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 89 genes and 12 molecular subtypes across 771 patients, 57 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'.

  • AKT1 mutation correlated to 'METHLYATION_CNMF' and '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',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • CBFB mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 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 89 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, 57 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
(7.81e-12) 		3.88e-10
(3.38e-07) 		1.68e-13
(1.47e-10) 		7.31e-11
(6.39e-08) 		1.64e-05
(0.014) 		1.06e-06
(0.000919) 		3.83e-29
(3.39e-26) 		6.84e-11
(5.99e-08) 		2.32e-10
(2.02e-07) 		3.16e-18
(2.78e-15) 		0.000184
(0.155) 		4.13e-07
(0.000358)
TP53 257 (33%) 514 7.08e-37
(6.28e-34) 		2.43e-33
(2.15e-30) 		8.75e-53
(7.8e-50) 		6.95e-21
(6.11e-18) 		1.87e-27
(1.66e-24) 		1.1e-23
(9.71e-21) 		3.31e-56
(2.95e-53) 		1.14e-48
(1.01e-45) 		2.65e-38
(2.35e-35) 		4e-43
(3.56e-40) 		2.88e-27
(2.54e-24) 		1.07e-27
(9.5e-25)
MAP3K1 57 (7%) 714 4.33e-06
(0.00371) 		4.38e-05
(0.0373) 		2.08e-05
(0.0177) 		0.0185
(1.00) 		0.000204
(0.171) 		1.99e-06
(0.00171) 		0.000118
(0.0999) 		1.99e-05
(0.017) 		4.24e-07
(0.000366) 		1.73e-05
(0.0148) 		2.48e-05
(0.0212) 		0.000284
(0.237)
CDH1 55 (7%) 716 1.67e-07
(0.000145) 		8.2e-05
(0.0695) 		2.2e-08
(1.91e-05) 		0.00103
(0.852) 		0.000255
(0.214) 		0.000579
(0.48) 		3.37e-06
(0.0029) 		5.15e-08
(4.47e-05) 		7.7e-11
(6.72e-08) 		7.42e-12
(6.5e-09) 		6.54e-05
(0.0555) 		8.56e-05
(0.0724)
GATA3 81 (11%) 690 0.000575
(0.477) 		0.000101
(0.0856) 		0.00404
(1.00) 		0.01
(1.00) 		0.00115
(0.949) 		0.000407
(0.34) 		4.65e-05
(0.0396) 		2.75e-09
(2.39e-06) 		3.5e-06
(0.00301) 		1.06e-06
(0.000913) 		1.18e-06
(0.00102) 		0.000102
(0.0857)
AKT1 19 (2%) 752 0.0634
(1.00) 		0.925
(1.00) 		0.00333
(1.00) 		0.000216
(0.181) 		0.162
(1.00) 		0.345
(1.00) 		0.00021
(0.176) 		0.348
(1.00) 		0.0633
(1.00) 		0.0167
(1.00) 		0.216
(1.00) 		0.125
(1.00)
TTN 122 (16%) 649 0.122
(1.00) 		0.0385
(1.00) 		0.00017
(0.143) 		0.0329
(1.00) 		6.23e-05
(0.0529) 		0.052
(1.00) 		0.000382
(0.319) 		0.00465
(1.00) 		0.0615
(1.00) 		0.00681
(1.00) 		0.0687
(1.00) 		0.0455
(1.00)
CBFB 16 (2%) 755 0.184
(1.00) 		0.648
(1.00) 		0.0245
(1.00) 		0.000863
(0.714) 		0.35
(1.00) 		0.569
(1.00) 		0.000563
(0.468) 		0.124
(1.00) 		0.0327
(1.00) 		6.12e-05
(0.052) 		0.0708
(1.00) 		0.034
(1.00)
PTEN 29 (4%) 742 0.226
(1.00) 		0.437
(1.00) 		0.162
(1.00) 		0.389
(1.00) 		0.882
(1.00) 		0.266
(1.00) 		0.177
(1.00) 		0.968
(1.00) 		0.674
(1.00) 		0.691
(1.00) 		0.102
(1.00) 		0.14
(1.00)
MLL3 61 (8%) 710 0.279
(1.00) 		0.922
(1.00) 		0.834
(1.00) 		0.704
(1.00) 		0.702
(1.00) 		0.968
(1.00) 		0.275
(1.00) 		0.922
(1.00) 		0.137
(1.00) 		0.221
(1.00) 		0.604
(1.00) 		0.926
(1.00)
NUDT11 8 (1%) 763 0.702
(1.00) 		0.179
(1.00) 		0.172
(1.00) 		0.897
(1.00) 		0.8
(1.00) 		0.275
(1.00) 		0.701
(1.00) 		0.272
(1.00)
GIGYF2 13 (2%) 758 0.454
(1.00) 		0.685
(1.00) 		0.546
(1.00) 		0.437
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.817
(1.00)
ZNF384 14 (2%) 757 0.487
(1.00) 		0.437
(1.00) 		0.51
