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 81 genes and 10 clinical features across 771 patients, 19 significant findings detected with Q value < 0.25.

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

  • DCP1B mutation correlated to 'NEOPLASM.DISEASESTAGE'.

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

  • 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'.

  • CCDC144NL mutation correlated to 'Time to Death'.

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

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

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

  • CTU2 mutation correlated to 'HISTOLOGICAL.TYPE' and 'NEOPLASM.DISEASESTAGE'.

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

  • ODF1 mutation correlated to 'HISTOLOGICAL.TYPE'.

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

  • ASXL2 mutation correlated to 'LYMPH.NODE.METASTASIS' and 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 81 genes and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 19 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		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 Chi-square test Fisher's exact test Fisher's exact test Chi-square test t-test t-test Chi-square test
CTU2 5 (1%) 766 0.556
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.000114
(0.0809) 		0.335
(1.00) 		1
(1.00) 		0.946
(1.00) 		0.058
(1.00) 		1.58e-09
(1.14e-06)
HLA-A 4 (1%) 767 0.211
(1.00) 		0.437
(1.00) 		1
(1.00) 		9.35e-06
(0.0067) 		0.275
(1.00) 		1
(1.00) 		2.91e-33
(2.11e-30) 		0.585
(1.00) 		0.807
(1.00)
ASXL2 8 (1%) 763 0.906
(1.00) 		0.947
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.432
(1.00) 		1
(1.00) 		7.73e-07
(0.000556) 		7.01e-05
(0.0498) 		0.978
(1.00)
ZNF384 14 (2%) 757 0.408
(1.00) 		0.0127
(1.00) 		1
(1.00) 		0.916
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.964
(1.00) 		1.16e-05
(0.00832) 		0.444
(1.00)
DCP1B 5 (1%) 766 0.55
(1.00) 		0.025
(1.00) 		1
(1.00) 		0.936
(1.00) 		0.335
(1.00) 		0.375
(1.00) 		0.512
(1.00) 		0.44
(1.00) 		1.08e-07
(7.79e-05)
PIK3R1 21 (3%) 750 0.174
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.842
(1.00) 		0.801
(1.00) 		0.484
(1.00) 		5.69e-05
(0.0404) 		0.0805
(1.00) 		0.286
(1.00)
GATA3 81 (11%) 690 0.739
(1.00) 		0.000217
(0.154) 		0.59
(1.00) 		0.147
(1.00) 		0.139
(1.00) 		0.0979
(1.00) 		0.781
(1.00) 		0.598
(1.00) 		0.22
(1.00)
TP53 257 (33%) 514 0.456
(1.00) 		0.0384
(1.00) 		0.0574
(1.00) 		1.03e-06
(0.000737) 		0.433
(1.00) 		0.0552
(1.00) 		0.379
(1.00) 		0.414
(1.00) 		0.732
(1.00)
CDH1 55 (7%) 716 0.418
(1.00) 		0.0861
(1.00) 		1
(1.00) 		3.17e-69
(2.3e-66) 		1
(1.00) 		0.799
(1.00) 		0.0257
(1.00) 		0.129
(1.00) 		0.134
(1.00)
MAP3K1 57 (7%) 714 0.782
(1.00) 		0.00183
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.753
(1.00) 		0.565
(1.00) 		0.103
(1.00) 		7.24e-07
(0.000522) 		0.679
(1.00)
CCDC144NL 8 (1%) 763 5.2e-05
(0.037) 		0.0508
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.41
(1.00) 		0.296
(1.00) 		0.448
(1.00)
AQP7 8 (1%) 763 0.0123
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.215
(1.00) 		1
(1.00) 		1.7e-06
(0.00122) 		0.196
(1.00) 		0.786
(1.00)
CDKN1B 7 (1%) 764 0.848
(1.00) 		0.945
(1.00) 		1
(1.00) 		0.967
(1.00) 		1
(1.00) 		0.0221
(1.00) 		4.09e-05
(0.0293) 		0.0478
(1.00) 		0.0512
(1.00)
CASP8 10 (1%) 761 0.93
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.714
(1.00) 		0.467
(1.00) 		0.611
(1.00) 		0.896
(1.00) 		5.57e-05
(0.0396) 		0.753
