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 89 genes and 10 clinical features across 771 patients, 13 significant findings detected with Q value < 0.25.

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

  • GATA3 mutation correlated to 'AGE'.

  • TP53 mutation correlated to 'HISTOLOGICAL.TYPE'.

  • CDH1 mutation correlated to 'HISTOLOGICAL.TYPE'.

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

  • RB1 mutation correlated to 'NEOPLASM.DISEASESTAGE'.

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

  • CTU2 mutation correlated to 'HISTOLOGICAL.TYPE'.

  • HLA-A mutation correlated to 'HISTOLOGICAL.TYPE'.

  • ODF1 mutation correlated to 'HISTOLOGICAL.TYPE'.

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

  • ATP13A4 mutation correlated to 'NEOPLASM.DISEASESTAGE'.

  • MED15 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 89 genes and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 13 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES
nMutated (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test
ZNF384 14 (2%) 757 0.337
(1.00) 		0.0127
(1.00) 		0.439
(1.00) 		0.26
(1.00) 		0.428
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.767
(1.00) 		1.16e-05
(0.0102)
GATA3 81 (11%) 690 0.612
(1.00) 		0.000217
(0.19) 		0.229
(1.00) 		0.00817
(1.00) 		0.664
(1.00) 		0.0979
(1.00) 		0.59
(1.00) 		0.145
(1.00) 		0.151
(1.00) 		0.598
(1.00)
TP53 257 (33%) 514 0.529
(1.00) 		0.0384
(1.00) 		0.655
(1.00) 		0.0647
(1.00) 		0.0687
(1.00) 		0.0552
(1.00) 		0.0574
(1.00) 		9.97e-07
(0.000882) 		0.498
(1.00) 		0.414
(1.00)
CDH1 55 (7%) 716 0.554
(1.00) 		0.0861
(1.00) 		0.148
(1.00) 		0.000345
(0.302) 		0.00513
(1.00) 		0.799
(1.00) 		1
(1.00) 		4.43e-69
(3.93e-66) 		1
(1.00) 		0.129
(1.00)
MAP3K1 57 (7%) 714 0.707
(1.00) 		0.00183
(1.00) 		0.652
(1.00) 		0.112
(1.00) 		0.976
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.634
(1.00) 		1
(1.00) 		7.24e-07
(0.000641)
RB1 14 (2%) 757 0.885
(1.00) 		0.12
(1.00) 		5.48e-05
(0.0483) 		0.521
(1.00) 		0.197
(1.00) 		0.719
(1.00) 		0.137
(1.00) 		0.921
(1.00) 		0.371
(1.00) 		0.459
(1.00)
CASP8 10 (1%) 761 0.793
(1.00) 		0.581
(1.00) 		0.724
(1.00) 		0.93
(1.00) 		0.313
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.732
(1.00) 		0.297
(1.00) 		5.57e-05
(0.0489)
CTU2 5 (1%) 766 0.542
(1.00) 		0.569
(1.00) 		0.187
(1.00) 		0.257
(1.00) 		0.594
(1.00) 		1
(1.00) 		1
(1.00) 		0.000116
(0.102) 		0.329
(1.00) 		0.058
(1.00)
HLA-A 4 (1%) 767 0.215
(1.00) 		0.437
(1.00) 		0.789
(1.00) 		1
(1.00) 		0.366
(1.00) 		1
(1.00) 		1
(1.00) 		9.52e-06
(0.00841) 		0.318
(1.00) 		0.585
(1.00)
ODF1 5 (1%) 766 0.0936
(1.00) 		0.569
(1.00) 		0.592
(1.00) 		0.106
(1.00) 		0.376