(1.00) 		0.67
(1.00) 		0.82
(1.00) 		0.396
(1.00) 		0.401
(1.00) 		0.71
(1.00)
DCP1B 5 (1%) 766 0.365
(1.00) 		0.126
(1.00) 		0.772
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.527
(1.00) 		0.588
(1.00) 		0.795
(1.00)
NCOA3 29 (4%) 742 0.549
(1.00) 		1
(1.00) 		0.975
(1.00) 		0.505
(1.00) 		1
(1.00) 		1
(1.00) 		0.611
(1.00) 		0.746
(1.00) 		0.496
(1.00) 		0.23
(1.00) 		0.0622
(1.00) 		0.773
(1.00)
AOAH 19 (2%) 752 0.426
(1.00) 		0.736
(1.00) 		0.646
(1.00) 		0.175
(1.00) 		0.0861
(1.00) 		0.871
(1.00) 		0.15
(1.00) 		0.721
(1.00)
RBMX 13 (2%) 758 0.00151
(1.00) 		0.236
(1.00) 		0.563
(1.00) 		0.183
(1.00) 		0.532
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.5
(1.00)
RUNX1 25 (3%) 746 0.00552
(1.00) 		0.0442
(1.00) 		0.000931
(0.769) 		0.0563
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.0222
(1.00) 		0.58
(1.00) 		0.0666
(1.00) 		0.305
(1.00) 		0.0593
(1.00) 		0.934
(1.00)
PIK3R1 21 (3%) 750 0.172
(1.00) 		0.616
(1.00) 		0.492
(1.00) 		0.709
(1.00) 		0.538
(1.00) 		0.297
(1.00) 		0.12
(1.00) 		0.385
(1.00) 		0.387
(1.00) 		0.871
(1.00) 		0.672
(1.00) 		0.617
(1.00)
MEF2A 14 (2%) 757 0.577
(1.00) 		0.377
(1.00) 		0.553
(1.00) 		0.271
(1.00) 		0.0352
(1.00) 		0.0386
(1.00) 		0.0606
(1.00) 		0.21
(1.00)
NCOR2 29 (4%) 742 0.676
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.483
(1.00) 		0.839
(1.00) 		0.69
(1.00) 		0.838
(1.00) 		0.593
(1.00) 		0.767
(1.00) 		0.462
(1.00) 		0.887
(1.00) 		0.777
(1.00)
NR1H2 18 (2%) 753 0.326
(1.00) 		0.267
(1.00) 		0.94
(1.00) 		0.163
(1.00) 		0.064
(1.00) 		0.116
(1.00) 		0.401
(1.00) 		0.246
(1.00) 		0.215
(1.00) 		0.292
(1.00) 		0.78
(1.00) 		0.0385
(1.00)
MAP3K4 18 (2%) 753 0.108
(1.00) 		0.721
(1.00) 		0.768
(1.00) 		0.172
(1.00) 		0.0733
(1.00) 		0.69
(1.00) 		0.223
(1.00) 		0.408
(1.00) 		0.509
(1.00) 		0.413
(1.00) 		0.272
(1.00) 		0.155
(1.00)
TPRX1 7 (1%) 764 0.205
(1.00) 		0.504
(1.00) 		0.958
(1.00) 		1
(1.00) 		0.742
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ATN1 17 (2%) 754 0.0643
(1.00) 		0.0545
(1.00) 		0.0631
(1.00) 		0.896
(1.00) 		0.169
(1.00) 		0.291
(1.00) 		0.0776
(1.00) 		0.855
(1.00) 		0.802
(1.00) 		0.257
(1.00) 		0.321
(1.00) 		0.115
(1.00)
MAP2K4 32 (4%) 739 0.0292
(1.00) 		0.00313
(1.00) 		0.0507
(1.00) 		0.0105
(1.00) 		0.00238
(1.00) 		0.0344
(1.00) 		0.00554
(1.00) 		0.000469
(0.39) 		0.00431
(1.00) 		0.000997
(0.822) 		0.00164
(1.00) 		0.0264
(1.00)
CTCF 18 (2%) 753 0.0265
(1.00) 		0.32
(1.00) 		0.00924
(1.00) 		0.0206
(1.00) 		0.0682
(1.00) 		0.369
(1.00) 		0.0045
(1.00) 		0.428
(1.00) 		0.0852
(1.00) 		0.184
(1.00) 		0.831
(1.00) 		0.426
(1.00)
CCDC144NL 8 (1%) 763 0.000916
(0.757) 		0.408
(1.00) 		0.664
(1.00) 		0.191
(1.00) 		0.273
(1.00) 		0.478
(1.00) 		0.443
(1.00) 		0.396
(1.00)
AKD1 19 (2%) 752 0.926
(1.00) 		0.437
(1.00) 		0.3
(1.00) 		0.23
(1.00) 		0.467
(1.00) 		0.242
(1.00) 		0.672
(1.00) 		0.0412
(1.00) 		0.129
(1.00) 		0.358
(1.00) 		0.0773
(1.00) 		0.146
(1.00)
RB1 14 (2%) 757 0.523
(1.00) 		0.172
(1.00) 		0.0727
(1.00) 		0.138
(1.00) 		0.483
(1.00) 		0.762
(1.00) 		0.329
(1.00) 		0.297
(1.00) 		0.333
(1.00) 		0.0375
(1.00) 		0.179
(1.00) 		0.0842
(1.00)
FOXA1 15 (2%) 756 0.736
(1.00) 		0.116
