Correlation between gene mutation status and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1Z31WJ3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1Z31WJ3
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, 44 significant findings detected with P value < 0.05 and Q value < 0.25.

  • AKT1 mutation correlated to 'METHLYATION_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'.

  • CDH1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', 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, 44 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 Fisher's exact 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
(3.09e-07) 		1.24e-12
(9.35e-10) 		9.27e-11
(6.98e-08) 		1.64e-05
(0.012) 		1.06e-06
(0.000788) 		8.13e-10
(6.1e-07) 		1.32e-12
(9.93e-10) 		8.02e-08
(5.98e-05) 		1.49e-11
(1.12e-08)
TP53 257 (33%) 515 3.29e-36
(2.51e-33) 		1.12e-32
(8.53e-30) 		7.85e-46
(6.01e-43) 		5.8e-21
(4.39e-18) 		1.87e-27
(1.42e-24) 		1.1e-23
(8.36e-21) 		2.24e-58
(1.72e-55) 		1.78e-49
(1.36e-46) 		7.46e-39
(5.69e-36) 		2.32e-44
(1.77e-41)
MAP3K1 57 (7%) 715 1.21e-07
(9.02e-05) 		4.93e-05
(0.0361) 		6.6e-05
(0.0481) 		0.028
(1.00) 		0.000204
(0.148) 		1.99e-06
(0.00146) 		0.000234
(0.169) 		5.52e-05
(0.0403) 		1.96e-05
(0.0144) 		4.16e-05
(0.0305)
CDH1 55 (7%) 717 1.45e-06
(0.00107) 		6.06e-05
(0.0443) 		7.09e-08
(5.29e-05) 		0.0034
(1.00) 		0.000255
(0.185) 		0.000579
(0.416) 		1.58e-07
(0.000118) 		1.48e-07
(0.00011) 		1.67e-06
(0.00123) 		5.92e-08
(4.43e-05)
GATA3 81 (10%) 691 0.00138
(0.989) 		0.000116
(0.0845) 		0.00425
(1.00) 		0.0146
(1.00) 		0.00115
(0.827) 		0.000407
(0.294) 		1.56e-09
(1.17e-06) 		9.97e-10
(7.48e-07) 		4.04e-07
(3e-04) 		1.27e-06
(0.000935)
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) 		0.188
(1.00) 		0.364
(1.00) 		0.0167
(1.00) 		0.0756
(1.00)
RUNX1 25 (3%) 747 0.00628
(1.00) 		0.0818
(1.00) 		7.89e-07
(0.000585) 		0.014
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.446
(1.00) 		0.0872
(1.00) 		0.00248
(1.00) 		0.133
(1.00)
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) 		0.18
(1.00) 		0.0799
(1.00) 		0.488
(1.00) 		0.311
(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) 		1
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.875
(1.00)
AOAH 19 (2%) 753 0.591
(1.00) 		0.722
(1.00) 		0.188
(1.00) 		0.0645
(1.00) 		0.109
(1.00) 		0.503
(1.00)
DCP1B 5 (1%) 767 0.35
(1.00) 		0.00648
(1.00) 		0.572
(1.00) 		0.84
(1.00) 		0.607
(1.00) 		0.606
(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) 		0.212
(1.00) 		0.443
(1.00) 		0.398
(1.00) 		0.209
(1.00)
MEF2A 14 (2%) 758 0.607
(1.00) 		0.399
(1.00) 		0.21
(1.00) 		0.351
(1.00) 		0.0531
(1.00) 		0.0127
(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) 		0.599
(1.00) 		0.588
(1.00) 		0.281
(1.00) 		0.0961
(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) 		0.776
(1.00) 		0.568
(1.00) 		0.542
(1.00) 		0.859
(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) 		0.559
(1.00) 		0.0447
(1.00) 		0.739
(1.00) 		0.44
(1.00)
RBMX 13 (2%) 759 0.00192
(1.00) 		0.0789
(1.00) 		0.162
(1.00) 		0.163
(1.00) 		0.276
(1.00) 		0.418
(1.00)
TPRX1 7 (1%) 765 0.315
(1.00) 		0.511
(1.00) 		0.866
(1.00) 		0.758
(1.00) 		0.694
(1.00) 		1
(1.00)
ZNF384 14 (2%) 758 0.456
(1.00) 		0.478
(1.00) 		0.929
(1.00) 		0.819
(1.00) 		0.881
(1.00) 		0.263
(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) 		0.964
(1.00) 		0.588
(1.00) 		0.38
(1.00) 		0.886
(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) 		0.212
(1.00) 		0.364
(1.00) 		0.489
(1.00) 		0.485
(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) 		0.051
(1.00) 		0.19
(1.00) 		0.0241
(1.00) 		0.00402
(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) 		0.00849
(1.00) 		0.000534
(0.384) 		0.00156
(1.00) 		0.00333
