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 91 genes and 10 molecular subtypes across 772 patients, 45 significant findings detected with P value < 0.05 and Q value < 0.25.

  • AKT1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

  • RUNX1 mutation correlated to 'CN_CNMF'.

  • MAP2K4 mutation correlated to 'MIRSEQ_CNMF'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 91 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 45 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
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
PIK3CA 261 (34%) 511 1.4e-14
(1.06e-11) 		4.1e-10
(3.08e-07) 		1.24e-12
(9.33e-10) 		9.27e-11
(6.97e-08) 		1.64e-05
(0.0121) 		1.06e-06
(0.00079) 		4.23e-29
(3.22e-26) 		1.1e-12
(8.3e-10) 		7.22e-07
(0.000537) 		4.84e-11
(3.64e-08)
TP53 257 (33%) 515 3.29e-36
(2.51e-33) 		1.12e-32
(8.53e-30) 		7.85e-46
(6e-43) 		5.8e-21
(4.39e-18) 		1.87e-27
(1.42e-24) 		1.1e-23
(8.35e-21) 		5.68e-52
(4.35e-49) 		2.6e-49
(1.99e-46) 		8.14e-38
(6.21e-35) 		8.23e-47
(6.29e-44)
MAP3K1 57 (7%) 715 1.21e-07
(9.03e-05) 		4.93e-05
(0.0361) 		6.6e-05
(0.0481) 		0.028
(1.00) 		0.000204
(0.148) 		1.99e-06
(0.00147) 		1.01e-07
(7.52e-05) 		3.28e-05
(0.0241) 		7.87e-06
(0.0058) 		4.46e-06
(0.00329)
CDH1 55 (7%) 717 1.45e-06
(0.00107) 		6.06e-05
(0.0443) 		7.09e-08
(5.32e-05) 		0.0034
(1.00) 		0.000255
(0.185) 		0.000579
(0.415) 		3.37e-05
(0.0247) 		9.24e-08
(6.92e-05) 		0.000873
(0.624) 		0.000137
(0.0994)
GATA3 81 (10%) 691 0.00138
(0.984) 		0.000116
(0.0845) 		0.00425
(1.00) 		0.0146
(1.00) 		0.00115
(0.822) 		0.000407
(0.294) 		1.14e-06
(0.000846) 		1.06e-07
(7.94e-05) 		2.3e-05
(0.0169) 		3.34e-07
(0.000249)
AKT1 19 (2%) 753 0.0507
(1.00) 		0.926
(1.00) 		0.00329
(1.00) 		0.000112
(0.0819) 		0.162
(1.00) 		0.345
(1.00) 		2.99e-05
(0.0219) 		0.384
(1.00) 		0.0226
(1.00) 		0.0225
(1.00)
RUNX1 25 (3%) 747 0.00628
(1.00) 		0.0818
(1.00) 		7.89e-07
(0.000587) 		0.014
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.133
(1.00) 		0.131
(1.00) 		0.067
(1.00) 		0.0392
(1.00)
MAP2K4 32 (4%) 740 0.0704
(1.00) 		0.00475
(1.00) 		0.0427
(1.00) 		0.0123
(1.00) 		0.00238
(1.00) 		0.0344
(1.00) 		0.00649
(1.00) 		0.000475
(0.341) 		0.000298
(0.215) 		0.000614
(0.439)
DSPP 26 (3%) 746 0.946
(1.00) 		0.42
(1.00) 		0.567
(1.00) 		0.975
(1.00) 		0.0987
(1.00) 		0.387
(1.00) 		0.593
(1.00) 		0.417
(1.00) 		0.096
(1.00) 		0.554
(1.00)
PIK3R1 21 (3%) 751 0.168
(1.00) 		0.437
(1.00) 		0.787
(1.00) 		0.572
(1.00) 		0.538
(1.00) 		0.297
(1.00) 		0.403
(1.00) 		0.923
(1.00) 		0.591
(1.00) 		0.849
(1.00)
AOAH 19 (2%) 753 0.591
(1.00) 		0.722
(1.00) 		0.442
(1.00) 		0.538
(1.00) 		0.0226
(1.00) 		0.849
(1.00)
DCP1B 5 (1%) 767 0.35
(1.00) 		0.00648
(1.00) 		0.714
(1.00) 		0.623
(1.00) 		0.384
(1.00) 		0.122
(1.00)
MAP3K4 18 (2%) 754 0.106