(1.00)
ODF1 5 (1%) 766 0.722
(1.00) 		0.569
(1.00) 		1
(1.00) 		4.38e-05
(0.0313) 		0.608
(1.00) 		0.0751
(1.00) 		0.698
(1.00) 		0.966
(1.00) 		0.592
(1.00)
KRT38 4 (1%) 767 0.5
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.975
(1.00) 		0.275
(1.00) 		1
(1.00) 		7.55e-15
(5.47e-12) 		0.0539
(1.00) 		0.991
(1.00)
PTEN 29 (4%) 742 0.889
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.554
(1.00) 		0.83
(1.00) 		0.0618
(1.00) 		0.387
(1.00) 		0.221
(1.00) 		0.0208
(1.00)
MLL3 56 (7%) 715 0.525
(1.00) 		0.0118
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.752
(1.00) 		0.418
(1.00) 		0.317
(1.00) 		0.918
(1.00) 		0.862
(1.00)
PIK3CA 261 (34%) 510 0.92
(1.00) 		0.0233
(1.00) 		1
(1.00) 		0.0217
(1.00) 		0.862
(1.00) 		0.357
(1.00) 		0.437
(1.00) 		0.339
(1.00) 		0.479
(1.00)
NCOA3 29 (4%) 742 0.464
(1.00) 		0.875
(1.00) 		1
(1.00) 		0.514
(1.00) 		0.667
(1.00) 		0.142
(1.00) 		0.221
(1.00) 		0.177
(1.00) 		0.478
(1.00)
AOAH 19 (2%) 752 0.283
(1.00) 		0.425
(1.00) 		1
(1.00) 		0.791
(1.00) 		0.0353
(1.00) 		0.276
(1.00) 		0.916
(1.00) 		0.282
(1.00) 		0.187
(1.00)
RBMX 13 (2%) 758 0.65
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.792
(1.00) 		0.337
(1.00) 		1
(1.00) 		0.95
(1.00) 		0.241
(1.00) 		0.972
(1.00)
RUNX1 25 (3%) 746 0.45
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.053
(1.00) 		0.353
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.532
(1.00) 		0.103
(1.00)
MEF2A 14 (2%) 757 0.788
(1.00) 		0.522
(1.00) 		1
(1.00) 		0.0174
(1.00) 		0.537
(1.00) 		0.719
(1.00) 		0.758
(1.00) 		0.0142
(1.00) 		0.436
(1.00)
NCOR2 29 (4%) 742 0.815
(1.00) 		0.709
(1.00) 		1
(1.00) 		0.864
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.93
(1.00) 		0.218
(1.00) 		0.957
(1.00)
AKT1 19 (2%) 752 0.196
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.984
(1.00) 		0.183
(1.00) 		0.597
(1.00) 		0.0405
(1.00) 		0.902
(1.00) 		0.541
(1.00)
NR1H2 18 (2%) 753 0.557
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.819
(1.00) 		1
(1.00) 		0.00281
(1.00) 		0.641
(1.00) 		0.954
(1.00) 		0.0163
(1.00)
MAP3K4 18 (2%) 753 0.989
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.585
(1.00) 		0.00145
(1.00) 		0.854
(1.00) 		0.912
(1.00) 		0.808
(1.00)
TPRX1 7 (1%) 764 0.695
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.00174
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.977
(1.00) 		0.205
(1.00) 		0.805
(1.00)
ATN1 17 (2%) 754 0.293
(1.00) 		0.959
(1.00) 		1
(1.00) 		0.727
(1.00) 		0.264
(1.00) 		0.104
(1.00) 		0.988
(1.00) 		0.609
(1.00) 		0.834
(1.00)
MAP2K4 32 (4%) 739 0.181
(1.00) 		0.386
(1.00) 		1
(1.00) 		0.526
(1.00) 		0.685
(1.00) 		0.647
(1.00) 		0.334
(1.00) 		0.911
(1.00) 		0.987
(1.00)
CBFB 16 (2%) 755 0.968
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.473
(1.00) 		0.821
(1.00) 		0.916
(1.00)
CTCF 18 (2%) 753 0.117
(1.00) 		0.931
(1.00) 		1
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.571
(1.00) 		0.991
(1.00) 		0.0498
(1.00) 		0.361
(1.00)
AKD1 19 (2%) 752 0.808
(1.00) 		0.469
(1.00) 		1
(1.00) 		0.0661
(1.00) 		0.794
(1.00) 		0.276
(1.00) 		0.372
(1.00) 		0.437
(1.00) 		0.708
(1.00)
RB1 14 (2%) 757 0.881
(1.00) 		0.12
(1.00) 		0.137
(1.00) 		0.911
(1.00) 		0.131
(1.00) 		0.719
(1.00) 		0.0714
(1.00) 		0.459
(1.00) 		0.00169
(1.00)
PHLDA1 9 (1%) 762 0.788
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.46
(1.00) 		0.198
(1.00) 		0.908
(1.00) 		0.000817
(0.575) 		0.249
(1.00)
FOXA1 15 (2%) 756 0.0781
(1.00) 		0.00249
(1.00) 		1
(1.00) 		0.00917