(1.00) 		0.135
(1.00) 		0.0262
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.892
(1.00) 		0.157
(1.00) 		0.478
(1.00) 		0.533
(1.00) 		0.532
(1.00) 		0.329
(1.00)
PHLDA1 9 (1%) 762 0.321
(1.00) 		0.275
(1.00) 		0.325
(1.00) 		0.691
(1.00) 		1
(1.00) 		0.28
(1.00) 		0.68
(1.00) 		0.814
(1.00) 		0.32
(1.00) 		0.909
(1.00) 		0.389
(1.00) 		0.382
(1.00)
VEZF1 8 (1%) 763 0.409
(1.00) 		0.548
(1.00) 		0.192
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.852
(1.00)
ZFP36L1 10 (1%) 761 0.839
(1.00) 		0.686
(1.00) 		0.028
(1.00) 		0.138
(1.00) 		0.0258
(1.00) 		0.392
(1.00) 		0.84
(1.00) 		0.599
(1.00) 		0.834
(1.00) 		0.417
(1.00) 		0.643
(1.00) 		0.735
(1.00)
NCOR1 31 (4%) 740 0.488
(1.00) 		0.33
(1.00) 		0.354
(1.00) 		0.745
(1.00) 		0.723
(1.00) 		0.726
(1.00) 		0.528
(1.00) 		0.154
(1.00) 		0.446
(1.00) 		0.281
(1.00) 		0.528
(1.00) 		0.747
(1.00)
AQP7 9 (1%) 762 0.638
(1.00) 		0.0682
(1.00) 		0.752
(1.00) 		0.719
(1.00) 		0.721
(1.00) 		0.509
(1.00) 		0.316
(1.00) 		0.657
(1.00) 		0.735
(1.00) 		0.434
(1.00)
TBX3 18 (2%) 753 0.612
(1.00) 		0.345
(1.00) 		0.791
(1.00) 		0.18
(1.00) 		0.16
(1.00) 		0.551
(1.00) 		0.395
(1.00) 		0.408
(1.00) 		0.902
(1.00) 		0.91
(1.00) 		0.791
(1.00) 		1
(1.00)
DSPP 26 (3%) 745 0.945
(1.00) 		0.416
(1.00) 		0.561
(1.00) 		0.939
(1.00) 		0.0987
(1.00) 		0.387
(1.00) 		0.71
(1.00) 		0.0544
(1.00) 		0.0992
(1.00) 		0.735
(1.00) 		0.261
(1.00) 		0.675
(1.00)
RPGR 16 (2%) 755 0.297
(1.00) 		0.205
(1.00) 		0.999
(1.00) 		0.724
(1.00) 		0.616
(1.00) 		0.373
(1.00) 		0.285
(1.00) 		0.269
(1.00) 		0.626
(1.00) 		0.148
(1.00) 		0.649
(1.00) 		0.51
(1.00)
BCL6B 8 (1%) 763 0.478
(1.00) 		0.63
(1.00) 		0.249
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.818
(1.00) 		0.735
(1.00) 		0.549
(1.00)
TBL1XR1 9 (1%) 762 0.109
(1.00) 		0.295
(1.00) 		0.156
(1.00) 		0.455
(1.00) 		0.569
(1.00) 		0.0432
(1.00) 		0.152
(1.00) 		0.446
(1.00) 		0.168
(1.00) 		0.864
(1.00) 		0.277
(1.00)
CRIPAK 13 (2%) 758 0.398
(1.00) 		0.459
(1.00) 		0.453
(1.00) 		0.292
(1.00) 		0.657
(1.00) 		0.55
(1.00) 		0.14
(1.00) 		0.132
(1.00)
MYB 11 (1%) 760 0.786
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.355
(1.00) 		1
(1.00) 		0.69
(1.00) 		0.798
(1.00) 		0.574
(1.00) 		0.726
(1.00) 		0.732
(1.00) 		0.547
(1.00) 		1
(1.00)
GPS2 6 (1%) 765 0.00768
(1.00) 		0.0284
(1.00) 		0.128
(1.00) 		0.283
(1.00) 		1
(1.00) 		1
(1.00) 		0.49
(1.00) 		0.559
(1.00) 		0.198
(1.00) 		0.278
(1.00)
PABPC3 8 (1%) 763 0.163
(1.00) 		0.801
(1.00) 		0.741
(1.00) 		0.981
(1.00) 		0.68
(1.00) 		0.897
(1.00) 		0.713
(1.00) 		0.909
(1.00) 		1
(1.00) 		1
(1.00)
E2F4 4 (1%) 767 0.929
(1.00) 		0.868
(1.00) 		0.687
(1.00) 		0.816
(1.00) 		1
(1.00)
DNAH12 12 (2%) 759 0.967
(1.00) 		0.266
(1.00) 		0.849
(1.00) 		0.541
(1.00) 		0.689
(1.00) 		0.69
(1.00) 		0.0799
(1.00) 		0.753
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.791
(1.00) 		0.324
(1.00)
CDKN1B 7 (1%) 764 0.358
(1.00) 		0.11
(1.00) 		0.00271
(1.00) 		0.0312
(1.00) 		0.331
(1.00) 		0.392
(1.00) 		0.268
(1.00) 		0.367
(1.00) 		0.041
(1.00) 		0.254
(1.00) 		0.502
(1.00) 		0.559
(1.00)
HNF1A 9 (1%) 762 0.194
(1.00) 		0.66
(1.00) 		0.336
(1.00) 		0.107
(1.00) 		0.13
(1.00) 		0.168
(1.00) 		0.63