(1.00) 		0.849
(1.00) 		0.763
(1.00) 		0.287
(1.00) 		0.0733
(1.00) 		0.69
(1.00) 		0.381
(1.00) 		0.423
(1.00) 		0.518
(1.00) 		0.0595
(1.00)
MEF2A 14 (2%) 758 0.607
(1.00) 		0.399
(1.00) 		0.701
(1.00) 		0.684
(1.00) 		0.134
(1.00) 		0.734
(1.00)
NCOA3 29 (4%) 743 0.615
(1.00) 		0.789
(1.00) 		0.925
(1.00) 		0.537
(1.00) 		1
(1.00) 		1
(1.00) 		0.505
(1.00) 		0.804
(1.00) 		0.814
(1.00) 		0.192
(1.00)
NCOR2 29 (4%) 743 0.693
(1.00) 		1
(1.00) 		0.0722
(1.00) 		0.631
(1.00) 		0.839
(1.00) 		0.69
(1.00) 		0.997
(1.00) 		0.608
(1.00) 		0.734
(1.00) 		0.276
(1.00)
NR1H2 18 (2%) 754 0.375
(1.00) 		0.58
(1.00) 		0.771
(1.00) 		0.0701
(1.00) 		0.064
(1.00) 		0.116
(1.00) 		0.0759
(1.00) 		0.0138
(1.00) 		0.313
(1.00) 		0.0832
(1.00)
RBMX 13 (2%) 759 0.00192
(1.00) 		0.0789
(1.00) 		0.306
(1.00) 		0.214
(1.00) 		0.472
(1.00) 		0.154
(1.00)
TPRX1 7 (1%) 765 0.315
(1.00) 		0.511
(1.00) 		0.989
(1.00) 		1
(1.00) 		1
(1.00) 		0.408
(1.00)
ZNF384 14 (2%) 758 0.456
(1.00) 		0.478
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.362
(1.00)
PTEN 29 (4%) 743 0.273
(1.00) 		0.445
(1.00) 		0.232
(1.00) 		0.431
(1.00) 		0.882
(1.00) 		0.266
(1.00) 		0.731
(1.00) 		0.804
(1.00) 		0.265
(1.00) 		0.617
(1.00)
TBX3 18 (2%) 754 0.847
(1.00) 		0.385
(1.00) 		0.481
(1.00) 		0.161
(1.00) 		0.16
(1.00) 		0.551
(1.00) 		0.49
(1.00) 		0.384
(1.00) 		0.805
(1.00) 		0.846
(1.00)
CBFB 16 (2%) 756 0.17
(1.00) 		0.739
(1.00) 		0.0322
(1.00) 		0.00425
(1.00) 		0.35
(1.00) 		0.569
(1.00) 		0.0149
(1.00) 		0.0851
(1.00) 		0.143
(1.00) 		0.058
(1.00)
FOXA1 15 (2%) 757 0.742
(1.00) 		0.097
(1.00) 		0.343
(1.00) 		0.0395
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.423
(1.00) 		0.334
(1.00) 		0.683
(1.00) 		0.302
(1.00)
MLL3 56 (7%) 716 0.233
(1.00) 		0.948
(1.00) 		0.505
(1.00) 		0.902
(1.00) 		0.74
(1.00) 		0.935
(1.00) 		0.591
(1.00) 		0.95
(1.00) 		0.0985
(1.00) 		0.191
(1.00)
ATN1 17 (2%) 755 0.314
(1.00) 		0.125
(1.00) 		0.0485
(1.00) 		0.874
(1.00) 		0.169
(1.00) 		0.291
(1.00) 		0.0545
(1.00) 		0.52
(1.00) 		0.844
(1.00) 		1
(1.00)
SF3B1 14 (2%) 758 0.759
(1.00) 		0.205
(1.00) 		0.396
(1.00) 		0.276
(1.00) 		0.253
(1.00) 		0.00499
(1.00) 		0.419
(1.00) 		0.422
(1.00) 		0.0875
(1.00) 		0.734
(1.00)
CCDC144NL 8 (1%) 764 0.000405
(0.292) 		0.325
(1.00) 		0.639
(1.00) 		0.0909
(1.00) 		0.33
(1.00) 		0.677
(1.00)
MUC12 44 (6%) 728 0.266
(1.00) 		0.038
(1.00) 		0.525
(1.00) 		0.132
(1.00) 		0.364
(1.00) 		0.499
(1.00) 		0.718
(1.00) 		0.0413
(1.00) 		0.175
(1.00) 		0.563
(1.00)
KRTAP4-7 7 (1%) 765 0.208
(1.00) 		0.599
(1.00) 		0.883
(1.00) 		0.582
(1.00) 		0.374
(1.00) 		1
(1.00)
ZFP36L1 10 (1%) 762 0.856
(1.00) 		0.616
(1.00) 		0.000412
(0.296) 		0.396
(1.00) 		0.0258
(1.00) 		0.392
(1.00) 		0.918
(1.00) 		0.301
(1.00) 		0.429
(1.00) 		0.372
(1.00)
NCOR1 31 (4%) 741 0.422
