Correlation between gene mutation status and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 81 genes and 12 molecular subtypes across 771 patients, 56 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PIK3CA mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RUNX1 mutation correlated to 'CN_CNMF'.

  • AKT1 mutation correlated to 'MRNASEQ_CNMF'.

  • GATA3 mutation correlated to 'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TP53 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CDH1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • MAP2K4 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • MAP3K1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • CCDC144NL mutation correlated to 'CN_CNMF'.

  • TTN mutation correlated to 'CN_CNMF' and 'RPPA_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 81 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 56 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PIK3CA 261 (34%) 510 8.9e-15
(7.27e-12) 		3.88e-10
(3.15e-07) 		1.13e-12
(9.19e-10) 		1.67e-09
(1.35e-06) 		1.64e-05
(0.013) 		1.06e-06
(0.000854) 		5.11e-28
(4.2e-25) 		2.61e-12
(2.13e-09) 		8.02e-08
(6.47e-05) 		1.49e-11
(1.21e-08) 		6.4e-05
(0.0502) 		1.9e-10
(1.54e-07)
TP53 257 (33%) 514 7.08e-37
(5.84e-34) 		2.43e-33
(2e-30) 		3.53e-49
(2.93e-46) 		6.18e-23
(5.05e-20) 		1.87e-27
(1.54e-24) 		1.1e-23
(9.03e-21) 		4.17e-55
(3.46e-52) 		4.18e-48
(3.46e-45) 		7.46e-39
(6.16e-36) 		2.32e-44
(1.92e-41) 		1.47e-30
(1.21e-27) 		4.95e-24
(4.06e-21)
MAP3K1 57 (7%) 714 4.33e-06
(0.00344) 		4.38e-05
(0.0344) 		7.22e-05
(0.0566) 		0.00117
(0.891) 		0.000204
(0.159) 		1.99e-06
(0.00159) 		1.08e-05
(0.00855) 		7.51e-05
(0.0587) 		1.96e-05
(0.0155) 		4.16e-05
(0.0327) 		0.00023
(0.179) 		0.00195
(1.00)
CDH1 55 (7%) 716 1.67e-07
(0.000135) 		8.2e-05
(0.0641) 		2.42e-08
(1.96e-05) 		0.000711
(0.545) 		0.000255
(0.198) 		0.000579
(0.444) 		1.29e-06
(0.00103) 		4.23e-07
(0.000339) 		1.67e-06
(0.00133) 		5.92e-08
(4.79e-05) 		0.000244
(0.19) 		0.0104
(1.00)
GATA3 81 (11%) 690 0.000575
(0.442) 		0.000101
(0.079) 		0.00409
(1.00) 		0.00887
(1.00) 		0.00115
(0.879) 		0.000407
(0.314) 		6.27e-06
(0.00498) 		1.22e-09
(9.92e-07) 		4.04e-07
(0.000325) 		1.27e-06
(0.00101) 		3.97e-07
(0.00032) 		1.46e-06
(0.00116)
TTN 122 (16%) 649 0.122
(1.00) 		0.0385
(1.00) 		1.02e-05
(0.00805) 		0.0397
(1.00) 		6.23e-05
(0.0489) 		0.052
(1.00) 		0.000335
(0.259) 		0.0009
(0.688) 		0.0434
(1.00) 		0.0193
(1.00) 		0.113
(1.00) 		0.00351
(1.00)
RUNX1 25 (3%) 746 0.00552
(1.00) 		0.0442
(1.00) 		1.85e-05
(0.0146) 		0.0369
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.0299
(1.00) 		0.141
(1.00) 		0.00248
(1.00) 		0.133
(1.00) 		0.106
(1.00) 		0.00803
(1.00)
AKT1 19 (2%) 752 0.0634
(1.00) 		0.925
(1.00) 		0.00312
(1.00) 		0.000363
(0.28) 		0.162
(1.00) 		0.345
(1.00) 		3.09e-05
(0.0244) 		0.288
(1.00) 		0.0167
(1.00) 		0.0756
(1.00) 		0.0813
(1.00) 		0.0402
(1.00)
MAP2K4 32 (4%) 739 0.0292
(1.00) 		0.00313
(1.00) 		0.0323
(1.00) 		0.009
(1.00) 		0.00238
(1.00) 		0.0344
(1.00) 		0.0281
(1.00) 		0.000313
(0.242) 		0.00156