(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) 		0.115
(1.00) 		0.152
(1.00) 		0.359
(1.00) 		0.229
(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) 		0.501
(1.00) 		0.851
(1.00) 		0.0396
(1.00) 		0.281
(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) 		0.496
(1.00) 		0.586
(1.00) 		0.853
(1.00) 		0.44
(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) 		0.115
(1.00) 		0.103
(1.00) 		0.0194
(1.00) 		0.185
(1.00)
CCDC144NL 8 (1%) 764 0.000405
(0.293) 		0.325
(1.00) 		0.559
(1.00) 		0.241
(1.00) 		0.809
(1.00) 		0.216
(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) 		0.517
(1.00) 		0.047
(1.00) 		0.0226
(1.00) 		0.527
(1.00)
KRTAP4-7 7 (1%) 765 0.208
(1.00) 		0.599
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.474
(1.00) 		0.89
(1.00)
ZFP36L1 10 (1%) 762 0.856
(1.00) 		0.616
(1.00) 		0.000412
(0.297) 		0.396
(1.00) 		0.0258
(1.00) 		0.392
(1.00) 		0.465
(1.00) 		0.702
(1.00) 		0.841
(1.00) 		0.393
(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) 		0.47
(1.00) 		0.443
(1.00) 		0.0941
(1.00) 		0.41
(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) 		0.532
(1.00) 		0.758
(1.00) 		0.752
(1.00) 		1
(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) 		0.493
(1.00) 		0.3
(1.00) 		0.331
(1.00) 		0.436
(1.00)
VEZF1 8 (1%) 764 0.653
(1.00) 		0.537
(1.00) 		0.87
(1.00) 		0.894
(1.00) 		0.902
(1.00) 		0.605
(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) 		0.225
(1.00) 		0.509
(1.00) 		0.269
(1.00) 		0.0665
(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) 		0.0748
(1.00) 		0.147
(1.00) 		0.2
(1.00) 		0.0621
(1.00)
KRTAP9-9 6 (1%) 766 0.262
(1.00) 		0.177
(1.00) 		0.866
(1.00) 		0.758
(1.00) 		0.298
(1.00) 		0.256
(1.00)
BCL6B 8 (1%) 764 0.135
(1.00) 		0.695
(1.00) 		0.44
(1.00) 		1
(1.00) 		0.809
(1.00) 		0.899
(1.00)
CTU2 5 (1%) 767 0.242
(1.00) 		0.577
(1.00) 		0.842
(1.00) 		0.443
(1.00) 		0.847
(1.00) 		0.07
(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) 		0.189
(1.00) 		0.294
(1.00) 		0.061
(1.00) 		0.00347
(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) 		0.87
(1.00) 		0.688
(1.00) 		0.474
(1.00) 		0.43
(1.00)
AQP7 8 (1%) 764 0.626
(1.00) 		0.138
(1.00) 		0.351
(1.00) 		0.641
(1.00) 		0.884
(1.00) 		0.724
(1.00) 		0.474
(1.00) 		0.632
(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) 		1
(1.00) 		0.53
(1.00) 		0.787
(1.00) 		0.687
(1.00)
E2F4 4 (1%) 768 0.934
(1.00) 		1
(1.00) 		0.812
(1.00) 		0.817
(1.00) 		0.491
(1.00)
MUC20 10 (1%) 762 0.0748
(1.00) 		0.103
(1.00) 		0.0704
(1.00) 		0.227
(1.00) 		0.135
(1.00) 		0.0893
(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) 		0.117
(1.00) 		0.0594
(1.00) 		0.322
(1.00) 		0.0662
(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) 		0.166
(1.00) 		0.326
(1.00) 		0.363
(1.00) 		0.368
(1.00)
KRTAP4-5 4 (1%) 768 0.473
(1.00) 		0.224
(1.00) 		0.0488
(1.00) 		0.0722
(1.00) 		0.0797
(1.00) 		0.814
(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) 		0.115
(1.00) 		0.282
(1.00) 		0.725
(1.00) 		0.283
(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) 		1
(1.00) 		0.495
(1.00) 		0.772
(1.00) 		0.166
(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) 		1
(1.00) 		0.616
(1.00) 		0.671
(1.00) 		0.293
(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) 		0.68
(1.00) 		0.37
(1.00) 		0.785
(1.00) 		1
(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) 		0.477
(1.00) 		0.239
(1.00) 		0.0794
(1.00) 		0.482
(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) 		0.252
(1.00) 		0.272
(1.00) 		0.866
(1.00) 		0.433
(1.00)
ZNF69 5 (1%) 767 0.613
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.75
(1.00) 		0.842
(1.00) 		0.443
(1.00) 		0.714
(1.00) 		0.732
(1.00)
GNRH2 3 (0%) 769 0.26
(1.00) 		0.264
(1.00) 		0.616
(1.00) 		0.125
(1.00) 		1
(1.00)