(1.00) 		0.377
(1.00) 		0.484
(1.00) 		0.99
(1.00) 		0.833
(1.00) 		0.0955
(1.00)
VEZF1 8 (1%) 763 0.581
(1.00) 		0.0879
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.432
(1.00) 		0.529
(1.00) 		0.995
(1.00) 		0.0425
(1.00) 		0.943
(1.00)
ZFP36L1 10 (1%) 761 0.981
(1.00) 		0.0124
(1.00) 		1
(1.00) 		0.962
(1.00) 		0.0718
(1.00) 		0.222
(1.00) 		0.943
(1.00) 		0.41
(1.00) 		0.668
(1.00)
NCOR1 31 (4%) 740 0.879
(1.00) 		0.934
(1.00) 		1
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.82
(1.00) 		0.462
(1.00) 		0.878
(1.00)
TBX3 18 (2%) 753 0.185
(1.00) 		0.0154
(1.00) 		1
(1.00) 		0.669
(1.00) 		1
(1.00) 		0.571
(1.00) 		0.989
(1.00) 		0.472
(1.00) 		0.673
(1.00)
DSPP 26 (3%) 745 0.868
(1.00) 		0.166
(1.00) 		1
(1.00) 		0.957
(1.00) 		1
(1.00) 		1
(1.00) 		0.479
(1.00) 		0.375
(1.00) 		0.839
(1.00)
BCL6B 8 (1%) 763 0.607
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.812
(1.00) 		0.121
(1.00) 		0.0408
(1.00) 		0.824
(1.00) 		0.805
(1.00) 		0.938
(1.00)
RPGR 14 (2%) 757 0.869
(1.00) 		0.459
(1.00) 		1
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.88
(1.00) 		0.856
(1.00) 		0.892
(1.00)
TBL1XR1 9 (1%) 762 0.565
(1.00) 		0.0223
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.702
(1.00) 		0.198
(1.00) 		0.413
(1.00) 		0.454
(1.00) 		0.447
(1.00)
MYB 11 (1%) 760 0.176
(1.00) 		0.18
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.487
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.0364
(1.00) 		0.758
(1.00)
PABPC3 8 (1%) 763 0.302
(1.00) 		0.941
(1.00) 		0.0804
(1.00) 		0.655
(1.00) 		1
(1.00) 		1
(1.00) 		0.973
(1.00) 		0.164
(1.00) 		0.885
(1.00)
GPS2 6 (1%) 765 0.219
(1.00) 		0.966
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.36
(1.00) 		0.638
(1.00) 		0.109
(1.00)
E2F4 4 (1%) 767 0.366
(1.00) 		1
(1.00) 		0.492
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.987
(1.00) 		0.982
(1.00)
DNAH12 12 (2%) 759 0.81
(1.00) 		0.98
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.518
(1.00) 		0.678
(1.00) 		0.886
(1.00) 		0.86
(1.00) 		0.881
(1.00)
HNF1A 9 (1%) 762 0.538
(1.00) 		0.205
(1.00) 		1
(1.00) 		0.00855
(1.00) 		0.247
(1.00) 		0.0654
(1.00) 		0.99
(1.00) 		0.636
(1.00) 		0.98
(1.00)
CRIPAK 6 (1%) 765 0.496
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.939
(1.00) 		1
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.00491
(1.00) 		0.82
(1.00)
STXBP2 9 (1%) 762 0.251
(1.00) 		0.0464
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.702
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.935
(1.00) 		0.7
(1.00)
CCDC66 9 (1%) 762 0.695
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.705
(1.00) 		0.702
(1.00) 		0.572
(1.00) 		0.809
(1.00) 		0.772
(1.00) 		0.749
(1.00)
HIST1H3B 7 (1%) 764 0.395
(1.00) 		0.285
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.383
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.452
(1.00) 		0.805
(1.00)
TTN 122 (16%) 649 0.0569
(1.00) 		0.00748
(1.00) 		0.369
(1.00) 		0.372
(1.00) 		0.91
(1.00) 		0.607
(1.00) 		0.949
(1.00) 		0.399
(1.00) 		0.0262
(1.00)
SLC25A5 3 (0%) 768 0.521
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.573
(1.00) 		0.245
(1.00) 		0.948
(1.00) 		0.932
(1.00) 		0.999
(1.00)
SELPLG 7 (1%) 764 0.662
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.383
(1.00) 		0.134
(1.00) 		0.71
(1.00) 		0.000817
(0.575) 		0.795
(1.00)
KRTAP9-9 6 (1%) 765 0.595
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.182
(1.00) 		0.431
(1.00) 		0.98
(1.00) 		0.293
(1.00) 		0.93
(1.00)