(1.00) 		0.00333
(1.00) 		0.00106
(0.807) 		0.0942
(1.00)
CCDC144NL 8 (1%) 763 6.29e-06
(0.00499) 		0.306
(1.00) 		0.705
(1.00) 		0.347
(1.00) 		0.809
(1.00) 		0.216
(1.00) 		0.246
(1.00) 		0.39
(1.00)
PTEN 29 (4%) 742 0.226
(1.00) 		0.437
(1.00) 		0.61
(1.00) 		0.603
(1.00) 		0.882
(1.00) 		0.266
(1.00) 		0.268
(1.00) 		0.901
(1.00) 		0.38
(1.00) 		0.886
(1.00) 		0.0597
(1.00) 		0.349
(1.00)
MLL3 56 (7%) 715 0.272
(1.00) 		0.973
(1.00) 		0.585
(1.00) 		0.789
(1.00) 		0.74
(1.00) 		0.935
(1.00) 		0.107
(1.00) 		0.86
(1.00) 		0.0396
(1.00) 		0.281
(1.00) 		0.151
(1.00) 		0.582
(1.00)
ZNF384 14 (2%) 757 0.61
(1.00) 		0.155
(1.00) 		0.535
(1.00) 		1
(1.00) 		0.881
(1.00) 		0.263
(1.00) 		0.466
(1.00) 		0.31
(1.00)
DCP1B 5 (1%) 766 0.395
(1.00) 		0.00475
(1.00) 		0.619
(1.00) 		0.719
(1.00) 		0.607
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.667
(1.00)
NCOA3 29 (4%) 742 0.549
(1.00) 		1
(1.00) 		0.993
(1.00) 		0.385
(1.00) 		1
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.287
(1.00) 		0.281
(1.00) 		0.0961
(1.00) 		0.24
(1.00) 		0.132
(1.00)
AOAH 19 (2%) 752 0.612
(1.00) 		0.654
(1.00) 		0.481
(1.00) 		0.228
(1.00) 		0.109
(1.00) 		0.503
(1.00) 		0.0498
(1.00) 		0.898
(1.00)
RBMX 13 (2%) 758 0.0058
(1.00) 		0.0706
(1.00) 		0.497
(1.00) 		0.127
(1.00) 		0.276
(1.00) 		0.418
(1.00) 		0.647
(1.00) 		0.948
(1.00)
PIK3R1 21 (3%) 750 0.172
(1.00) 		0.616
(1.00) 		0.687
(1.00) 		0.647
(1.00) 		0.538
(1.00) 		0.297
(1.00) 		0.165
(1.00) 		0.913
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.803
(1.00) 		0.786
(1.00)
MEF2A 14 (2%) 757 0.659
(1.00) 		0.335
(1.00) 		0.63
(1.00) 		0.149
(1.00) 		0.0531
(1.00) 		0.0127
(1.00) 		0.169
(1.00) 		0.0332
(1.00)
NCOR2 29 (4%) 742 0.676
(1.00) 		1
(1.00) 		0.111
(1.00) 		0.4
(1.00) 		0.839
(1.00) 		0.69
(1.00) 		0.695
(1.00) 		0.549
(1.00) 		0.542
(1.00) 		0.859
(1.00) 		0.413
(1.00) 		0.256
(1.00)
NR1H2 18 (2%) 753 0.326
(1.00) 		0.267
(1.00) 		0.789
(1.00) 		0.0487
(1.00) 		0.064
(1.00) 		0.116
(1.00) 		0.56
(1.00) 		0.0728
(1.00) 		0.739
(1.00) 		0.44
(1.00) 		0.484
(1.00) 		0.0856
(1.00)
MAP3K4 18 (2%) 753 0.108
(1.00) 		0.721
(1.00) 		0.788
(1.00) 		0.0248
(1.00) 		0.0733
(1.00) 		0.69
(1.00) 		0.464
(1.00) 		0.214
(1.00) 		0.398
(1.00) 		0.209
(1.00) 		0.781
(1.00) 		0.765
(1.00)
TPRX1 7 (1%) 764 0.343
(1.00) 		0.561
(1.00) 		0.983
(1.00) 		0.737
(1.00) 		0.694
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.712
(1.00)
ATN1 17 (2%) 754 0.0643
(1.00) 		0.0545
(1.00) 		0.0642
(1.00) 		0.835
(1.00) 		0.169
(1.00) 		0.291
(1.00) 		0.16
(1.00) 		0.569
(1.00) 		0.853
(1.00) 		0.44
(1.00) 		0.0767
(1.00) 		0.353
(1.00)
CBFB 16 (2%) 755 0.184
(1.00) 		0.648
(1.00) 		0.0266
(1.00) 		0.0107
(1.00) 		0.35
(1.00) 		0.569
(1.00) 		0.000473
(0.364) 		0.583
(1.00) 		0.0241
(1.00) 		0.00402
(1.00) 		0.0114
(1.00) 		0.000733
(0.56)
CTCF 18 (2%) 753 0.0265
(1.00) 		0.32
(1.00) 		0.00297
(1.00) 		0.00459
(1.00) 		0.0682
(1.00) 		0.369
(1.00) 		0.000386
(0.298) 		0.0891
(1.00) 		0.2
(1.00) 		0.0621
(1.00) 		0.778
(1.00) 		0.532
(1.00)
AKD1 19 (2%) 752 0.926