HLA-DRB1 8 (1%) 764 0.524
(1.00) 		0.444
(1.00) 		0.223
(1.00) 		0.209
(1.00) 		0.592
(1.00) 		0.789
(1.00) 		0.192
(1.00) 		0.425
(1.00)
DENND4B 8 (1%) 764 0.188
(1.00) 		0.0515
(1.00) 		0.28
(1.00) 		0.456
(1.00) 		0.467
(1.00) 		0.239
(1.00)
CCDC66 9 (1%) 763 0.389
(1.00) 		0.332
(1.00) 		0.876
(1.00) 		0.673
(1.00) 		0.0553
(1.00) 		0.239
(1.00) 		0.091
(1.00) 		0.482
(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) 		0.391
(1.00) 		0.421
(1.00) 		0.103
(1.00) 		0.15
(1.00)
HNF1A 9 (1%) 763 0.0685
(1.00) 		0.603
(1.00) 		0.135
(1.00) 		0.27
(1.00) 		0.406
(1.00) 		0.0699
(1.00)
RAI1 7 (1%) 765 0.225
(1.00) 		0.912
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.68
(1.00) 		0.37
(1.00) 		0.474
(1.00) 		0.797
(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) 		0.105
(1.00) 		0.0314
(1.00) 		0.752
(1.00) 		1
(1.00)
PCMTD1 3 (0%) 769 0.495
(1.00) 		0.657
(1.00) 		0.415
(1.00) 		0.807
(1.00) 		0.598
(1.00) 		0.798
(1.00)
SLC25A5 3 (0%) 769 0.255
(1.00) 		0.693
(1.00) 		0.78
(1.00) 		0.354
(1.00)
STXBP2 9 (1%) 763 0.793
(1.00) 		0.692
(1.00) 		0.587
(1.00) 		0.557
(1.00) 		0.406
(1.00) 		0.917
(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) 		0.455
(1.00) 		0.221
(1.00) 		0.318
(1.00) 		0.336
(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) 		0.00327
(1.00) 		0.0264
(1.00) 		0.0229
(1.00) 		0.0781
(1.00)
POLR2J3 3 (0%) 769 0.701
(1.00) 		0.693
(1.00) 		0.264
(1.00) 		0.299
(1.00) 		0.442
(1.00) 		0.354
(1.00)
AXL 6 (1%) 766 0.255
(1.00) 		0.413
(1.00) 		0.236
(1.00) 		0.0799
(1.00) 		0.752
(1.00) 		0.384
(1.00)
MUC21 6 (1%) 766 0.377
(1.00) 		0.806
(1.00) 		0.147
(1.00) 		0.00908
(1.00) 		0.252
(1.00) 		0.495
(1.00) 		0.298
(1.00) 		1
(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) 		0.0538
(1.00) 		0.0156
(1.00) 		0.191
(1.00) 		0.247
(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) 		1
(1.00) 		1
(1.00) 		0.817
(1.00) 		1
(1.00)
HS6ST1 5 (1%) 767 0.013
(1.00) 		0.683
(1.00) 		0.572
(1.00) 		0.84
(1.00) 		0.294
(1.00) 		0.606
(1.00)
RALY 6 (1%) 766 0.647
(1.00) 		0.76
(1.00) 		1
(1.00) 		0.877
(1.00) 		0.18
(1.00) 		0.336
(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) 		0.493
(1.00) 		1
(1.00) 		0.717
(1.00) 		0.741
(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) 		0.751
(1.00) 		0.647
(1.00) 		0.336
(1.00) 		0.434
(1.00)
ODF1 5 (1%) 767 0.934
(1.00) 		0.683
(1.00) 		0.636
(1.00) 		0.55
(1.00) 		0.671
(1.00) 		0.491
(1.00)
PABPC3 8 (1%) 764 0.162
(1.00) 		0.806
(1.00) 		0.711
(1.00) 		0.824
(1.00) 		0.701
(1.00) 		0.81
(1.00) 		0.641
(1.00) 		0.899
(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) 		0.165
(1.00) 		0.308
(1.00) 		0.517
(1.00) 		0.743
(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) 		0.806
(1.00) 		0.828
(1.00) 		0.242
(1.00) 		0.53
(1.00)
ASPHD1 3 (0%) 769 0.701
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.807
(1.00) 		1
(1.00) 		0.626
(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) 		0.309
(1.00) 		0.789
(1.00) 		0.883
(1.00) 		1
(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) 		0.655
(1.00) 		0.601
(1.00) 		0.352
(1.00) 		0.249
(1.00)
ZIC3 4 (1%) 768 0.83
(1.00) 		0.52
(1.00) 		0.636
(1.00) 		0.55
(1.00) 		0.817
(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) 		0.00355
(1.00) 		0.00287
(1.00) 		0.00735
(1.00) 		0.0946
(1.00)
VSTM2B 3 (0%) 769 0.97
(1.00) 		1
(1.00) 		0.616
(1.00) 		1
(1.00) 		1
(1.00)
SELPLG 7 (1%) 765 0.266
(1.00) 		0.14
(1.00) 		0.0854
(1.00) 		0.035
(1.00) 		0.474
(1.00) 		0.304
(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) 		0.184
(1.00) 		0.362
(1.00) 		0.238
(1.00) 		0.0412
(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) 		0.884
(1.00) 		0.724
(1.00) 		0.521
(1.00) 		0.274
(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'