(1.00) 		0.505
(1.00) 		0.389
(1.00) 		0.31
(1.00) 		0.723
(1.00) 		0.726
(1.00) 		0.634
(1.00) 		0.467
(1.00) 		0.307
(1.00) 		0.535
(1.00)
KRAS 6 (1%) 766 0.577
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.184
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.476
(1.00) 		1
(1.00) 		0.47
(1.00) 		0.578
(1.00)
PHLDA1 9 (1%) 763 0.352
(1.00) 		0.315
(1.00) 		0.338
(1.00) 		0.702
(1.00) 		1
(1.00) 		0.28
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.585
(1.00) 		1
(1.00)
VEZF1 8 (1%) 764 0.653
(1.00) 		0.537
(1.00) 		0.243
(1.00) 		0.799
(1.00) 		1
(1.00) 		0.562
(1.00)
ERBB2 12 (2%) 760 0.308
(1.00) 		0.893
(1.00) 		0.000568
(0.408) 		0.00785
(1.00) 		0.451
(1.00) 		0.773
(1.00) 		0.00235
(1.00) 		0.437
(1.00) 		0.479
(1.00) 		0.183
(1.00)
CTCF 18 (2%) 754 0.0239
(1.00) 		0.289
(1.00) 		0.0132
(1.00) 		0.0137
(1.00) 		0.0682
(1.00) 		0.369
(1.00) 		0.000931
(0.665) 		0.163
(1.00) 		0.0551
(1.00) 		0.0342
(1.00)
KRTAP9-9 6 (1%) 766 0.262
(1.00) 		0.177
(1.00) 		0.0683
(1.00) 		1
(1.00) 		0.21
(1.00) 		0.185
(1.00)
BCL6B 8 (1%) 764 0.135
(1.00) 		0.695
(1.00) 		0.273
(1.00) 		0.625
(1.00) 		0.89
(1.00) 		0.562
(1.00)
CTU2 5 (1%) 767 0.242
(1.00) 		0.577
(1.00) 		0.749
(1.00) 		0.732
(1.00) 		0.847
(1.00) 		0.725
(1.00)
RB1 14 (2%) 758 0.513
(1.00) 		0.093
(1.00) 		0.179
(1.00) 		0.327
(1.00) 		0.483
(1.00) 		0.762
(1.00) 		0.412
(1.00) 		0.262
(1.00) 		0.202
(1.00) 		0.25
(1.00)
HIST1H3B 7 (1%) 765 0.379
(1.00) 		1
(1.00) 		0.539
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.269
(1.00) 		0.387
(1.00) 		0.776
(1.00) 		1
(1.00)
AQP7 8 (1%) 764 0.626
(1.00) 		0.138
(1.00) 		0.351
(1.00) 		0.641
(1.00) 		0.732
(1.00) 		0.737
(1.00) 		0.684
(1.00) 		0.511
(1.00)
MYB 11 (1%) 761 0.758
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.407
(1.00) 		1
(1.00) 		0.69
(1.00) 		0.19
(1.00) 		0.549
(1.00) 		0.705
(1.00) 		1
(1.00)
E2F4 4 (1%) 768 0.934
(1.00) 		0.852
(1.00) 		0.369
(1.00) 		1
(1.00) 		1
(1.00)
MUC20 10 (1%) 762 0.0748
(1.00) 		0.103
(1.00) 		0.0542
(1.00) 		0.16
(1.00) 		0.228
(1.00) 		0.0281
(1.00)
AKD1 19 (2%) 753 0.771
(1.00) 		0.449
(1.00) 		0.0586
(1.00) 		0.368
(1.00) 		0.467
(1.00) 		0.242
(1.00) 		0.341
(1.00) 		0.0761
(1.00) 		0.253
(1.00) 		0.849
(1.00)
CDKN1B 7 (1%) 765 0.316
(1.00) 		0.203
(1.00) 		0.00331
(1.00) 		0.0247
(1.00) 		0.331
(1.00) 		0.392
(1.00) 		0.122
(1.00) 		0.237
(1.00) 		0.0783
(1.00) 		0.233
(1.00)
KRTAP4-5 4 (1%) 768 0.473
(1.00) 		0.224
(1.00) 		0.824
(1.00) 		0.346
(1.00) 		0.817
(1.00) 		1
(1.00)
RPGR 14 (2%) 758 0.597
(1.00) 		0.299
(1.00) 		0.923
(1.00) 		0.706
(1.00) 		0.745
(1.00) 		0.606
(1.00) 		0.524
(1.00) 		0.27
(1.00) 		0.433
(1.00) 		0.211
(1.00)
CASP8 10 (1%) 762 0.324
(1.00) 		0.332
(1.00) 		0.917
(1.00) 		0.505
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.84