(1.00) 		0.437
(1.00) 		0.112
(1.00) 		0.176
(1.00) 		0.467
(1.00) 		0.242
(1.00) 		0.415
(1.00) 		0.305
(1.00) 		0.322
(1.00) 		0.0662
(1.00) 		0.114
(1.00) 		0.201
(1.00)
RB1 14 (2%) 757 0.523
(1.00) 		0.172
(1.00) 		0.158
(1.00) 		0.171
(1.00) 		0.483
(1.00) 		0.762
(1.00) 		0.339
(1.00) 		0.231
(1.00) 		0.061
(1.00) 		0.00347
(1.00) 		0.137
(1.00) 		0.137
(1.00)
PHLDA1 9 (1%) 762 0.321
(1.00) 		0.275
(1.00) 		0.395
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.28
(1.00) 		0.89
(1.00) 		0.894
(1.00) 		0.331
(1.00) 		0.436
(1.00) 		0.256
(1.00) 		0.548
(1.00)
FOXA1 15 (2%) 756 0.736
(1.00) 		0.116
(1.00) 		0.175
(1.00) 		0.0334
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.636
(1.00) 		0.167
(1.00) 		0.359
(1.00) 		0.229
(1.00) 		0.456
(1.00) 		0.6
(1.00)
VEZF1 8 (1%) 763 0.48
(1.00) 		0.509
(1.00) 		0.183
(1.00) 		0.88
(1.00) 		0.902
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.904
(1.00)
ZFP36L1 10 (1%) 761 0.839
(1.00) 		0.686
(1.00) 		0.0118
(1.00) 		0.164
(1.00) 		0.0258
(1.00) 		0.392
(1.00) 		0.884
(1.00) 		0.831
(1.00) 		0.841
(1.00) 		0.393
(1.00) 		0.695
(1.00) 		0.126
(1.00)
NCOR1 31 (4%) 740 0.488
(1.00) 		0.33
(1.00) 		0.266
(1.00) 		0.412
(1.00) 		0.723
(1.00) 		0.726
(1.00) 		0.799
(1.00) 		0.484
(1.00) 		0.0941
(1.00) 		0.41
(1.00) 		0.593
(1.00) 		0.455
(1.00)
TBX3 18 (2%) 753 0.612
(1.00) 		0.345
(1.00) 		0.602
(1.00) 		0.0562
(1.00) 		0.16
(1.00) 		0.551
(1.00) 		0.184
(1.00) 		0.444
(1.00) 		0.489
(1.00) 		0.485
(1.00) 		0.651
(1.00) 		1
(1.00)
DSPP 26 (3%) 745 0.945
(1.00) 		0.416
(1.00) 		0.647
(1.00) 		0.792
(1.00) 		0.0987
(1.00) 		0.387
(1.00) 		0.703
(1.00) 		0.053
(1.00) 		0.488
(1.00) 		0.311
(1.00) 		0.132
(1.00) 		0.607
(1.00)
AQP7 8 (1%) 763 0.638
(1.00) 		0.0682
(1.00) 		0.0396
(1.00) 		0.662
(1.00) 		0.768
(1.00) 		0.347
(1.00) 		0.474
(1.00) 		0.632
(1.00) 		0.612
(1.00) 		0.412
(1.00)
BCL6B 8 (1%) 763 0.476
(1.00) 		0.692
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.809
(1.00) 		0.899
(1.00) 		0.49
(1.00) 		0.537
(1.00)
RPGR 14 (2%) 757 0.605
(1.00) 		0.392
(1.00) 		0.995
(1.00) 		0.628
(1.00) 		0.745
(1.00) 		0.606
(1.00) 		0.332
(1.00) 		0.51
(1.00) 		0.725
(1.00) 		0.283
(1.00) 		0.902
(1.00) 		0.501
(1.00)
TBL1XR1 9 (1%) 762 0.109
(1.00) 		0.295
(1.00) 		0.0611
(1.00) 		0.455
(1.00) 		0.569
(1.00) 		0.0215
(1.00) 		0.2
(1.00) 		0.0794
(1.00) 		0.482
(1.00) 		0.869
(1.00) 		0.229
(1.00)
MYB 11 (1%) 760 0.786
(1.00) 		1
(1.00) 		0.086
(1.00) 		0.421
(1.00) 		1
(1.00) 		0.69
(1.00) 		0.758
(1.00) 		0.656
(1.00) 		0.787
(1.00) 		0.687
(1.00) 		0.278
(1.00) 		1
(1.00)
PABPC3 8 (1%) 763 0.163
(1.00) 		0.801
(1.00) 		0.703
(1.00) 		0.73
(1.00) 		0.888
(1.00) 		0.395
(1.00) 		0.641
(1.00) 		0.899
(1.00) 		1
(1.00) 		1
(1.00)
GPS2 6 (1%) 765 0.00768
(1.00) 		0.0284
(1.00) 		0.147
(1.00) 		0.293
(1.00) 		1
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.184
(1.00) 		0.752
(1.00) 		1
(1.00)
E2F4 4 (1%) 767 0.932
(1.00) 		0.896
(1.00) 		0.817
(1.00) 		0.817
(1.00) 		0.491
(1.00)
DNAH12 12 (2%) 759 0.967
(1.00) 		0.266
(1.00) 		0.836
(1.00) 		0.672