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S2.  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 S2.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.56e-09 (Fisher's exact test), Q value = 1.2e-06

Table S3.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 123 419
GATA3 MUTATED 2 15 63
GATA3 WILD-TYPE 211 108 356

Figure S3.  Get High-res Image Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.97e-10 (Fisher's exact test), Q value = 7.5e-07

Table S4.  Gene #6: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 183 386 186
GATA3 MUTATED 18 61 1
GATA3 WILD-TYPE 165 325 185

Figure S4.  Get High-res Image Gene #6: '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 = 3e-04

Table S5.  Gene #6: '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 S5.  Get High-res Image Gene #6: '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 = 0.00093

Table S6.  Gene #6: '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 S6.  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 S7.  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 S7.  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 S8.  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 S8.  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 = 9.4e-10

Table S9.  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 S9.  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 S10.  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 S10.  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 S11.  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 S11.  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 S12.  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 S12.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8.13e-10 (Fisher's exact test), Q value = 6.1e-07

Table S13.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 123 419
PIK3CA MUTATED 39 62 157
PIK3CA WILD-TYPE 174 61 262

Figure S13.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-12 (Fisher's exact test), Q value = 9.9e-10

Table S14.  Gene #12: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 183 386 186
PIK3CA MUTATED 92 138 28
PIK3CA WILD-TYPE 91 248 158

Figure S14.  Get High-res Image Gene #12: '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 = 6e-05

Table S15.  Gene #12: '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 S15.  Get High-res Image Gene #12: '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 = 1.1e-08

Table S16.  Gene #12: '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 S16.  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 S17.  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 S17.  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 S18.  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 S18.  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 S19.  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 S19.  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 S20.  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 S20.  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 S21.  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 S21.  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 S22.  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 S22.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.24e-58 (Fisher's exact test), Q value = 1.7e-55

Table S23.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 123 419
TP53 MUTATED 166 14 72
TP53 WILD-TYPE 47 109 347

Figure S23.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-49 (Fisher's exact test), Q value = 1.4e-46

Table S24.  Gene #14: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 183 386 186
TP53 MUTATED 26 80 146
TP53 WILD-TYPE 157 306 40

Figure S24.  Get High-res Image Gene #14: '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 = 5.7e-36

Table S25.  Gene #14: '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 S25.  Get High-res Image Gene #14: '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 = 1.8e-41

Table S26.  Gene #14: '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 S26.  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 = 0.00058

Table S27.  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 S27.  Get High-res Image Gene #17: 'RUNX1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S28.  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 S28.  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 S29.  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 S29.  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 S30.  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 S30.  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 S31.  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 S31.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.58e-07 (Fisher's exact test), Q value = 0.00012

Table S32.  Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 123 419
CDH1 MUTATED 3 22 30
CDH1 WILD-TYPE 210 101 389

Figure S32.  Get High-res Image Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.48e-07 (Fisher's exact test), Q value = 0.00011

Table S33.  Gene #22: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 183 386 186
CDH1 MUTATED 29 24 2
CDH1 WILD-TYPE 154 362 184

Figure S33.  Get High-res Image Gene #22: '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 = 0.0012

Table S34.  Gene #22: '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 S34.  Get High-res Image Gene #22: '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 = 4.4e-05

Table S35.  Gene #22: '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 S35.  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 S36.  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 S36.  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 S37.  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 S37.  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 S38.  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 S38.  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 S39.  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 S39.  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 S40.  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 S40.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.17

Table S41.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 123 419
MAP3K1 MUTATED 4 11 42
MAP3K1 WILD-TYPE 209 112 377

Figure S41.  Get High-res Image Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.52e-05 (Fisher's exact test), Q value = 0.04

Table S42.  Gene #23: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 183 386 186
MAP3K1 MUTATED 16 39 2
MAP3K1 WILD-TYPE 167 347 184

Figure S42.  Get High-res Image Gene #23: '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 = 0.014

Table S43.  Gene #23: '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 S43.  Get High-res Image Gene #23: '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 = 0.03

Table S44.  Gene #23: '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 S44.  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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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