(1.00) 		0.511
(1.00) 		0.16
(1.00)
HLA-A 4 (1%) 768 0.806
(1.00) 		0.275
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.00324
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.448
(1.00)
FGFR2 7 (1%) 765 0.591
(1.00) 		0.37
(1.00) 		0.86
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.2
(1.00) 		0.625
(1.00) 		0.238
(1.00) 		0.0718
(1.00)
TBL1XR1 9 (1%) 763 0.0917
(1.00) 		0.269
(1.00) 		0.034
(1.00) 		0.455
(1.00) 		0.569
(1.00) 		0.0756
(1.00) 		0.212
(1.00) 		0.153
(1.00) 		0.266
(1.00)
PRRX1 6 (1%) 766 0.552
(1.00) 		0.606
(1.00) 		0.468
(1.00) 		0.122
(1.00) 		0.839
(1.00) 		0.392
(1.00) 		0.362
(1.00) 		0.148
(1.00) 		0.254
(1.00) 		0.185
(1.00)
ZNF69 5 (1%) 767 0.613
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.75
(1.00) 		0.358
(1.00) 		0.732
(1.00) 		0.847
(1.00) 		0.725
(1.00)
GNRH2 3 (0%) 769 0.26
(1.00) 		0.411
(1.00) 		1
(1.00) 		0.0995
(1.00) 		0.209
(1.00)
HLA-DRB1 8 (1%) 764 0.524
(1.00) 		0.444
(1.00) 		0.223
(1.00) 		0.209
(1.00) 		0.407
(1.00) 		1
(1.00) 		0.0488
(1.00) 		0.826
(1.00)
DENND4B 8 (1%) 764 0.188
(1.00) 		0.0515
(1.00) 		0.399
(1.00) 		0.204
(1.00) 		0.218
(1.00) 		0.187
(1.00)
CCDC66 9 (1%) 763 0.389
(1.00) 		0.332
(1.00) 		0.876
(1.00) 		0.673
(1.00) 		0.0534
(1.00) 		0.192
(1.00) 		0.061
(1.00) 		0.495
(1.00)
AFF2 15 (2%) 757 0.687
(1.00) 		0.0503
(1.00) 		0.188
(1.00) 		0.229
(1.00) 		0.0623
(1.00) 		0.015
(1.00) 		0.501
(1.00) 		0.334
(1.00) 		0.247
(1.00) 		0.241
(1.00)
HNF1A 9 (1%) 763 0.0685
(1.00) 		0.603
(1.00) 		0.212
(1.00) 		0.124
(1.00) 		0.532
(1.00) 		0.266
(1.00)
RAI1 7 (1%) 765 0.225
(1.00) 		0.912
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.721
(1.00) 		0.878
(1.00) 		0.74
(1.00) 		0.77
(1.00)
GPS2 6 (1%) 766 0.00759
(1.00) 		0.102
(1.00) 		0.147
(1.00) 		0.35
(1.00) 		1
(1.00) 		1
(1.00) 		0.54
(1.00) 		0.246
(1.00) 		0.863
(1.00) 		0.578
(1.00)
PCMTD1 3 (0%) 769 0.495
(1.00) 		0.657
(1.00) 		0.584
(1.00) 		0.792
(1.00) 		0.743
(1.00) 		0.209
(1.00)
SLC25A5 3 (0%) 769 0.255
(1.00) 		0.693
(1.00) 		0.286
(1.00) 		0.321
(1.00)
STXBP2 9 (1%) 763 0.793
(1.00) 		0.692
(1.00) 		0.676
(1.00) 		0.636
(1.00) 		0.901
(1.00) 		1
(1.00)
FAM21A 7 (1%) 765 0.475
(1.00) 		0.225
(1.00) 		0.0504
(1.00) 		0.115
(1.00) 		0.111
(1.00) 		0.497
(1.00) 		0.292
(1.00) 		0.122
(1.00) 		0.325
(1.00) 		0.134
(1.00)
ZNF587 9 (1%) 763 0.0576
(1.00) 		0.721
(1.00) 		0.256
(1.00) 		0.191
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.00748
(1.00) 		0.0272
(1.00) 		0.121
(1.00) 		0.0747
(1.00)
POLR2J3 3 (0%) 769 0.701
(1.00) 		0.693
(1.00) 		0.929
(1.00) 		0.113
(1.00) 		0.286
(1.00) 		0.321
(1.00)
AXL 6 (1%) 766 0.255
(1.00) 		0.413
(1.00) 		0.502
(1.00) 		0.0316
(1.00) 		1
(1.00) 		0.262
(1.00)
MUC21 6 (1%) 766 0.377
(1.00) 		0.806
(1.00) 		0.147
(1.00) 		0.00908
(1.00) 		0.778