(1.00) 		0.689
(1.00) 		0.69
(1.00) 		0.302
(1.00) 		0.532
(1.00) 		0.863
(1.00) 		1
(1.00) 		1
(1.00) 		0.52
(1.00)
CDKN1B 7 (1%) 764 0.358
(1.00) 		0.11
(1.00) 		0.00229
(1.00) 		0.0428
(1.00) 		0.331
(1.00) 		0.392
(1.00) 		0.114
(1.00) 		0.306
(1.00) 		0.363
(1.00) 		0.368
(1.00) 		0.453
(1.00) 		0.215
(1.00)
HNF1A 9 (1%) 762 0.0661
(1.00) 		0.622
(1.00) 		0.076
(1.00) 		0.0353
(1.00) 		0.406
(1.00) 		0.0699
(1.00) 		0.471
(1.00) 		0.28
(1.00)
CRIPAK 6 (1%) 765 0.821
(1.00) 		0.113
(1.00) 		0.285
(1.00) 		0.184
(1.00) 		0.258
(1.00) 		0.569
(1.00) 		0.869
(1.00) 		0.73
(1.00)
CASP8 10 (1%) 761 0.355
(1.00) 		0.197
(1.00) 		0.919
(1.00) 		0.561
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.737
(1.00) 		0.772
(1.00) 		0.166
(1.00) 		0.0985
(1.00) 		0.388
(1.00)
STXBP2 9 (1%) 762 0.905
(1.00) 		0.819
(1.00) 		0.876
(1.00) 		0.48
(1.00) 		0.406
(1.00) 		0.917
(1.00) 		0.902
(1.00) 		0.749
(1.00)
CTU2 5 (1%) 766 0.203
(1.00) 		0.542
(1.00) 		0.743
(1.00) 		0.605
(1.00) 		0.847
(1.00) 		0.07
(1.00) 		0.449
(1.00) 		0.213
(1.00)
CCDC66 9 (1%) 762 0.368
(1.00) 		0.197
(1.00) 		0.675
(1.00) 		0.675
(1.00) 		0.0682
(1.00) 		0.157
(1.00) 		0.091
(1.00) 		0.482
(1.00) 		0.484
(1.00) 		0.125
(1.00)
HIST1H3B 7 (1%) 764 0.383
(1.00) 		1
(1.00) 		0.554
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.339
(1.00) 		0.401
(1.00) 		0.474
(1.00) 		0.43
(1.00) 		0.605
(1.00) 		0.0788
(1.00)
SLC25A5 3 (0%) 768 0.329
(1.00) 		0.71
(1.00) 		0.78
(1.00) 		0.354
(1.00) 		0.456
(1.00) 		0.23
(1.00)
SELPLG 7 (1%) 764 0.0783
(1.00) 		0.00372
(1.00) 		0.108
(1.00) 		0.0801
(1.00) 		0.474
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.092
(1.00)
KRTAP9-9 6 (1%) 765 0.249
(1.00) 		0.253
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.256
(1.00) 		0.256
(1.00) 		0.156
(1.00)
KRTAP4-5 4 (1%) 767 0.478
(1.00) 		0.251
(1.00) 		0.26
(1.00) 		0.0534
(1.00) 		0.0797
(1.00) 		0.814
(1.00) 		0.154
(1.00) 		0.852
(1.00)
SF3B1 14 (2%) 757 0.629
(1.00) 		0.0949
(1.00) 		0.347
(1.00) 		0.24
(1.00) 		0.253
(1.00) 		0.00499
(1.00) 		0.186
(1.00) 		0.0216
(1.00) 		0.0194
(1.00) 		0.185
(1.00) 		0.369
(1.00) 		0.133
(1.00)
HLA-A 4 (1%) 767 0.816
(1.00) 		0.543
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.0167
(1.00) 		0.315
(1.00) 		0.671
(1.00) 		0.293
(1.00)
FGFR2 7 (1%) 764 0.602
(1.00) 		0.543
(1.00) 		0.857
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.302
(1.00) 		0.515
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.0746
(1.00) 		0.0111
(1.00)
SHROOM4 11 (1%) 760 0.432
(1.00) 		0.182
(1.00) 		0.0315
(1.00) 		0.562
(1.00) 		0.402
(1.00) 		0.633
(1.00) 		0.362
(1.00) 		0.269
(1.00) 		0.618
(1.00) 		0.925
(1.00) 		0.386
(1.00) 		0.904
(1.00)
MED12 20 (3%) 751 0.603
(1.00) 		0.326
(1.00) 		0.304
(1.00) 		0.623
(1.00) 		0.455
(1.00) 		0.803
(1.00) 		0.452
(1.00) 		0.95
(1.00) 		0.835
(1.00) 		0.647
(1.00) 		0.335
(1.00) 		0.0946
(1.00)
DENND4B 8 (1%) 763 0.148
(1.00) 		0.0156
(1.00) 		0.0749
(1.00) 		0.631
(1.00) 		0.467
(1.00) 		0.239
(1.00) 		0.587
(1.00) 		0.192
(1.00)
ODF1 5 (1%) 766 0.932
(1.00) 		0.501