KRTAP4-5 4 (1%) 767 0.596
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.275
(1.00) 		0.313
(1.00) 		0.972
(1.00) 		0.466
(1.00) 		0.905
(1.00)
SF3B1 14 (2%) 757 0.291
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.369
(1.00) 		0.719
(1.00) 		0.982
(1.00) 		0.778
(1.00) 		0.298
(1.00)
FGFR2 7 (1%) 764 0.000464
(0.327) 		0.751
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.684
(1.00) 		0.134
(1.00) 		0.789
(1.00) 		0.0471
(1.00) 		0.755
(1.00)
SHROOM4 11 (1%) 760 0.302
(1.00) 		0.619
(1.00) 		0.109
(1.00) 		0.804
(1.00) 		0.163
(1.00) 		0.353
(1.00) 		0.894
(1.00) 		0.72
(1.00) 		0.933
(1.00)
MED12 20 (3%) 751 0.607
(1.00) 		0.777
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.313
(1.00) 		0.366
(1.00) 		0.959
(1.00) 		0.489
(1.00) 		0.669
(1.00)
DENND4B 8 (1%) 763 0.546
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.00359
(1.00) 		1
(1.00) 		0.529
(1.00) 		0.998
(1.00) 		0.806
(1.00) 		0.925
(1.00)
AXL 6 (1%) 765 0.438
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.00305
(1.00) 		0.347
(1.00) 		0.431
(1.00) 		0.635
(1.00) 		0.447
(1.00) 		0.614
(1.00)
RPL18 4 (1%) 767 0.794
(1.00) 		0.857
(1.00) 		1
(1.00) 		0.492
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.767
(1.00) 		0.027
(1.00) 		0.751
(1.00)
RAI1 7 (1%) 764 0.679
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.383
(1.00) 		1
(1.00) 		0.963
(1.00) 		0.0482
(1.00) 		0.38
(1.00)
ERBB2 12 (2%) 759 0.139
(1.00) 		0.542
(1.00) 		0.118
(1.00) 		0.383
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.522
(1.00) 		0.932
(1.00)
TICAM1 5 (1%) 766 0.563
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.959
(1.00) 		0.608
(1.00) 		0.0751
(1.00) 		0.0376
(1.00) 		0.724
(1.00) 		0.0683
(1.00)
ASPHD1 3 (0%) 768 0.0443
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.879
(1.00) 		0.727
(1.00) 		0.966
(1.00)
FAM171B 8 (1%) 763 0.745
(1.00) 		0.00375
(1.00) 		0.0804
(1.00) 		0.891
(1.00) 		0.432
(1.00) 		0.529
(1.00) 		0.999
(1.00) 		0.383
(1.00) 		0.885
(1.00)
MUC20 10 (1%) 761 0.421
(1.00) 		0.169
(1.00) 		1
(1.00) 		0.0697
(1.00) 		0.724
(1.00) 		0.611
(1.00) 		0.813
(1.00) 		0.533
(1.00) 		0.97
(1.00)
PPEF1 8 (1%) 763 0.748
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.891
(1.00) 		1
(1.00) 		1
(1.00) 		0.885
(1.00) 		0.164
(1.00) 		0.982
(1.00)
PRRX1 6 (1%) 765 0.487
(1.00) 		0.9
(1.00) 		1
(1.00) 		0.939
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.722
(1.00) 		0.988
(1.00)
ATP13A4 9 (1%) 762 0.301
(1.00) 		0.545
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.702
(1.00) 		1
(1.00) 		0.988
(1.00) 		0.0558
(1.00) 		0.000397
(0.28)
MUC2 18 (2%) 753 0.466
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.0972
(1.00) 		0.19
(1.00) 		0.547
(1.00) 		0.445
(1.00) 		0.529
(1.00)
UBC 8 (1%) 763 0.216
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.891
(1.00) 		1
(1.00) 		1
(1.00) 		0.906
(1.00) 		0.844
(1.00) 		0.934
(1.00)
KCNN3 6 (1%) 765 0.619
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.237
(1.00) 		0.347
(1.00) 		0.431
(1.00) 		0.981
(1.00) 		0.019
(1.00) 		0.669
(1.00)
RBM23 6 (1%) 765 0.663
(1.00) 		0.746
(1.00) 		1
(1.00) 		0.000403
(0.285) 		0.182
(1.00) 		0.103
(1.00) 		0.89
(1.00) 		0.794
(1.00) 		0.792
(1.00)
GNRH2 3 (0%) 768 0.91
(1.00) 		0.178
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.573
(1.00) 		0.245
(1.00) 		0.205
(1.00) 		0.434
(1.00) 		0.999
(1.00)
'ZNF384 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-05 (t-test), Q value = 0.0083