(1.00) 		0.448
(1.00) 		0.863
(1.00) 		0.461
(1.00)
MED23 13 (2%) 759 0.00902
(1.00) 		0.0201
(1.00) 		0.264
(1.00) 		0.22
(1.00) 		0.121
(1.00) 		0.191
(1.00) 		0.154
(1.00) 		0.0271
(1.00) 		0.109
(1.00) 		0.0914
(1.00)
KRT38 4 (1%) 768 0.591
(1.00) 		0.69
(1.00) 		0.251
(1.00) 		0.748
(1.00) 		0.402
(1.00) 		0.633
(1.00) 		0.655
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
HS6ST1 5 (1%) 767 0.013
(1.00) 		0.683
(1.00) 		0.838
(1.00) 		0.623
(1.00) 		0.111
(1.00) 		0.725
(1.00)
RALY 6 (1%) 766 0.647
(1.00) 		0.76
(1.00) 		0.0903
(1.00) 		0.673
(1.00) 		0.142
(1.00) 		0.77
(1.00)
UBC 8 (1%) 764 0.286
(1.00) 		0.789
(1.00) 		0.0144
(1.00) 		0.339
(1.00) 		0.556
(1.00) 		0.827
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.89
(1.00) 		0.826
(1.00)
TLR4 11 (1%) 761 0.364
(1.00) 		0.326
(1.00) 		0.763
(1.00) 		0.988
(1.00) 		0.28
(1.00) 		0.332
(1.00) 		0.984
(1.00) 		0.393
(1.00) 		0.705
(1.00) 		1
(1.00)
ODF1 5 (1%) 767 0.934
(1.00) 		0.683
(1.00) 		0.409
(1.00) 		0.295
(1.00) 		1
(1.00) 		1
(1.00)
PABPC3 8 (1%) 764 0.162
(1.00) 		0.806
(1.00) 		0.711
(1.00) 		0.824
(1.00) 		0.522
(1.00) 		0.816
(1.00) 		1
(1.00) 		0.455
(1.00)
KCNT2 11 (1%) 761 0.332
(1.00) 		0.371
(1.00) 		0.129
(1.00) 		0.543
(1.00) 		0.524
(1.00) 		1
(1.00) 		0.148
(1.00) 		0.287
(1.00) 		0.45
(1.00) 		0.35
(1.00)
NEK5 9 (1%) 763 0.807
(1.00) 		0.332
(1.00) 		0.775
(1.00) 		0.72
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.914
(1.00) 		0.911
(1.00) 		0.901
(1.00) 		0.399
(1.00)
ASPHD1 3 (0%) 769 0.701
(1.00) 		0.887
(1.00) 		0.845
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.209
(1.00)
FAM47B 7 (1%) 765 0.62
(1.00) 		0.315
(1.00) 		0.756
(1.00) 		0.573
(1.00) 		0.522
(1.00) 		1
(1.00) 		0.777
(1.00) 		0.709
(1.00) 		0.325
(1.00) 		0.813
(1.00)
PCDH19 14 (2%) 758 0.22
(1.00) 		0.919
(1.00) 		0.79
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.379
(1.00) 		0.621
(1.00) 		0.712
(1.00) 		0.816
(1.00)
ZIC3 4 (1%) 768 0.83
(1.00) 		0.52
(1.00) 		0.613
(1.00) 		0.57
(1.00) 		0.294
(1.00) 		1
(1.00)
FAM21C 6 (1%) 766 0.475
(1.00) 		0.0145
(1.00) 		0.0268
(1.00) 		0.00648
(1.00) 		0.099
(1.00) 		0.00333
(1.00) 		0.00455
(1.00) 		0.0654
(1.00)
VSTM2B 3 (0%) 769 0.97
(1.00) 		0.945
(1.00) 		1
(1.00) 		1
(1.00) 		0.66
(1.00)
SELPLG 7 (1%) 765 0.266
(1.00) 		0.14
(1.00) 		0.0445
(1.00) 		0.205
(1.00) 		0.684
(1.00) 		0.233
(1.00)
SLC30A10 5 (1%) 767 0.68
(1.00) 		0.806
(1.00) 		0.555
(1.00) 		0.665
(1.00) 		0.402
(1.00) 		0.379
(1.00) 		0.948
(1.00) 		0.538
(1.00) 		1
(1.00) 		0.542
(1.00)
RGS7 8 (1%) 764 0.578
(1.00) 		0.24
(1.00) 		0.089
(1.00) 		0.439
(1.00) 		0.743
(1.00) 		0.625
(1.00) 		0.675
(1.00) 		0.388
(1.00) 		0.33
(1.00) 		0.00844
(1.00)
'AKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000112 (Chi-square test), Q value = 0.082