(1.00) 		0.454
(1.00) 		0.517
(1.00) 		0.671
(1.00) 		0.491
(1.00) 		0.695
(1.00) 		0.806
(1.00)
AXL 6 (1%) 765 0.266
(1.00) 		0.33
(1.00) 		0.887
(1.00) 		0.251
(1.00) 		0.752
(1.00) 		0.384
(1.00) 		1
(1.00) 		0.511
(1.00)
RPL18 4 (1%) 767 0.504
(1.00) 		0.241
(1.00) 		0.119
(1.00) 		0.0917
(1.00) 		0.542
(1.00) 		0.121
(1.00) 		0.456
(1.00) 		0.615
(1.00)
RAI1 7 (1%) 764 0.269
(1.00) 		0.875
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.748
(1.00) 		0.515
(1.00) 		0.474
(1.00) 		0.797
(1.00) 		0.869
(1.00) 		0.6
(1.00)
ERBB2 12 (2%) 759 0.287
(1.00) 		0.891
(1.00) 		0.121
(1.00) 		0.0121
(1.00) 		0.451
(1.00) 		0.773
(1.00) 		0.746
(1.00) 		0.294
(1.00) 		0.269
(1.00) 		0.0665
(1.00) 		0.471
(1.00) 		0.402
(1.00)
KRT38 4 (1%) 767 0.602
(1.00) 		0.812
(1.00) 		0.288
(1.00) 		0.786
(1.00) 		0.402
(1.00) 		0.633
(1.00) 		0.633
(1.00) 		0.817
(1.00) 		0.817
(1.00) 		1
(1.00)
TICAM1 5 (1%) 766 0.774
(1.00) 		0.869
(1.00) 		0.977
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.608
(1.00)
ASXL2 8 (1%) 763 0.36
(1.00) 		0.214
(1.00) 		0.799
(1.00) 		0.431
(1.00) 		0.749
(1.00) 		0.305
(1.00) 		0.531
(1.00) 		0.336
(1.00) 		1
(1.00) 		0.468
(1.00)
ASPHD1 3 (0%) 768 0.711
(1.00) 		0.886
(1.00) 		0.661
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.626
(1.00) 		1
(1.00) 		1
(1.00)
FAM171B 8 (1%) 763 0.925
(1.00) 		0.291
(1.00) 		0.941
(1.00) 		0.047
(1.00) 		0.193
(1.00) 		0.00277
(1.00) 		0.318
(1.00) 		0.0997
(1.00) 		0.0322
(1.00) 		0.188
(1.00)
MUC20 10 (1%) 761 0.105
(1.00) 		0.147
(1.00) 		0.000539
(0.414) 		0.193
(1.00) 		0.135
(1.00) 		0.0893
(1.00) 		0.342
(1.00) 		0.109
(1.00)
PPEF1 8 (1%) 763 0.853
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.183
(1.00) 		1
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.711
(1.00) 		0.255
(1.00) 		0.385
(1.00) 		0.203
(1.00) 		0.241
(1.00)
PRRX1 6 (1%) 765 0.577
(1.00) 		0.522
(1.00) 		0.0472
(1.00) 		0.0567
(1.00) 		0.839
(1.00) 		0.392
(1.00) 		0.559
(1.00) 		0.407
(1.00) 		0.866
(1.00) 		0.433
(1.00) 		0.326
(1.00) 		0.73
(1.00)
ATP13A4 9 (1%) 762 0.602
(1.00) 		0.356
(1.00) 		0.157
(1.00) 		0.33
(1.00) 		0.873
(1.00) 		0.428
(1.00) 		0.826
(1.00) 		0.835
(1.00) 		0.789
(1.00) 		0.67
(1.00)
MUC2 18 (2%) 753 0.83
(1.00) 		0.259
(1.00) 		0.325
(1.00) 		0.487
(1.00) 		0.778
(1.00) 		0.881
(1.00) 		0.488
(1.00) 		0.288
(1.00) 		0.951
(1.00) 		1
(1.00) 		1
(1.00) 		0.303
(1.00)
UBC 8 (1%) 763 0.336
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.35
(1.00) 		0.556
(1.00) 		0.827
(1.00) 		0.29
(1.00) 		0.894
(1.00) 		0.717
(1.00) 		0.741
(1.00)
KCNN3 6 (1%) 765 0.968
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.36
(1.00) 		0.143
(1.00) 		0.635
(1.00) 		0.415
(1.00) 		0.769
(1.00) 		0.456
(1.00) 		0.138
(1.00)
RBM23 6 (1%) 765 0.693
(1.00) 		0.404
(1.00) 		0.795
(1.00) 		0.0722
(1.00) 		0.415
(1.00) 		0.0581
(1.00) 		0.695
(1.00) 		0.19
(1.00)
GNRH2 3 (0%) 768 0.319
(1.00) 		0.958
(1.00) 		1
(1.00) 		0.125
(1.00) 		1
(1.00)
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 8.9e-15 (Chi-square test), Q value = 7.3e-12