(1.00) 		0.0751
(1.00) 		1
(1.00) 		4.19e-05
(0.0369) 		0.625
(1.00) 		0.966
(1.00)
ASXL2 8 (1%) 763 0.968
(1.00) 		0.947
(1.00) 		0.976
(1.00) 		0.75
(1.00) 		0.417
(1.00) 		1
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.694
(1.00) 		7.01e-05
(0.0616)
ATP13A4 9 (1%) 762 0.248
(1.00) 		0.545
(1.00) 		1.54e-06
(0.00136) 		0.851
(1.00) 		0.501
(1.00) 		1
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.718
(1.00) 		0.0558
(1.00)
MED15 7 (1%) 764 0.38
(1.00) 		0.721
(1.00) 		0.26
(1.00) 		0.5
(1.00) 		0.844
(1.00) 		0.483
(1.00) 		0.0707
(1.00) 		0.916
(1.00) 		1
(1.00) 		7.01e-05
(0.0616)
PTEN 29 (4%) 742 0.578
(1.00) 		0.458
(1.00) 		0.00561
(1.00) 		0.421
(1.00) 		0.278
(1.00) 		0.0618
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.834
(1.00) 		0.221
(1.00)
MLL3 61 (8%) 710 0.455
(1.00) 		0.00965
(1.00) 		0.923
(1.00) 		0.684
(1.00) 		0.222
(1.00) 		0.518
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.238
(1.00) 		0.62
(1.00)
NUDT11 8 (1%) 763 0.615
(1.00) 		0.575
(1.00) 		0.998
(1.00) 		0.416
(1.00) 		0.868
(1.00) 		0.0408
(1.00) 		1
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.513
(1.00)
GIGYF2 13 (2%) 758 0.313
(1.00) 		0.649
(1.00) 		0.328
(1.00) 		0.00367
(1.00) 		0.0598
(1.00) 		0.136
(1.00) 		1
(1.00) 		0.915
(1.00) 		0.0577
(1.00) 		0.968
(1.00)
DCP1B 5 (1%) 766 0.538
(1.00) 		0.025
(1.00) 		0.991
(1.00) 		0.69
(1.00) 		0.776
(1.00) 		0.375
(1.00) 		1
(1.00) 		0.937
(1.00) 		0.329
(1.00) 		0.44
(1.00)
PIK3CA 261 (34%) 510 0.865
(1.00) 		0.0233
(1.00) 		0.523
(1.00) 		0.796
(1.00) 		0.951
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.0299
(1.00) 		1
(1.00) 		0.339
(1.00)
NCOA3 29 (4%) 742 0.68
(1.00) 		0.875
(1.00) 		0.562
(1.00) 		0.335
(1.00) 		0.35
(1.00) 		0.142
(1.00) 		1
(1.00) 		0.473
(1.00) 		0.681
(1.00) 		0.177
(1.00)
AOAH 19 (2%) 752 0.352
(1.00) 		0.425
(1.00) 		0.197
(1.00) 		0.0516
(1.00) 		0.907
(1.00) 		0.276
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.119
(1.00) 		0.282
(1.00)
RBMX 13 (2%) 758 0.709
(1.00) 		0.874
(1.00) 		0.971
(1.00) 		0.1
(1.00) 		0.401
(1.00) 		1
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.534
(1.00) 		0.241
(1.00)
RUNX1 25 (3%) 746 0.445
(1.00) 		0.603
(1.00) 		0.0208
(1.00) 		0.122
(1.00) 		0.654
(1.00) 		1
(1.00) 		1
(1.00) 		0.0572
(1.00) 		0.498
(1.00) 		0.532
(1.00)
PIK3R1 21 (3%) 750 0.283
(1.00) 		0.686
(1.00) 		0.3
(1.00) 		0.0681
(1.00) 		0.411
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.0805
(1.00)
MEF2A 14 (2%) 757 0.246
(1.00) 		0.522
(1.00) 		0.42
(1.00) 		0.541
(1.00) 		0.37
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.0202
(1.00) 		1
(1.00) 		0.0142
(1.00)
NCOR2 29 (4%) 742 0.793
(1.00) 		0.709