Table S1.  Gene #3: 'AKT1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 77 111 69 120 31 57
AKT1 MUTATED 0 11 2 0 0 1
AKT1 WILD-TYPE 77 100 67 120 31 56

Figure S1.  Get High-res Image Gene #3: 'AKT1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'AKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.99e-05 (Chi-square test), Q value = 0.022

Table S2.  Gene #3: 'AKT1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 134 65 94 121 166 12 136 25
AKT1 MUTATED 0 0 3 2 1 0 12 0
AKT1 WILD-TYPE 134 65 91 119 165 12 124 25

Figure S2.  Get High-res Image Gene #3: 'AKT1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000116 (Fisher's exact test), Q value = 0.085

Table S3.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 125 246
GATA3 MUTATED 18 2 34
GATA3 WILD-TYPE 121 123 212

Figure S3.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.14e-06 (Chi-square test), Q value = 0.00085

Table S4.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 134 65 94 121 166 12 136 25
GATA3 MUTATED 1 10 6 6 31 0 23 2
GATA3 WILD-TYPE 133 55 88 115 135 12 113 23

Figure S4.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-07 (Fisher's exact test), Q value = 7.9e-05

Table S5.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 316 187 250
GATA3 MUTATED 45 2 32
GATA3 WILD-TYPE 271 185 218

Figure S5.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.3e-05 (Fisher's exact test), Q value = 0.017

Table S6.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 403 224
GATA3 MUTATED 11 59 8
GATA3 WILD-TYPE 114 344 216

Figure S6.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.34e-07 (Fisher's exact test), Q value = 0.00025