Table S1.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 118 95 105 74 20 40
PIK3CA MUTATED 7 12 24 7 62 25 9 23
PIK3CA WILD-TYPE 14 24 94 88 43 49 11 17

Figure S1.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 3.88e-10 (Fisher's exact test), Q value = 3.2e-07

Table S2.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 125 264
PIK3CA MUTATED 61 16 92
PIK3CA WILD-TYPE 59 109 172

Figure S2.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 1.13e-12 (Chi-square test), Q value = 9.2e-10

Table S3.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 261 190 58 203 47
PIK3CA MUTATED 122 44 36 47 11
PIK3CA WILD-TYPE 139 146 22 156 36

Figure S3.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.67e-09 (Chi-square test), Q value = 1.4e-06

Table S4.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 81 121 76 102 28 57
PIK3CA MUTATED 9 67 30 24 9 19
PIK3CA WILD-TYPE 72 54 46 78 19 38

Figure S4.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.013

Table S5.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 133 119
PIK3CA MUTATED 26 53 49
PIK3CA WILD-TYPE 118 80 70

Figure S5.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00085

Table S6.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 114 125
PIK3CA MUTATED 55 53 20
PIK3CA WILD-TYPE 102 61 105

Figure S6.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.11e-28 (Chi-square test), Q value = 4.2e-25

Table S7.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 130 55 196 129 199 34 15
PIK3CA MUTATED 6 20 115 55 35 18 9
PIK3CA WILD-TYPE 124 35 81 74 164 16 6

Figure S7.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.61e-12 (Fisher's exact test), Q value = 2.1e-09

Table S8.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 153 417
PIK3CA MUTATED 28 77 153
PIK3CA WILD-TYPE 160 76 264

Figure S8.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 8.02e-08 (Fisher's exact test), Q value = 6.5e-05

Table S9.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 378 221
PIK3CA MUTATED 67 149 43
PIK3CA WILD-TYPE 90 229 178

Figure S9.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.49e-11 (Fisher's exact test), Q value = 1.2e-08

Table S10.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 347 205 204
PIK3CA MUTATED 110 108 41
PIK3CA WILD-TYPE 237 97 163

Figure S10.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.05

Table S11.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 103 137
PIK3CA MUTATED 81 44 27
PIK3CA WILD-TYPE 126 59 110

Figure S11.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.9e-10 (Fisher's exact test), Q value = 1.5e-07

Table S12.  Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 108 114 178
PIK3CA MUTATED 23 25 17 87
PIK3CA WILD-TYPE 24 83 97 91

Figure S12.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.85e-05 (Chi-square test), Q value = 0.015

Table S13.  Gene #9: 'RUNX1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 261 190 58 203 47
RUNX1 MUTATED 10 4 8 2 0
RUNX1 WILD-TYPE 251 186 50 201 47

Figure S13.  Get High-res Image Gene #9: 'RUNX1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'AKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.09e-05 (Chi-square test), Q value = 0.024

Table S14.  Gene #13: 'AKT1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 130 55 196 129 199 34 15
AKT1 MUTATED 0 0 15 3 1 0 0
AKT1 WILD-TYPE 130 55 181 126 198 34 15

Figure S14.  Get High-res Image Gene #13: 'AKT1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000101 (Fisher's exact test), Q value = 0.079

Table S15.  Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 125 264
GATA3 MUTATED 15 2 37
GATA3 WILD-TYPE 105 123 227