(1.00) 		0.957
(1.00) 		0.431
(1.00) 		0.605
(1.00) 		0.375
(1.00) 		1
(1.00) 		0.884
(1.00) 		1
(1.00) 		0.218
(1.00)
AKT1 19 (2%) 752 0.182
(1.00) 		0.133
(1.00) 		0.541
(1.00) 		0.321
(1.00) 		0.646
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.119
(1.00) 		0.902
(1.00)
NR1H2 18 (2%) 753 0.147
(1.00) 		0.714
(1.00) 		0.00131
(1.00) 		0.274
(1.00) 		0.589
(1.00) 		0.00281
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.792
(1.00) 		0.954
(1.00)
MAP3K4 18 (2%) 753 0.553
(1.00) 		0.542
(1.00) 		0.786
(1.00) 		0.0598
(1.00) 		0.787
(1.00) 		0.00145
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.792
(1.00) 		0.912
(1.00)
TPRX1 7 (1%) 764 0.615
(1.00) 		0.123
(1.00) 		0.795
(1.00) 		0.0165
(1.00) 		1
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.00236
(1.00) 		0.41
(1.00) 		0.205
(1.00)
ATN1 17 (2%) 754 0.342
(1.00) 		0.959
(1.00) 		0.839
(1.00) 		0.466
(1.00) 		0.772
(1.00) 		0.104
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.422
(1.00) 		0.609
(1.00)
MAP2K4 32 (4%) 739 0.174
(1.00) 		0.386
(1.00) 		0.974
(1.00) 		0.421
(1.00) 		0.461
(1.00) 		0.647
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.548
(1.00) 		0.911
(1.00)
CBFB 16 (2%) 755 0.929
(1.00) 		0.725
(1.00) 		0.907
(1.00) 		0.204
(1.00) 		0.118
(1.00) 		0.203
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.821
(1.00)
CTCF 18 (2%) 753 0.101
(1.00) 		0.931
(1.00) 		0.379
(1.00) 		0.128
(1.00) 		0.655
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.792
(1.00) 		0.0498
(1.00)
CCDC144NL 8 (1%) 763 0.0518
(1.00) 		0.0508
(1.00) 		0.45
(1.00) 		0.484
(1.00) 		0.135
(1.00) 		1
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.452
(1.00) 		0.296
(1.00)
AKD1 19 (2%) 752 0.325
(1.00) 		0.469
(1.00) 		0.706
(1.00) 		0.182
(1.00) 		0.722
(1.00) 		0.276
(1.00) 		1
(1.00) 		0.0816
(1.00) 		0.441
(1.00) 		0.437
(1.00)
FOXA1 15 (2%) 756 0.0139
(1.00) 		0.00249
(1.00) 		0.0997
(1.00) 		0.00214
(1.00) 		0.877
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.00959
(1.00) 		0.255
(1.00) 		0.833
(1.00)
PHLDA1 9 (1%) 762 0.0283
(1.00) 		0.752
(1.00) 		0.227
(1.00) 		0.356
(1.00) 		0.798
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.458
(1.00) 		0.000817
(0.713)
VEZF1 8 (1%) 763 0.492
(1.00) 		0.0879
(1.00) 		0.923
(1.00) 		0.912
(1.00) 		0.928
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.89
(1.00) 		0.232
(1.00) 		0.0425
(1.00)
ZFP36L1 10 (1%) 761 0.958
(1.00) 		0.0124
(1.00) 		0.662
(1.00) 		0.591
(1.00) 		0.531
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.962
(1.00) 		0.0701
(1.00) 		0.41
(1.00)
NCOR1 31 (4%) 740 0.996
(1.00) 		0.934
(1.00) 		0.889
(1.00) 		0.817
(1.00) 		0.619
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.684