(1.00) 		0.156
(1.00)
CCDC66 14 (2%) 757 0.367
(1.00) 		0.446
(1.00) 		0.268
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.0514
(1.00) 		0.279
(1.00) 		0.516
(1.00) 		0.19
(1.00) 		0.371
(1.00) 		0.0992
(1.00)
CASP8 10 (1%) 761 0.355
(1.00) 		0.197
(1.00) 		0.608
(1.00) 		0.473
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.266
(1.00) 		0.55
(1.00) 		0.0593
(1.00) 		0.033
(1.00) 		0.189
(1.00) 		0.227
(1.00)
STXBP2 10 (1%) 761 0.923
(1.00) 		0.954
(1.00) 		0.807
(1.00) 		0.503
(1.00) 		0.475
(1.00) 		0.505
(1.00) 		0.814
(1.00) 		0.884
(1.00)
HIST1H3B 7 (1%) 764 0.383
(1.00) 		1
(1.00) 		0.553
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.215
(1.00) 		0.691
(1.00) 		1
(1.00) 		0.796
(1.00) 		0.429
(1.00) 		0.3
(1.00)
CTU2 5 (1%) 766 0.26
(1.00) 		0.534
(1.00) 		0.717
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.0754
(1.00) 		0.466
(1.00) 		0.0304
(1.00)
SHROOM4 12 (2%) 759 0.64
(1.00) 		0.183
(1.00) 		0.107
(1.00) 		0.435
(1.00) 		0.158
(1.00) 		0.314
(1.00) 		0.245
(1.00) 		0.419
(1.00) 		0.74
(1.00) 		0.701
(1.00) 		0.914
(1.00) 		0.486
(1.00)
HLA-A 4 (1%) 767 0.816
(1.00) 		0.543
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.0116
(1.00) 		0.277
(1.00) 		0.659
(1.00) 		0.214
(1.00)
SLC25A5 3 (0%) 768 0.243
(1.00) 		0.7
(1.00)
SELPLG 7 (1%) 764 0.278
(1.00) 		0.1
(1.00) 		0.079
(1.00) 		0.166
(1.00) 		0.31
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.229
(1.00)
KRTAP9-9 6 (1%) 765 0.262
(1.00) 		0.228
(1.00) 		0.138
(1.00) 		1
(1.00) 		0.869
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.0731
(1.00)
KRTAP4-5 4 (1%) 767 0.448
(1.00) 		0.282
(1.00) 		0.146
(1.00) 		0.128
(1.00) 		0.248
(1.00) 		0.691
(1.00) 		0.0949
(1.00) 		1
(1.00)
SF3B1 14 (2%) 757 0.629
(1.00) 		0.0949
(1.00) 		0.378
(1.00) 		0.224
(1.00) 		0.253
(1.00) 		0.00499
(1.00) 		0.254
(1.00) 		0.157
(1.00) 		0.119
(1.00) 		0.475
(1.00) 		0.631
(1.00) 		0.067
(1.00)
FGFR2 7 (1%) 764 0.602
(1.00) 		0.543
(1.00) 		0.848
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.249
(1.00) 		0.791
(1.00) 		0.603
(1.00) 		0.494
(1.00) 		0.39
(1.00) 		0.0688
(1.00)
MUC2 22 (3%) 749 0.83
(1.00) 		0.259
(1.00) 		0.328
(1.00) 		0.309
(1.00) 		0.778
(1.00) 		0.881
(1.00) 		0.5
(1.00) 		0.422
(1.00) 		0.598
(1.00) 		0.725
(1.00) 		0.752
(1.00) 		0.287
(1.00)
MED12 20 (3%) 751 0.603
(1.00) 		0.326
(1.00) 		0.352
(1.00) 		0.723
(1.00) 		0.455
(1.00) 		0.803
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.803
(1.00) 		0.294
(1.00) 		0.23
(1.00)
USP36 13 (2%) 758 0.668
(1.00) 		0.429
(1.00) 		0.653
(1.00) 		0.388
(1.00) 		0.778
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.922
(1.00) 		0.817
(1.00)
DENND4B 8 (1%) 763 0.209
(1.00) 		0.0346
(1.00) 		0.0773
(1.00) 		0.457
(1.00) 		0.107
(1.00) 		0.147
(1.00) 		0.165
(1.00) 		0.0853
(1.00)
RAI1 7 (1%) 764 0.375
(1.00) 		0.899
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.826
(1.00) 		0.326
(1.00) 		0.52
(1.00) 		0.163
(1.00) 		0.631
(1.00) 		0.83
(1.00)
ODF1 5 (1%) 766 0.929
(1.00) 		0.445
(1.00) 		0.689
(1.00) 		0.277
(1.00) 		0.816
(1.00) 		0.356
(1.00) 		0.643
(1.00) 		1
(1.00)
AXL 6 (1%) 765 0.377
(1.00) 		0.21
(1.00) 		0.826
(1.00) 		0.0816