Figure S15.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 6.27e-06 (Chi-square test), Q value = 0.005

Table S16.  Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 130 55 196 129 199 34 15
GATA3 MUTATED 1 8 29 6 34 2 0
GATA3 WILD-TYPE 129 47 167 123 165 32 15

Figure S16.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-09 (Fisher's exact test), Q value = 9.9e-07

Table S17.  Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 153 417
GATA3 MUTATED 1 15 64
GATA3 WILD-TYPE 187 138 353

Figure S17.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 4.04e-07 (Fisher's exact test), Q value = 0.00032

Table S18.  Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 378 221
GATA3 MUTATED 17 57 5
GATA3 WILD-TYPE 140 321 216

Figure S18.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.001

Table S19.  Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 347 205 204
GATA3 MUTATED 48 27 4
GATA3 WILD-TYPE 299 178 200

Figure S19.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.97e-07 (Fisher's exact test), Q value = 0.00032

Table S20.  Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 103 137
GATA3 MUTATED 39 15 2
GATA3 WILD-TYPE 168 88 135

Figure S20.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.0012

Table S21.  Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 108 114 178
GATA3 MUTATED 4 22 1 29
GATA3 WILD-TYPE 43 86 113 149

Figure S21.  Get High-res Image Gene #14: 'GATA3 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 7.08e-37 (Chi-square test), Q value = 5.8e-34

Table S22.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 118 95 105 74 20 40
TP53 MUTATED 6 6 23 77 6 50 10 6
TP53 WILD-TYPE 15 30 95 18 99 24 10 34

Figure S22.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 2.43e-33 (Fisher's exact test), Q value = 2e-30

Table S23.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 125 264
TP53 MUTATED 16 101 67
TP53 WILD-TYPE 104 24 197

Figure S23.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.53e-49 (Chi-square test), Q value = 2.9e-46

Table S24.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 261 190 58 203 47
TP53 MUTATED 32 48 8 154 13
TP53 WILD-TYPE 229 142 50 49 34

Figure S24.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.18e-23 (Chi-square test), Q value = 5.1e-20

Table S25.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 81 121 76 102 28 57
TP53 MUTATED 63 11 27 24 5 18
TP53 WILD-TYPE 18 110 49 78 23 39

Figure S25.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.87e-27 (Fisher's exact test), Q value = 1.5e-24

Table S26.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 133 119
TP53 MUTATED 102 12 38
TP53 WILD-TYPE 42 121 81

Figure S26.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1.1e-23 (Fisher's exact test), Q value = 9e-21

Table S27.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 114 125
TP53 MUTATED 35 23 94
TP53 WILD-TYPE 122 91 31

Figure S27.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.17e-55 (Chi-square test), Q value = 3.5e-52

Table S28.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 130 55 196 129 199 34 15
TP53 MUTATED 102 8 14 81 34 6 8
TP53 WILD-TYPE 28 47 182 48 165 28 7

Figure S28.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.18e-48 (Fisher's exact test), Q value = 3.5e-45

Table S29.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 153 417
TP53 MUTATED 146 22 85
TP53 WILD-TYPE 42 131 332

Figure S29.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.46e-39 (Fisher's exact test), Q value = 6.2e-36

Table S30.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 378 221
TP53 MUTATED 34 65 152
TP53 WILD-TYPE 123 313 69

Figure S30.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.32e-44 (Fisher's exact test), Q value = 1.9e-41

Table S31.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 347 205 204
TP53 MUTATED 75 27 149
TP53 WILD-TYPE 272 178 55

Figure S31.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.47e-30 (Fisher's exact test), Q value = 1.2e-27

Table S32.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 103 137
TP53 MUTATED 35 12 98
TP53 WILD-TYPE 172 91 39

Figure S32.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.95e-24 (Fisher's exact test), Q value = 4.1e-21

Table S33.  Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 108 114 178
TP53 MUTATED 13 25 82 25
TP53 WILD-TYPE 34 83 32 153

Figure S33.  Get High-res Image Gene #17: 'TP53 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1.67e-07 (Chi-square test), Q value = 0.00013

Table S34.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 118 95 105 74 20 40
CDH1 MUTATED 0 5 1 0 12 4 1 10
CDH1 WILD-TYPE 21 31 117 95 93 70 19 30

Figure S34.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 8.2e-05 (Fisher's exact test), Q value = 0.064

Table S35.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 125 264
CDH1 MUTATED 18 2 13
CDH1 WILD-TYPE 102 123 251

Figure S35.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.42e-08 (Chi-square test), Q value = 2e-05

Table S36.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 261 190 58 203 47
CDH1 MUTATED 26 9 14 2 4
CDH1 WILD-TYPE 235 181 44 201 43

Figure S36.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.2

Table S37.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 133 119
CDH1 MUTATED 3 4 16
CDH1 WILD-TYPE 141 129 103