(1.00) 		0.462
(1.00)
AQP7 9 (1%) 762 0.00822
(1.00) 		0.481
(1.00) 		0.803
(1.00) 		0.543
(1.00) 		0.215
(1.00) 		1
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.127
(1.00) 		0.155
(1.00)
TBX3 18 (2%) 753 0.522
(1.00) 		0.0154
(1.00) 		0.691
(1.00) 		0.597
(1.00) 		0.884
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.669
(1.00) 		0.792
(1.00) 		0.472
(1.00)
DSPP 26 (3%) 745 0.597
(1.00) 		0.166
(1.00) 		0.839
(1.00) 		0.314
(1.00) 		0.654
(1.00) 		1
(1.00) 		1
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.375
(1.00)
RPGR 16 (2%) 755 0.991
(1.00) 		0.763
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.279
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.408
(1.00) 		0.851
(1.00)
BCL6B 8 (1%) 763 0.547
(1.00) 		0.749
(1.00) 		0.943
(1.00) 		0.385
(1.00) 		0.868
(1.00) 		0.0408
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.114
(1.00) 		0.805
(1.00)
TBL1XR1 9 (1%) 762 0.54
(1.00) 		0.0223
(1.00) 		0.422
(1.00) 		0.0827
(1.00) 		0.138
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.712
(1.00) 		0.718
(1.00) 		0.454
(1.00)
CRIPAK 13 (2%) 758 0.959
(1.00) 		0.746
(1.00) 		0.953
(1.00) 		0.364
(1.00) 		0.092
(1.00) 		0.707
(1.00) 		0.128
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.218
(1.00)
MYB 11 (1%) 760 0.169
(1.00) 		0.18
(1.00) 		0.783
(1.00) 		0.24
(1.00) 		0.878
(1.00) 		1
(1.00) 		1
(1.00) 		0.24
(1.00) 		0.516
(1.00) 		0.0364
(1.00)
GPS2 6 (1%) 765 0.209
(1.00) 		0.966
(1.00) 		0.105
(1.00) 		0.284
(1.00) 		0.0566
(1.00) 		1
(1.00) 		1
(1.00) 		0.678
(1.00) 		0.678
(1.00) 		0.638
(1.00)
PABPC3 8 (1%) 763 0.339
(1.00) 		0.941
(1.00) 		0.909
(1.00) 		0.75
(1.00) 		0.868
(1.00) 		1
(1.00) 		0.0804
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.164
(1.00)
E2F4 4 (1%) 767 0.366
(1.00) 		0.982
(1.00) 		0.136
(1.00) 		0.314
(1.00) 		1
(1.00) 		1
(1.00) 		0.47
(1.00) 		0.582
(1.00)
DNAH12 12 (2%) 759 0.983
(1.00) 		0.98
(1.00) 		0.882
(1.00) 		0.283
(1.00) 		0.775
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.335
(1.00) 		0.86
(1.00)
CDKN1B 7 (1%) 764 0.855
(1.00) 		0.945
(1.00) 		0.0513
(1.00) 		0.0222
(1.00) 		0.00173
(1.00) 		0.0221
(1.00) 		1
(1.00) 		0.967
(1.00) 		1
(1.00) 		0.0478
(1.00)
HNF1A 9 (1%) 762 0.397
(1.00) 		0.205
(1.00) 		0.982
(1.00) 		0.851
(1.00) 		0.407
(1.00) 		0.0654
(1.00) 		1
(1.00) 		0.00912
(1.00) 		0.28
(1.00) 		0.636
(1.00)
CCDC66 14 (2%) 757 0.0639
(1.00) 		0.667
(1.00) 		0.958
(1.00) 		0.176
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00) 		0.513
(1.00) 		1
(1.00) 		0.606
(1.00)
STXBP2 10 (1%) 761 0.23
(1.00) 		0.0636
(1.00) 		0.875
(1.00) 		0.93
(1.00) 		0.822
(1.00) 		1
(1.00) 		1
(1.00) 		0.962
(1.00) 		1
(1.00) 		0.935