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.278
(1.00)
RPL18 4 (1%) 767 0.501
(1.00) 		0.192
(1.00) 		0.121
(1.00) 		0.0944
(1.00) 		0.11
(1.00) 		0.0496
(1.00) 		0.274
(1.00) 		0.441
(1.00)
KRT38 4 (1%) 767 0.602
(1.00) 		0.812
(1.00) 		0.238
(1.00) 		0.755
(1.00) 		0.402
(1.00) 		0.633
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.0823
(1.00)
ASXL2 8 (1%) 763 0.36
(1.00) 		0.214
(1.00) 		0.781
(1.00) 		0.42
(1.00) 		0.812
(1.00) 		0.523
(1.00) 		0.603
(1.00) 		0.441
(1.00) 		0.75
(1.00) 		0.18
(1.00)
TICAM1 5 (1%) 766 0.755
(1.00) 		0.873
(1.00) 		0.949
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.527
(1.00) 		0.819
(1.00) 		1
(1.00)
RBM5 12 (2%) 759 0.758
(1.00) 		0.772
(1.00) 		0.75
(1.00) 		0.809
(1.00) 		0.308
(1.00) 		0.207
(1.00) 		0.0514
(1.00) 		0.523
(1.00)
ASPHD1 3 (0%) 768 0.686
(1.00) 		0.876
(1.00) 		0.564
(1.00) 		0.81
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PPEF1 8 (1%) 763 0.853
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.472
(1.00) 		1
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.592
(1.00) 		0.273
(1.00) 		0.384
(1.00) 		0.103
(1.00) 		0.12
(1.00)
MUC20 10 (1%) 761 0.0149
(1.00) 		0.178
(1.00) 		0.00043
(0.358) 		0.0546
(1.00) 		0.36
(1.00) 		0.125
(1.00) 		0.649
(1.00) 		0.14
(1.00)
TMEM184A 4 (1%) 767 0.543
(1.00) 		0.00609
(1.00) 		0.958
(1.00) 		0.687
(1.00) 		1
(1.00) 		0.278
(1.00) 		0.00677
(1.00) 		0.00125
(1.00)
FAM171B 8 (1%) 763 0.925
(1.00) 		0.291
(1.00) 		0.552
(1.00) 		0.0565
(1.00) 		0.2
(1.00) 		0.00175
(1.00) 		0.603
(1.00) 		0.0374
(1.00) 		0.173
(1.00) 		0.128
(1.00)
PRRX1 6 (1%) 765 0.577
(1.00) 		0.522
(1.00) 		0.398
(1.00) 		0.0939
(1.00) 		0.839
(1.00) 		0.392
(1.00) 		0.489
(1.00) 		0.496
(1.00) 		0.293
(1.00) 		0.435
(1.00) 		0.588
(1.00) 		0.68
(1.00)
ATP13A4 9 (1%) 762 0.602
(1.00) 		0.356
(1.00) 		0.134
(1.00) 		0.362
(1.00) 		0.865
(1.00) 		0.335
(1.00) 		0.907
(1.00) 		0.631
(1.00) 		0.443
(1.00) 		0.506
(1.00)
MUC21 6 (1%) 765 0.317
(1.00) 		0.429
(1.00) 		0.128
(1.00) 		0.277
(1.00) 		0.649
(1.00) 		0.496
(1.00) 		0.869
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.3
(1.00)
HLA-B 4 (1%) 767 0.612
(1.00) 		0.7
(1.00) 		0.381
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.356
(1.00) 		1
(1.00) 		1
(1.00)
RBM23 6 (1%) 765 0.667
(1.00) 		0.328
(1.00) 		0.789
(1.00) 		0.0358
(1.00) 		0.351
(1.00) 		0.0872
(1.00) 		0.643
(1.00) 		0.735
(1.00)
UBC 8 (1%) 763 0.336
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.309
(1.00) 		0.556
(1.00) 		0.827
(1.00) 		0.215
(1.00) 		1
(1.00) 		0.899
(1.00) 		0.275
(1.00)
SPRED3 4 (1%) 767 0.845
(1.00) 		0.751
(1.00) 		0.958
(1.00) 		0.469
(1.00) 		0.536
(1.00) 		0.278
(1.00) 		0.429
(1.00) 		0.3
(1.00)
KCNN3 6 (1%) 765 0.968
(1.00) 		1
(1.00) 		0.0707
(1.00) 		0.311
(1.00) 		0.102
(1.00) 		0.379
(1.00) 		0.351
(1.00) 		0.673
(1.00) 		0.274
(1.00) 		0.18
(1.00)
GNRH2 3 (0%) 768 0.247
(1.00) 		0.822
(1.00) 		1
(1.00) 		0.775
(1.00) 		0.801
(1.00)
MED15 7 (1%) 764 0.437
(1.00) 		0.124
(1.00) 		0.524
(1.00) 		0.288
(1.00) 		0.235
(1.00) 		0.254
(1.00) 		0.179
(1.00) 		0.229
(1.00)
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 8.9e-15 (Chi-square test), Q value = 7.8e-12