Table S7.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 525 53
GATA3 MUTATED 2 72 4
GATA3 WILD-TYPE 172 453 49

Figure S7.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1.4e-14 (Chi-square test), Q value = 1.1e-11

Table S8.  Gene #12: '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 123 36 23 94 74 20 100 40
PIK3CA MUTATED 25 12 9 7 25 9 60 22
PIK3CA WILD-TYPE 98 24 14 87 49 11 40 18

Figure S8.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4.1e-10 (Fisher's exact test), Q value = 3.1e-07

Table S9.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 125 246
PIK3CA MUTATED 69 16 84
PIK3CA WILD-TYPE 70 109 162

Figure S9.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 1.24e-12 (Chi-square test), Q value = 9.3e-10

Table S10.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 262 202 61 193 42
PIK3CA MUTATED 124 48 36 43 9
PIK3CA WILD-TYPE 138 154 25 150 33

Figure S10.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.27e-11 (Chi-square test), Q value = 7e-08

Table S11.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 77 111 69 120 31 57
PIK3CA MUTATED 6 63 30 31 10 18
PIK3CA WILD-TYPE 71 48 39 89 21 39

Figure S11.  Get High-res Image Gene #12: '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 = 0.012

Table S12.  Gene #12: '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 S12.  Get High-res Image Gene #12: '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 = 0.00079

Table S13.  Gene #12: '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 S13.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.23e-29 (Chi-square test), Q value = 3.2e-26

Table S14.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 134 65 94 121 166 12 136 25
PIK3CA MUTATED 8 25 63 48 23 7 70 13
PIK3CA WILD-TYPE 126 40 31 73 143 5 66 12

Figure S14.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.1e-12 (Fisher's exact test), Q value = 8.3e-10

Table S15.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 316 187 250
PIK3CA MUTATED 109 28 120
PIK3CA WILD-TYPE 207 159 130

Figure S15.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.22e-07 (Fisher's exact test), Q value = 0.00054

Table S16.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 403 224
PIK3CA MUTATED 49 163 46
PIK3CA WILD-TYPE 76 240 178

Figure S16.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.84e-11 (Fisher's exact test), Q value = 3.6e-08

Table S17.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 525 53
PIK3CA MUTATED 24 211 23
PIK3CA WILD-TYPE 150 314 30

Figure S17.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.29e-36 (Chi-square test), Q value = 2.5e-33

Table S18.  Gene #14: '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 123 36 23 94 74 20 100 40
TP53 MUTATED 24 6 6 76 50 10 6 6
TP53 WILD-TYPE 99 30 17 18 24 10 94 34

Figure S18.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.12e-32 (Fisher's exact test), Q value = 8.5e-30

Table S19.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 125 246
TP53 MUTATED 22 101 61
TP53 WILD-TYPE 117 24 185

Figure S19.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.85e-46 (Chi-square test), Q value = 6e-43

Table S20.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 262 202 61 193 42
TP53 MUTATED 36 49 9 146 15
TP53 WILD-TYPE 226 153 52 47 27

Figure S20.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5.8e-21 (Chi-square test), Q value = 4.4e-18

Table S21.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 77 111 69 120 31 57
TP53 MUTATED 59 10 26 31 5 17
TP53 WILD-TYPE 18 101 43 89 26 40

Figure S21.  Get High-res Image Gene #14: '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 = 1.4e-24

Table S22.  Gene #14: '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 S22.  Get High-res Image Gene #14: '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 = 8.4e-21

Table S23.  Gene #14: '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 S23.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.68e-52 (Chi-square test), Q value = 4.4e-49

Table S24.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 134 65 94 121 166 12 136 25
TP53 MUTATED 105 9 21 74 27 6 6 4
TP53 WILD-TYPE 29 56 73 47 139 6 130 21

Figure S24.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.6e-49 (Fisher's exact test), Q value = 2e-46

Table S25.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 316 187 250
TP53 MUTATED 71 146 35
TP53 WILD-TYPE 245 41 215

Figure S25.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 8.14e-38 (Fisher's exact test), Q value = 6.2e-35

Table S26.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 403 224
TP53 MUTATED 31 68 152
TP53 WILD-TYPE 94 335 72