(1.00)
HIST1H3B 7 (1%) 764 0.603
(1.00) 		0.285
(1.00) 		0.795
(1.00) 		0.39
(1.00) 		0.434
(1.00) 		1
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.104
(1.00) 		0.452
(1.00)
TTN 122 (16%) 649 0.161
(1.00) 		0.00748
(1.00) 		0.0254
(1.00) 		0.0412
(1.00) 		0.745
(1.00) 		0.607
(1.00) 		0.369
(1.00) 		0.373
(1.00) 		0.913
(1.00) 		0.399
(1.00)
SHROOM4 12 (2%) 759 0.198
(1.00) 		0.481
(1.00) 		0.952
(1.00) 		0.269
(1.00) 		0.314
(1.00) 		0.387
(1.00) 		0.118
(1.00) 		0.833
(1.00) 		0.109
(1.00) 		0.786
(1.00)
SLC25A5 3 (0%) 768 0.521
(1.00) 		0.999
(1.00) 		0.388
(1.00) 		0.607
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.13
(1.00) 		1
(1.00) 		0.932
(1.00)
SELPLG 7 (1%) 764 0.582
(1.00) 		0.266
(1.00) 		0.804
(1.00) 		0.716
(1.00) 		0.844
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.41
(1.00) 		0.000817
(0.713)
KRTAP9-9 6 (1%) 765 0.541
(1.00) 		0.408
(1.00) 		0.923
(1.00) 		0.565
(1.00) 		0.388
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.359
(1.00) 		0.293
(1.00)
KRTAP4-5 4 (1%) 767 0.572
(1.00) 		0.194
(1.00) 		0.906
(1.00) 		0.395
(1.00) 		0.143
(1.00) 		0.313
(1.00) 		1
(1.00) 		0.291
(1.00) 		0.318
(1.00) 		0.466
(1.00)
SF3B1 14 (2%) 757 0.232
(1.00) 		0.74
(1.00) 		0.238
(1.00) 		0.326
(1.00) 		0.866
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.554
(1.00) 		0.778
(1.00)
FGFR2 7 (1%) 764 0.00758
(1.00) 		0.751
(1.00) 		0.756
(1.00) 		0.122
(1.00) 		0.467
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.68
(1.00) 		0.0471
(1.00)
MUC2 22 (3%) 749 0.667
(1.00) 		0.52
(1.00) 		0.401
(1.00) 		0.563
(1.00) 		0.203
(1.00) 		0.332
(1.00) 		0.208
(1.00) 		0.976
(1.00) 		0.0905
(1.00) 		0.153
(1.00)
MED12 20 (3%) 751 0.583
(1.00) 		0.777
(1.00) 		0.681
(1.00) 		0.52
(1.00) 		0.485
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.991
(1.00) 		0.217
(1.00) 		0.489
(1.00)
USP36 13 (2%) 758 0.601
(1.00) 		0.0796
(1.00) 		0.665
(1.00) 		0.485
(1.00) 		0.145
(1.00) 		0.136
(1.00) 		1
(1.00) 		0.933
(1.00) 		0.37
(1.00) 		0.634
(1.00)
DENND4B 8 (1%) 763 0.494
(1.00) 		0.734
(1.00) 		0.926
(1.00) 		0.484
(1.00) 		0.868
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.00386
(1.00) 		1
(1.00) 		0.806
(1.00)
RAI1 7 (1%) 764 0.566
(1.00) 		0.917
(1.00) 		0.388
(1.00) 		0.425
(1.00) 		0.844
(1.00) 		1
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.41
(1.00) 		0.0482
(1.00)
AXL 6 (1%) 765 0.0255
(1.00) 		0.734
(1.00) 		0.615
(1.00) 		0.485
(1.00) 		0.102
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.00431
(1.00) 		0.192
(1.00) 		0.447
(1.00)
RPL18 4 (1%) 767 0.714
(1.00) 		0.857
(1.00) 		0.755
(1.00) 		0.78
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.47
(1.00) 		0.318
(1.00) 		0.027