Table S1.  Gene #7: '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 #7: '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 = 3.4e-07

Table S2.  Gene #7: '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 #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 1.68e-13 (Chi-square test), Q value = 1.5e-10

Table S3.  Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 254 206 60 198 41
PIK3CA MUTATED 121 49 37 45 8
PIK3CA WILD-TYPE 133 157 23 153 33

Figure S3.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.31e-11 (Chi-square test), Q value = 6.4e-08

Table S4.  Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 115 74 113 27 61
PIK3CA MUTATED 5 65 30 29 10 19
PIK3CA WILD-TYPE 70 50 44 84 17 42

Figure S4.  Get High-res Image Gene #7: '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 = 0.014

Table S5.  Gene #7: '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 #7: '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 = 0.00092

Table S6.  Gene #7: '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 #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.83e-29 (Chi-square test), Q value = 3.4e-26

Table S7.  Gene #7: '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 131 96 172 131 193 23 14
PIK3CA MUTATED 6 47 101 55 30 10 9
PIK3CA WILD-TYPE 125 49 71 76 163 13 5

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

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.84e-11 (Fisher's exact test), Q value = 6e-08

Table S8.  Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 196 188 376
PIK3CA MUTATED 91 29 138
PIK3CA WILD-TYPE 105 159 238

Figure S8.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.32e-10 (Fisher's exact test), Q value = 2e-07

Table S9.  Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 396 205
PIK3CA MUTATED 73 151 35
PIK3CA WILD-TYPE 80 245 170

Figure S9.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.16e-18 (Fisher's exact test), Q value = 2.8e-15

Table S10.  Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 250 334
PIK3CA MUTATED 23 135 101
PIK3CA WILD-TYPE 147 115 233