Figure S26.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.23e-47 (Fisher's exact test), Q value = 6.3e-44

Table S27.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 525 53
TP53 MUTATED 131 90 30
TP53 WILD-TYPE 43 435 23

Figure S27.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.89e-07 (Chi-square test), Q value = 0.00059

Table S28.  Gene #17: 'RUNX1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 262 202 61 193 42
RUNX1 MUTATED 10 4 9 1 0
RUNX1 WILD-TYPE 252 198 52 192 42

Figure S28.  Get High-res Image Gene #17: 'RUNX1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000298 (Fisher's exact test), Q value = 0.22

Table S29.  Gene #21: 'MAP2K4 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 403 224
MAP2K4 MUTATED 5 26 1
MAP2K4 WILD-TYPE 120 377 223

Figure S29.  Get High-res Image Gene #21: 'MAP2K4 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1.45e-06 (Chi-square test), Q value = 0.0011

Table S30.  Gene #22: '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 123 36 23 94 74 20 100 40
CDH1 MUTATED 2 5 1 0 4 1 10 10
CDH1 WILD-TYPE 121 31 22 94 70 19 90 30

Figure S30.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 6.06e-05 (Fisher's exact test), Q value = 0.044

Table S31.  Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 125 246
CDH1 MUTATED 20 2 11
CDH1 WILD-TYPE 119 123 235

Figure S31.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.09e-08 (Chi-square test), Q value = 5.3e-05

Table S32.  Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 262 202 61 193 42
CDH1 MUTATED 26 9 14 2 4
CDH1 WILD-TYPE 236 193 47 191 38

Figure S32.  Get High-res Image Gene #22: '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 = 0.18

Table S33.  Gene #22: '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 S33.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.37e-05 (Chi-square test), Q value = 0.025

Table S34.  Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 134 65 94 121 166 12 136 25
CDH1 MUTATED 0 13 11 8 7 1 12 3
CDH1 WILD-TYPE 134 52 83 113 159 11 124 22

Figure S34.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.24e-08 (Fisher's exact test), Q value = 6.9e-05

Table S35.  Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 316 187 250
CDH1 MUTATED 17 2 36
CDH1 WILD-TYPE 299 185 214

Figure S35.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.099

Table S36.  Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 525 53
CDH1 MUTATED 2 49 2
CDH1 WILD-TYPE 172 476 51

Figure S36.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1.21e-07 (Chi-square test), Q value = 9e-05

Table S37.  Gene #23: '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 123 36 23 94 74 20 100 40
MAP3K1 MUTATED 12 1 8 0 1 0 14 3
MAP3K1 WILD-TYPE 111 35 15 94 73 20 86 37

Figure S37.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.036

Table S38.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 125 246
MAP3K1 MUTATED 13 0 26
MAP3K1 WILD-TYPE 126 125 220

Figure S38.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 6.6e-05 (Chi-square test), Q value = 0.048

Table S39.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 262 202 61 193 42
MAP3K1 MUTATED 34 7 7 5 4
MAP3K1 WILD-TYPE 228 195 54 188 38

Figure S39.  Get High-res Image Gene #23: '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 = 0.15

Table S40.  Gene #23: '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 S40.  Get High-res Image Gene #23: '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 = 0.0015

Table S41.  Gene #23: '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 S41.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.01e-07 (Chi-square test), Q value = 7.5e-05

Table S42.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 134 65 94 121 166 12 136 25
MAP3K1 MUTATED 1 3 21 3 14 0 12 3
MAP3K1 WILD-TYPE 133 62 73 118 152 12 124 22

Figure S42.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.28e-05 (Fisher's exact test), Q value = 0.024

Table S43.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 316 187 250
MAP3K1 MUTATED 34 2 21
MAP3K1 WILD-TYPE 282 185 229

Figure S43.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.87e-06 (Fisher's exact test), Q value = 0.0058

Table S44.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 403 224
MAP3K1 MUTATED 10 44 3
MAP3K1 WILD-TYPE 115 359 221

Figure S44.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0033

Table S45.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 525 53
MAP3K1 MUTATED 1 54 2
MAP3K1 WILD-TYPE 173 471 51

Figure S45.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 772

  • Number of significantly mutated genes = 91

  • Number of Molecular subtypes = 10

  • 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)
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