(1.00)
KRT38 4 (1%) 767 0.476
(1.00) 		0.242
(1.00) 		0.991
(1.00) 		0.395
(1.00) 		0.496
(1.00) 		1
(1.00) 		1
(1.00) 		0.974
(1.00) 		0.318
(1.00) 		0.0539
(1.00)
TICAM1 5 (1%) 766 0.542
(1.00) 		0.54
(1.00) 		0.0716
(1.00) 		0.69
(1.00) 		0.0175
(1.00) 		0.0751
(1.00) 		1
(1.00) 		0.958
(1.00) 		0.625
(1.00) 		0.724
(1.00)
RBM5 12 (2%) 759 0.252
(1.00) 		0.866
(1.00) 		0.98
(1.00) 		0.341
(1.00) 		0.231
(1.00) 		1
(1.00) 		1
(1.00) 		0.303
(1.00) 		1
(1.00) 		0.245
(1.00)
ASPHD1 3 (0%) 768 0.0394
(1.00) 		0.782
(1.00) 		0.966
(1.00) 		0.719
(1.00) 		0.772
(1.00) 		1
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.563
(1.00) 		0.727
(1.00)
PPEF1 8 (1%) 763 0.783
(1.00) 		0.704
(1.00) 		0.979
(1.00) 		1
(1.00) 		0.372
(1.00) 		1
(1.00) 		1
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.164
(1.00)
MUC20 10 (1%) 761 0.349
(1.00) 		0.169
(1.00) 		0.967
(1.00) 		0.494
(1.00) 		0.248
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.0839
(1.00) 		0.481
(1.00) 		0.533
(1.00)
TMEM184A 4 (1%) 767 0.907
(1.00) 		0.981
(1.00) 		0.996
(1.00) 		0.78
(1.00) 		0.112
(1.00) 		1
(1.00) 		1
(1.00) 		0.974
(1.00) 		0.582
(1.00) 		0.632
(1.00)
FAM171B 8 (1%) 763 0.865
(1.00) 		0.00375
(1.00) 		0.855
(1.00) 		0.75
(1.00) 		0.928
(1.00) 		0.529
(1.00) 		0.0804
(1.00) 		0.89
(1.00) 		0.694
(1.00) 		0.383
(1.00)
PRRX1 6 (1%) 765 0.439
(1.00) 		0.9
(1.00) 		0.99
(1.00) 		0.755
(1.00) 		0.425
(1.00) 		1
(1.00) 		1
(1.00) 		0.939
(1.00) 		0.0569
(1.00) 		0.722
(1.00)
MUC21 6 (1%) 765 0.372
(1.00) 		0.462
(1.00) 		0.802
(1.00) 		0.36
(1.00) 		0.904
(1.00) 		1
(1.00) 		1
(1.00) 		0.939
(1.00) 		1
(1.00) 		0.00268
(1.00)
HLA-B 4 (1%) 767 0.648
(1.00) 		0.744
(1.00) 		0.982
(1.00) 		0.26
(1.00) 		0.702
(1.00) 		1
(1.00) 		1
(1.00) 		0.291
(1.00) 		1
(1.00) 		0.799
(1.00)
RBM23 6 (1%) 765 0.915
(1.00) 		0.746
(1.00) 		0.778
(1.00) 		0.052
(1.00) 		0.464
(1.00) 		0.103
(1.00) 		1
(1.00) 		0.000389
(0.34) 		0.359
(1.00) 		0.794
(1.00)
UBC 8 (1%) 763 0.201
(1.00) 		0.671
(1.00) 		0.94
(1.00) 		0.912
(1.00) 		0.816
(1.00) 		1
(1.00) 		1
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.844
(1.00)
SPRED3 4 (1%) 767 0.768
(1.00) 		0.707
(1.00) 		0.972
(1.00) 		1
(1.00) 		0.421
(1.00) 		1
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.318
(1.00) 		0.694
(1.00)
KCNN3 6 (1%) 765 0.634
(1.00) 		0.744
(1.00) 		0.67
(1.00) 		0.485
(1.00) 		0.818
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.244
(1.00) 		0.192
(1.00) 		0.019
(1.00)
GNRH2 3 (0%) 768 0.881
(1.00) 		0.178
(1.00) 		0.999
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.563
(1.00) 		0.434
(1.00)
'ZNF384 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-05 (t-test), Q value = 0.01