Figure S10.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000184 (Fisher's exact test), Q value = 0.15

Table S11.  Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 78 126
PIK3CA MUTATED 96 32 25
PIK3CA WILD-TYPE 146 46 101

Figure S11.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.13e-07 (Fisher's exact test), Q value = 0.00036

Table S12.  Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 277 123
PIK3CA MUTATED 26 106 21
PIK3CA WILD-TYPE 20 171 102

Figure S12.  Get High-res Image Gene #7: 'PIK3CA MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000216 (Chi-square test), Q value = 0.18

Table S13.  Gene #15: 'AKT1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 115 74 113 27 61
AKT1 MUTATED 0 11 2 0 0 1
AKT1 WILD-TYPE 75 104 72 113 27 60

Figure S13.  Get High-res Image Gene #15: 'AKT1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'AKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Chi-square test), Q value = 0.18

Table S14.  Gene #15: '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 131 96 172 131 193 23 14
AKT1 MUTATED 0 3 13 2 1 0 0
AKT1 WILD-TYPE 131 93 159 129 192 23 14

Figure S14.  Get High-res Image Gene #15: '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 = 0.086

Table S15.  Gene #16: '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 #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.65e-05 (Chi-square test), Q value = 0.04

Table S16.  Gene #16: '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 131 96 172 131 193 23 14
GATA3 MUTATED 1 14 25 7 31 2 0
GATA3 WILD-TYPE 130 82 147 124 162 21 14

Figure S16.  Get High-res Image Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.75e-09 (Fisher's exact test), Q value = 2.4e-06

Table S17.  Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 196 188 376
GATA3 MUTATED 22 1 57
GATA3 WILD-TYPE 174 187 319

Figure S17.  Get High-res Image Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.003

Table S18.  Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 396 205
GATA3 MUTATED 17 57 5
GATA3 WILD-TYPE 136 339 200

Figure S18.  Get High-res Image Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00091

Table S19.  Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 250 334
GATA3 MUTATED 2 31 46
GATA3 WILD-TYPE 168 219 288

Figure S19.  Get High-res Image Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.001

Table S20.  Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 78 126
GATA3 MUTATED 45 9 2
GATA3 WILD-TYPE 197 69 124

Figure S20.  Get High-res Image Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.086

Table S21.  Gene #16: 'GATA3 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 277 123
GATA3 MUTATED 4 48 4
GATA3 WILD-TYPE 42 229 119

Figure S21.  Get High-res Image Gene #16: '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 = 6.3e-34

Table S22.  Gene #19: '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 #19: '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 = 2.1e-30

Table S23.  Gene #19: '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 #19: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.75e-53 (Chi-square test), Q value = 7.8e-50

Table S24.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 254 206 60 198 41
TP53 MUTATED 29 51 7 154 14
TP53 WILD-TYPE 225 155 53 44 27

Figure S24.  Get High-res Image Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.95e-21 (Chi-square test), Q value = 6.1e-18

Table S25.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 115 74 113 27 61
TP53 MUTATED 58 11 27 29 4 19
TP53 WILD-TYPE 17 104 47 84 23 42

Figure S25.  Get High-res Image Gene #19: '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 = 1.7e-24

Table S26.  Gene #19: '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 #19: '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 = 9.7e-21

Table S27.  Gene #19: '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 #19: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.31e-56 (Chi-square test), Q value = 3e-53

Table S28.  Gene #19: '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 131 96 172 131 193 23 14
TP53 MUTATED 103 12 11 82 33 5 8
TP53 WILD-TYPE 28 84 161 49 160 18 6

Figure S28.  Get High-res Image Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-48 (Fisher's exact test), Q value = 1e-45

Table S29.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 196 188 376
TP53 MUTATED 26 146 82
TP53 WILD-TYPE 170 42 294

Figure S29.  Get High-res Image Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.65e-38 (Fisher's exact test), Q value = 2.4e-35

Table S30.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 396 205
TP53 MUTATED 16 92 142
TP53 WILD-TYPE 137 304 63

Figure S30.  Get High-res Image Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-43 (Fisher's exact test), Q value = 3.6e-40

Table S31.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 250 334
TP53 MUTATED 128 28 94
TP53 WILD-TYPE 42 222 240

Figure S31.  Get High-res Image Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.88e-27 (Fisher's exact test), Q value = 2.5e-24

Table S32.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 78 126
TP53 MUTATED 45 9 90
TP53 WILD-TYPE 197 69 36

Figure S32.  Get High-res Image Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.07e-27 (Fisher's exact test), Q value = 9.5e-25

Table S33.  Gene #19: 'TP53 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 277 123
TP53 MUTATED 11 44 89
TP53 WILD-TYPE 35 233 34