Figure S37.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.29e-06 (Chi-square test), Q value = 0.001

Table S38.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 130 55 196 129 199 34 15
CDH1 MUTATED 0 11 23 7 7 5 2
CDH1 WILD-TYPE 130 44 173 122 192 29 13

Figure S38.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.23e-07 (Fisher's exact test), Q value = 0.00034

Table S39.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 153 417
CDH1 MUTATED 3 26 26
CDH1 WILD-TYPE 185 127 391

Figure S39.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0013

Table S40.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 378 221
CDH1 MUTATED 23 27 3
CDH1 WILD-TYPE 134 351 218

Figure S40.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.92e-08 (Fisher's exact test), Q value = 4.8e-05

Table S41.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 347 205 204
CDH1 MUTATED 18 32 3
CDH1 WILD-TYPE 329 173 201

Figure S41.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000244 (Fisher's exact test), Q value = 0.19

Table S42.  Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 103 137
CDH1 MUTATED 13 15 2
CDH1 WILD-TYPE 194 88 135

Figure S42.  Get High-res Image Gene #19: 'CDH1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000313 (Fisher's exact test), Q value = 0.24

Table S43.  Gene #21: 'MAP2K4 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 153 417
MAP2K4 MUTATED 0 6 25
MAP2K4 WILD-TYPE 188 147 392

Figure S43.  Get High-res Image Gene #21: 'MAP2K4 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.33e-06 (Chi-square test), Q value = 0.0034

Table S44.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 118 95 105 74 20 40
MAP3K1 MUTATED 6 1 11 0 16 1 0 4
MAP3K1 WILD-TYPE 15 35 107 95 89 73 20 36

Figure S44.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.034

Table S45.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 125 264
MAP3K1 MUTATED 13 0 26
MAP3K1 WILD-TYPE 107 125 238

Figure S45.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.22e-05 (Chi-square test), Q value = 0.057

Table S46.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 261 190 58 203 47
MAP3K1 MUTATED 34 7 6 5 5
MAP3K1 WILD-TYPE 227 183 52 198 42

Figure S46.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.16

Table S47.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 133 119
MAP3K1 MUTATED 3 20 13
MAP3K1 WILD-TYPE 141 113 106

Figure S47.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1.99e-06 (Fisher's exact test), Q value = 0.0016

Table S48.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 114 125
MAP3K1 MUTATED 20 16 0
MAP3K1 WILD-TYPE 137 98 125

Figure S48.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.08e-05 (Chi-square test), Q value = 0.0085

Table S49.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 130 55 196 129 199 34 15
MAP3K1 MUTATED 0 4 30 4 17 2 0
MAP3K1 WILD-TYPE 130 51 166 125 182 32 15

Figure S49.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.51e-05 (Fisher's exact test), Q value = 0.059

Table S50.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 153 417
MAP3K1 MUTATED 3 9 45
MAP3K1 WILD-TYPE 185 144 372

Figure S50.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.015

Table S51.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 378 221
MAP3K1 MUTATED 15 39 3
MAP3K1 WILD-TYPE 142 339 218

Figure S51.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.16e-05 (Fisher's exact test), Q value = 0.033

Table S52.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 347 205 204
MAP3K1 MUTATED 30 24 3
MAP3K1 WILD-TYPE 317 181 201

Figure S52.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.18

Table S53.  Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 103 137
MAP3K1 MUTATED 19 12 1
MAP3K1 WILD-TYPE 188 91 136

Figure S53.  Get High-res Image Gene #22: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'CCDC144NL MUTATION STATUS' versus 'CN_CNMF'

P value = 6.29e-06 (Chi-square test), Q value = 0.005

Table S54.  Gene #25: 'CCDC144NL MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 261 190 58 203 47
CCDC144NL MUTATED 1 3 0 0 4
CCDC144NL WILD-TYPE 260 187 58 203 43

Figure S54.  Get High-res Image Gene #25: 'CCDC144NL MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TTN MUTATION STATUS' versus 'CN_CNMF'

P value = 1.02e-05 (Chi-square test), Q value = 0.0081

Table S55.  Gene #52: 'TTN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 261 190 58 203 47
TTN MUTATED 27 29 3 53 5
TTN WILD-TYPE 234 161 55 150 42

Figure S55.  Get High-res Image Gene #52: 'TTN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TTN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 6.23e-05 (Fisher's exact test), Q value = 0.049

Table S56.  Gene #52: 'TTN MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 133 119
TTN MUTATED 38 10 15
TTN WILD-TYPE 106 123 104

Figure S56.  Get High-res Image Gene #52: 'TTN MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

Methods & Data
Input

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

  • Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 771

  • Number of significantly mutated genes = 81

  • Number of Molecular subtypes = 12

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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