Correlation between gene mutation status and selected clinical features
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.

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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