Table S1.  Gene #3: 'ZNF384 MUTATION STATUS' versus Clinical Feature #8: '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 #3: 'ZNF384 MUTATION STATUS' versus Clinical Feature #8: 'NUMBER.OF.LYMPH.NODES'

'DCP1B MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.08e-07 (Chi-square test), Q value = 7.8e-05

Table S2.  Gene #4: 'DCP1B MUTATION STATUS' versus Clinical Feature #10: '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 3 267 167 117 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 2 267 165 116 23 33 15 1 16

Figure S2.  Get High-res Image Gene #4: 'DCP1B MUTATION STATUS' versus Clinical Feature #10: 'NEOPLASM.DISEASESTAGE'

'PIK3R1 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 5.69e-05 (Chi-square test), Q value = 0.04

Table S3.  Gene #10: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B N3C NX
ALL 224 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 219 19 110 0 88 115 30 2 17 47 47 15 25 2 1 13

Figure S3.  Get High-res Image Gene #10: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'GATA3 MUTATION STATUS' versus 'AGE'

P value = 0.000217 (t-test), Q value = 0.15

Table S4.  Gene #14: '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 S4.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-06 (Chi-square test), Q value = 0.00074

Table S5.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 638 64 4 25 6 34
TP53 MUTATED 236 3 3 5 0 10
TP53 WILD-TYPE 402 61 1 20 6 24

Figure S5.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'CDH1 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.17e-69 (Chi-square test), Q value = 2.3e-66

Table S6.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 638 64 4 25 6 34
CDH1 MUTATED 11 40 1 3 0 0
CDH1 WILD-TYPE 627 24 3 22 6 34

Figure S6.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

Table S7.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: '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 S7.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'NUMBER.OF.LYMPH.NODES'

'CCDC144NL MUTATION STATUS' versus 'Time to Death'

P value = 5.2e-05 (logrank test), Q value = 0.037

Table S8.  Gene #25: 'CCDC144NL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 714 91 0.0 - 223.4 (18.3)
CCDC144NL MUTATED 6 1 1.6 - 15.0 (7.5)
CCDC144NL WILD-TYPE 708 90 0.0 - 223.4 (18.9)