Table S1.  Gene #5: 'ZNF384 MUTATION STATUS' versus Clinical Feature #10: '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 S1.  Get High-res Image Gene #5: 'ZNF384 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'GATA3 MUTATION STATUS' versus 'AGE'

P value = 0.000217 (t-test), Q value = 0.19

Table S2.  Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 771 58.0 (13.1)
GATA3 MUTATED 81 52.8 (13.0)
GATA3 WILD-TYPE 690 58.6 (13.0)

Figure S2.  Get High-res Image Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 9.97e-07 (Chi-square test), Q value = 0.00088

Table S3.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 637 64 4 26 6 33
TP53 MUTATED 235 3 3 5 0 10
TP53 WILD-TYPE 402 61 1 21 6 23

Figure S3.  Get High-res Image Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'CDH1 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.43e-69 (Chi-square test), Q value = 3.9e-66

Table S4.  Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 637 64 4 26 6 33
CDH1 MUTATED 11 40 1 3 0 0
CDH1 WILD-TYPE 626 24 3 23 6 33

Figure S4.  Get High-res Image Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 7.24e-07 (t-test), Q value = 0.00064

Table S5.  Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: '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 #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'RB1 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.48e-05 (Chi-square test), Q value = 0.048

Table S6.  Gene #29: 'RB1 MUTATION STATUS' versus Clinical Feature #3: '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 65 57 6 2 268 167 117 23 33 15 1 16
RB1 MUTATED 2 0 1 1 5 3 0 1 1 0 0 0
RB1 WILD-TYPE 63 57 5 1 263 164 117 22 32 15 1 16

Figure S6.  Get High-res Image Gene #29: 'RB1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 5.57e-05 (t-test), Q value = 0.049

Table S7.  Gene #50: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: '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 S7.  Get High-res Image Gene #50: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'CTU2 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000116 (Chi-square test), Q value = 0.1

Table S8.  Gene #53: 'CTU2 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 637 64 4 26 6 33
CTU2 MUTATED 3 1 0 0 1 0
CTU2 WILD-TYPE 634 63 4 26 5 33

Figure S8.  Get High-res Image Gene #53: 'CTU2 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'HLA-A MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 9.52e-06 (Chi-square test), Q value = 0.0084

Table S9.  Gene #56: 'HLA-A MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 637 64 4 26 6 33
HLA-A MUTATED 3 0 0 0 1 0
HLA-A WILD-TYPE 634 64 4 26 5 33

Figure S9.  Get High-res Image Gene #56: 'HLA-A MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'ODF1 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.19e-05 (Chi-square test), Q value = 0.037

Table S10.  Gene #68: 'ODF1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 637 64 4 26 6 33
ODF1 MUTATED 3 0 0 0 1 1
ODF1 WILD-TYPE 634 64 4 26 5 32

Figure S10.  Get High-res Image Gene #68: 'ODF1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 7.01e-05 (t-test), Q value = 0.062

Table S11.  Gene #72: 'ASXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
ASXL2 MUTATED 6 0.5 (0.5)
ASXL2 WILD-TYPE 629 2.2 (4.0)

Figure S11.  Get High-res Image Gene #72: 'ASXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'ATP13A4 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.54e-06 (Chi-square test), Q value = 0.0014

Table S12.  Gene #81: 'ATP13A4 MUTATION STATUS' versus Clinical Feature #3: '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 65 57 6 2 268 167 117 23 33 15 1 16
ATP13A4 MUTATED 2 0 0 1 4 1 0 0 1 0 0 0
ATP13A4 WILD-TYPE 63 57 6 1 264 166 117 23 32 15 1 16

Figure S12.  Get High-res Image Gene #81: 'ATP13A4 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'MED15 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.01e-05 (t-test), Q value = 0.062

Table S13.  Gene #89: 'MED15 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 635 2.1 (4.0)
MED15 MUTATED 6 0.5 (0.5)
MED15 WILD-TYPE 629 2.2 (4.0)

Figure S13.  Get High-res Image Gene #89: 'MED15 MUTATION STATUS' versus Clinical Feature #10: '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 = 771

  • Number of significantly mutated genes = 89

  • Number of selected clinical features = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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