Figure S33.  Get High-res Image Gene #19: '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 = 0.00014

Table S34.  Gene #21: '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 #21: '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 = 0.069

Table S35.  Gene #21: '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 #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.2e-08 (Chi-square test), Q value = 1.9e-05

Table S36.  Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 254 206 60 198 41
CDH1 MUTATED 27 9 14 2 3
CDH1 WILD-TYPE 227 197 46 196 38

Figure S36.  Get High-res Image Gene #21: '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 = 0.21

Table S37.  Gene #21: '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 #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.37e-06 (Chi-square test), Q value = 0.0029

Table S38.  Gene #21: '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 131 96 172 131 193 23 14
CDH1 MUTATED 0 17 18 7 8 4 1
CDH1 WILD-TYPE 131 79 154 124 185 19 13

Figure S38.  Get High-res Image Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.15e-08 (Fisher's exact test), Q value = 4.5e-05

Table S39.  Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 196 188 376
CDH1 MUTATED 31 2 22
CDH1 WILD-TYPE 165 186 354

Figure S39.  Get High-res Image Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.7e-11 (Fisher's exact test), Q value = 6.7e-08

Table S40.  Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 396 205
CDH1 MUTATED 29 23 1
CDH1 WILD-TYPE 124 373 204

Figure S40.  Get High-res Image Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.42e-12 (Fisher's exact test), Q value = 6.5e-09

Table S41.  Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 250 334
CDH1 MUTATED 0 40 13
CDH1 WILD-TYPE 170 210 321

Figure S41.  Get High-res Image Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.54e-05 (Fisher's exact test), Q value = 0.055

Table S42.  Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 78 126
CDH1 MUTATED 14 14 2
CDH1 WILD-TYPE 228 64 124

Figure S42.  Get High-res Image Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.56e-05 (Fisher's exact test), Q value = 0.072

Table S43.  Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 277 123
CDH1 MUTATED 6 24 0
CDH1 WILD-TYPE 40 253 123

Figure S43.  Get High-res Image Gene #21: 'CDH1 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.33e-06 (Chi-square test), Q value = 0.0037

Table S44.  Gene #24: '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 #24: '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 = 0.037

Table S45.  Gene #24: '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 #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.08e-05 (Chi-square test), Q value = 0.018

Table S46.  Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 254 206 60 198 41
MAP3K1 MUTATED 34 8 7 4 4
MAP3K1 WILD-TYPE 220 198 53 194 37

Figure S46.  Get High-res Image Gene #24: '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 = 0.17

Table S47.  Gene #24: '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 #24: '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 = 0.0017

Table S48.  Gene #24: '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 #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000118 (Chi-square test), Q value = 0.1

Table S49.  Gene #24: '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 131 96 172 131 193 23 14
MAP3K1 MUTATED 0 11 23 4 18 1 0
MAP3K1 WILD-TYPE 131 85 149 127 175 22 14

Figure S49.  Get High-res Image Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.017

Table S50.  Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 196 188 376
MAP3K1 MUTATED 14 2 41
MAP3K1 WILD-TYPE 182 186 335

Figure S50.  Get High-res Image Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 4.24e-07 (Fisher's exact test), Q value = 0.00037

Table S51.  Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 396 205
MAP3K1 MUTATED 19 37 1
MAP3K1 WILD-TYPE 134 359 204

Figure S51.  Get High-res Image Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.015

Table S52.  Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 250 334
MAP3K1 MUTATED 1 27 29
MAP3K1 WILD-TYPE 169 223 305

Figure S52.  Get High-res Image Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.021

Table S53.  Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 78 126
MAP3K1 MUTATED 23 10 0
MAP3K1 WILD-TYPE 219 68 126

Figure S53.  Get High-res Image Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000284 (Fisher's exact test), Q value = 0.24

Table S54.  Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 277 123
MAP3K1 MUTATED 7 25 1
MAP3K1 WILD-TYPE 39 252 122

Figure S54.  Get High-res Image Gene #24: 'MAP3K1 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.052

Table S55.  Gene #25: 'CBFB MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 250 334
CBFB MUTATED 0 13 2
CBFB WILD-TYPE 170 237 332

Figure S55.  Get High-res Image Gene #25: 'CBFB MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'TTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00017 (Chi-square test), Q value = 0.14

Table S56.  Gene #54: 'TTN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 254 206 60 198 41
TTN MUTATED 26 33 4 49 5
TTN WILD-TYPE 228 173 56 149 36

Figure S56.  Get High-res Image Gene #54: '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 = 0.053

Table S57.  Gene #54: '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 S57.  Get High-res Image Gene #54: '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 = 89

  • 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)
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