Figure S8.  Get High-res Image Gene #25: 'CCDC144NL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

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

P value = 1.7e-06 (Chi-square test), Q value = 0.0012

Table S9.  Gene #35: 'AQP7 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B N3C NX
ALL 224 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 223 18 113 1 91 115 30 2 18 49 48 15 25 1 1 13

Figure S9.  Get High-res Image Gene #35: 'AQP7 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

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

P value = 4.09e-05 (Chi-square test), Q value = 0.029

Table S10.  Gene #44: 'CDKN1B MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B N3C NX
ALL 224 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 224 19 112 1 93 116 29 2 18 50 47 15 22 2 1 13

Figure S10.  Get High-res Image Gene #44: 'CDKN1B MUTATION STATUS' versus Clinical Feature #7: '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 #47: 'CASP8 MUTATION STATUS' versus Clinical Feature #8: '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 #47: 'CASP8 MUTATION STATUS' versus Clinical Feature #8: 'NUMBER.OF.LYMPH.NODES'

'CTU2 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000114 (Chi-square test), Q value = 0.081

Table S12.  Gene #49: 'CTU2 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 638 64 4 25 6 34
CTU2 MUTATED 3 1 0 0 1 0
CTU2 WILD-TYPE 635 63 4 25 5 34

Figure S12.  Get High-res Image Gene #49: 'CTU2 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'CTU2 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.58e-09 (Chi-square test), Q value = 1.1e-06

Table S13.  Gene #49: 'CTU2 MUTATION STATUS' versus Clinical Feature #10: '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 3 267 167 117 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 2 266 167 117 22 33 15 1 16

Figure S13.  Get High-res Image Gene #49: 'CTU2 MUTATION STATUS' versus Clinical Feature #10: 'NEOPLASM.DISEASESTAGE'

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

P value = 9.35e-06 (Chi-square test), Q value = 0.0067

Table S14.  Gene #58: 'HLA-A MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 638 64 4 25 6 34
HLA-A MUTATED 3 0 0 0 1 0
HLA-A WILD-TYPE 635 64 4 25 5 34

Figure S14.  Get High-res Image Gene #58: 'HLA-A MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

P value = 2.91e-33 (Chi-square test), Q value = 2.1e-30

Table S15.  Gene #58: 'HLA-A MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B N3C NX
ALL 224 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 223 19 112 1 92 116 30 2 18 50 49 15 25 2 0 13

Figure S15.  Get High-res Image Gene #58: 'HLA-A MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'ODF1 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.38e-05 (Chi-square test), Q value = 0.031

Table S16.  Gene #63: 'ODF1 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 638 64 4 25 6 34
ODF1 MUTATED 3 0 0 0 1 1
ODF1 WILD-TYPE 635 64 4 25 5 33

Figure S16.  Get High-res Image Gene #63: 'ODF1 MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

P value = 7.55e-15 (Chi-square test), Q value = 5.5e-12

Table S17.  Gene #68: 'KRT38 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B N3C NX
ALL 224 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 224 19 112 1 93 114 30 1 18 50 49 15 25 2 1 13

Figure S17.  Get High-res Image Gene #68: 'KRT38 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'ASXL2 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 7.73e-07 (Chi-square test), Q value = 0.00056

Table S18.  Gene #70: 'ASXL2 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N0 (I+) N0 (I-) N0 (MOL+) N1 N1A N1B N1C N1MI N2 N2A N3 N3A N3B N3C NX
ALL 224 19 113 1 93 116 30 2 18 50 49 15 25 2 1 13
ASXL2 MUTATED 1 0 2 0 0 2 0 1 1 0 0 0 1 0 0 0
ASXL2 WILD-TYPE 223 19 111 1 93 114 30 1 17 50 49 15 24 2 1 13

Figure S18.  Get High-res Image Gene #70: 'ASXL2 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

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

P value = 7.01e-05 (t-test), Q value = 0.05

Table S19.  Gene #70: 'ASXL2 MUTATION STATUS' versus Clinical Feature #8: '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 S19.  Get High-res Image Gene #70: 'ASXL2 MUTATION STATUS' versus Clinical Feature #8: '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 = 81

  • 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

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)
Made with Nozzle