.0994
(1.00) 		0.229
(1.00) 		1
(1.00) 		1
(1.00) 		0.283
(1.00) 		0.966
(1.00) 		0.774
(1.00) 		0.775
(1.00)
POLR2J3 3 (0%) 769 0.889
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		1
(1.00) 		0.148
(1.00) 		0.99
(1.00)
AXL 6 (1%) 766 0.438
(1.00) 		0.733
(1.00) 		1
(1.00) 		0.347
(1.00) 		0.431
(1.00) 		0.633
(1.00) 		0.447
(1.00) 		0.613
(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) 		0.813
(1.00)
MED23 13 (2%) 759 0.426
(1.00) 		0.0131
(1.00) 		1
(1.00) 		0.109
(1.00) 		1
(1.00) 		0.93
(1.00) 		0.168
(1.00) 		0.523
(1.00)
HS6ST1 5 (1%) 767 0.688
(1.00) 		0.685
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.984
(1.00) 		0.0133
(1.00) 		0.981
(1.00)
RALY 6 (1%) 766 0.728
(1.00) 		0.523
(1.00) 		1
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.932
(1.00) 		0.437
(1.00) 		0.759
(1.00)
UBC 8 (1%) 764 0.216
(1.00) 		0.672
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.906
(1.00) 		0.844
(1.00) 		0.935
(1.00)
TLR4 11 (1%) 761 0.41
(1.00) 		0.457
(1.00) 		1
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.843
(1.00) 		0.656
(1.00) 		0.978
(1.00)
ODF1 5 (1%) 767 0.722
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.0749
(1.00) 		0.697
(1.00) 		0.966
(1.00) 		0.591
(1.00)
PABPC3 8 (1%) 764 0.302
(1.00) 		0.94
(1.00) 		0.0803
(1.00) 		1
(1.00) 		1
(1.00) 		0.973
(1.00) 		0.164
(1.00) 		0.884
(1.00)
NEK5 9 (1%) 763 0.899
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.571
(1.00) 		0.0203
(1.00) 		0.832
(1.00) 		0.24
(1.00)
ASPHD1 3 (0%) 769 0.0442
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.879
(1.00) 		0.727
(1.00) 		0.966
(1.00)
FAM47B 7 (1%) 765 0.434
(1.00) 		0.729
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.482
(1.00) 		0.572
(1.00) 		0.418
(1.00) 		0.962
(1.00)
PCDH19 14 (2%) 758 0.517
(1.00) 		0.876
(1.00) 		1
(1.00) 		1
(1.00) 		0.236
(1.00) 		0.956
(1.00) 		0.482
(1.00) 		0.802
(1.00)
ZIC3 4 (1%) 768 0.625
(1.00) 		0.869
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.513
(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) 		0.431
(1.00) 		0.956
(1.00) 		0.058
(1.00) 		0.984
(1.00)
SELPLG 7 (1%) 765 0.662
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.134
(1.00) 		0.71
(1.00) 		0.000817
(0.576) 		0.794
(1.00)
SLC30A10 5 (1%) 767 0.449
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.242
(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) 		0.815
(1.00) 		0.594
(1.00) 		0.864
(1.00)
'PIK3R1 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 5.55e-05 (Chi-square test), Q value = 0.04

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 N3C NX
ALL 225 19 113 1 93 116 30 2 18 50 49 15 25 2 1 13
PIK3R1 MUTATED 5 0 3 1 5 1 0 0 1 3 2 0 0 0 0 0
PIK3R1 WILD-TYPE 220 19 110 0 88 115 30 2 17 47 47 15 25 2 1 13

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 = 1.04e-07 (Chi-square test), Q value = 7.5e-05

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 TIS STAGE X
ALL 61 61 6 3 268 167 117 23 33 15 1 16
DCP1B MUTATED 1 0 0 1 0 2 1 0 0 0 0 0
DCP1B WILD-TYPE 60 61 6 2 268 165 116 23 33 15 1 16

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 = 0.0083

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 = 0.000329 (Fisher's exact test), Q value = 0.23

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

nPatients CM0 (I+) M0 M1 MX
ALL 2 703 15 52
MUC12 MUTATED 0 32 1 11
MUC12 WILD-TYPE 2 671 14 41

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 = 1.52e-09 (Chi-square test), Q value = 1.1e-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 TIS STAGE X
ALL 61 61 6 3 268 167 117 23 33 15 1 16
CTU2 MUTATED 0 2 0 1 1 0 0 1 0 0 0 0
CTU2 WILD-TYPE 61 59 6 2 267 167 117 22 33 15 1 16

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 = 1.65e-06 (Chi-square test), Q value = 0.0012

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 N3C NX
ALL 225 19 113 1 93 116 30 2 18 50 49 15 25 2 1 13
AQP7 MUTATED 1 1 0 0 2 1 0 0 0 1 1 0 0 1 0 0
AQP7 WILD-TYPE 224 18 113 1 91 115 30 2 18 49 48 15 25 1 1 13

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

'CDKN1B MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 3.99e-05 (Chi-square test), Q value = 0.028

Table S10.  Gene #48: 'CDKN1B 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 N3C NX
ALL 225 19 113 1 93 116 30 2 18 50 49 15 25 2 1 13
CDKN1B MUTATED 0 0 1 0 0 0 1 0 0 0 2 0 3 0 0 0
CDKN1B WILD-TYPE 225 19 112 1 93 116 29 2 18 50 47 15 22 2 1 13

Figure S10.  Get High-res Image Gene #48: 'CDKN1B 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 = 0.04

Table S11.  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 S11.  Get High-res Image Gene #51: 'CASP8 MUTATION STATUS' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

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

P value = 2.59e-33 (Chi-square test), Q value = 1.9e-30

Table S12.  Gene #52: 'HLA-A 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 N3C NX
ALL 225 19 113 1 93 116 30 2 18 50 49 15 25 2 1 13
HLA-A MUTATED 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0
HLA-A WILD-TYPE 224 19 112 1 92 116 30 2 18 50 49 15 25 2 0 13

Figure S12.  Get High-res Image Gene #52: 'HLA-A MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'ZNF69 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.9e-05 (Chi-square test), Q value = 0.07

Table S13.  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 TIS STAGE X
ALL 61 61 6 3 268 167 117 23 33 15 1 16
ZNF69 MUTATED 0 0 1 0 1 1 0 0 1 1 0 0
ZNF69 WILD-TYPE 61 61 5 3 267 166 117 23 32 14 1 16

Figure S13.  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 = 8.54e-08 (Chi-square test), Q value = 6.1e-05

Table S14.  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 N3C NX
ALL 225 19 113 1 93 116 30 2 18 50 49 15 25 2 1 13
HLA-DRB1 MUTATED 1 0 0 0 1 3 2 0 0 0 0 0 0 1 0 0
HLA-DRB1 WILD-TYPE 224 19 113 1 92 113 28 2 18 50 49 15 25 1 1 13

Figure S14.  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 S15.  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 S15.  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 = 7.11e-15 (Chi-square test), Q value = 5.1e-12

Table S16.  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 N3C NX
ALL 225 19 113 1 93 116 30 2 18 50 49 15 25 2 1 13
KRT38 MUTATED 0 0 1 0 0 2 0 1 0 0 0 0 0 0 0 0
KRT38 WILD-TYPE 225 19 112 1 93 114 30 1 18 50 49 15 25 2 1 13

Figure S16.  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 S17.  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 S17.  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 S18.  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 S18.  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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