Correlation between copy number variations of arm-level result and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C15D8PWQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C15D8PWQ
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 80 arm-level results and 14 molecular subtypes across 569 patients, 53 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 2q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 13q gain cnv correlated to 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'METHLYATION_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 22q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
2p gain 0 (0%) 440 3.7e-09
(4.09e-06) 		1.75e-08
(1.93e-05) 		0.615
(1.00) 		1.31e-05
(0.0142) 		3.02e-11
(3.35e-08) 		8.24e-12
(9.17e-09) 		0.0363
(1.00) 		0.439
(1.00) 		8.7e-05
(0.0933) 		0.00457
(1.00) 		0.426
(1.00) 		0.209
(1.00) 		0.801
(1.00) 		0.25
(1.00)
12p gain 0 (0%) 361 3.25e-05
(0.035) 		1.13e-05
(0.0122) 		0.306
(1.00) 		4.46e-05
(0.0481) 		4.27e-13
(4.76e-10) 		1.24e-07
(0.000136) 		0.362
(1.00) 		0.825
(1.00) 		1.46e-05
(0.0158) 		0.00033
(0.351) 		0.183
(1.00) 		0.194
(1.00) 		0.0904
(1.00) 		0.0642
(1.00)
20q gain 0 (0%) 296 1.02e-05
(0.0111) 		9.09e-05
(0.0975) 		0.497
(1.00) 		1.6e-06
(0.00175) 		3.3e-20
(3.69e-17) 		2.09e-14
(2.33e-11) 		0.456
(1.00) 		0.175
(1.00) 		0.0033
(1.00) 		0.395
(1.00) 		0.351
(1.00) 		0.877
(1.00) 		0.733
(1.00) 		0.522
(1.00)
2q gain 0 (0%) 466 1.24e-06
(0.00135) 		5.25e-06
(0.00572) 		0.648
(1.00) 		0.00255
(1.00) 		1.43e-08
(1.58e-05) 		2.57e-06
(0.00282) 		0.0338
(1.00) 		0.329
(1.00) 		0.00183
(1.00) 		0.00447
(1.00) 		0.535
(1.00) 		0.481
(1.00) 		0.388
(1.00) 		0.414
(1.00)
12q gain 0 (0%) 447 0.000395
(0.42) 		8.66e-06
(0.00941) 		0.533
(1.00) 		0.00204
(1.00) 		1.22e-14
(1.36e-11) 		4e-06
(0.00437) 		0.00933
(1.00) 		0.663
(1.00) 		0.000731
(0.773) 		0.00235
(1.00) 		0.102
(1.00) 		0.119
(1.00) 		0.0442
(1.00) 		0.0762
(1.00)
20p gain 0 (0%) 335 0.00166
(1.00) 		0.00161
(1.00) 		0.207
(1.00) 		4.08e-06
(0.00446) 		3.87e-15
(4.32e-12) 		3.68e-10
(4.08e-07) 		0.322
(1.00) 		0.572
(1.00) 		0.00375
(1.00) 		0.144
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.686
(1.00)
5q loss 0 (0%) 397 0.000136
(0.145) 		0.00431
(1.00) 		0.655
(1.00) 		0.00138
(1.00) 		0.000173
(0.185) 		1.51e-07
(0.000166) 		0.00843
(1.00) 		0.0604
(1.00) 		0.000664
(0.702) 		0.284
(1.00) 		0.533
(1.00) 		0.595
(1.00) 		0.528
(1.00) 		0.637
(1.00)
22q loss 0 (0%) 182 4.52e-05
(0.0486) 		0.000128
(0.137) 		0.056
(1.00) 		0.0363
(1.00) 		0.000176
(0.188) 		0.00852
(1.00) 		0.0395
(1.00) 		0.101
(1.00) 		0.0806
(1.00) 		0.191
(1.00) 		0.00279
(1.00) 		0.39
(1.00) 		0.00511
(1.00) 		0.501
(1.00)
6q gain 0 (0%) 507 0.738
(1.00) 		0.109
(1.00) 		0.896
(1.00) 		0.0396
(1.00) 		1.01e-05
(0.011) 		7.2e-05
(0.0775) 		0.14
(1.00) 		0.857
(1.00) 		0.00314
(1.00) 		0.354
(1.00) 		0.93
(1.00) 		0.416
(1.00) 		1
(1.00) 		0.451
(1.00)
7p gain 0 (0%) 444 0.211
(1.00) 		0.298
(1.00) 		0.0456
(1.00) 		0.00843
(1.00) 		9.19e-08
(0.000101) 		4.53e-06
(0.00494) 		0.407
(1.00) 		0.158
(1.00) 		0.0836
(1.00) 		0.109
(1.00) 		0.944
(1.00) 		0.371
(1.00) 		0.417
(1.00) 		0.469
(1.00)
15q loss 0 (0%) 349 0.00173
(1.00) 		0.00281
(1.00) 		0.000914
(0.96) 		0.0035
(1.00) 		7.17e-11
(7.96e-08) 		7.7e-05
(0.0828) 		0.884
(1.00) 		0.885
(1.00) 		0.0245
(1.00) 		0.449
(1.00) 		0.00638
(1.00) 		0.375
(1.00) 		0.0926
(1.00) 		0.467
(1.00)
1q gain 0 (0%) 408 0.442
(1.00) 		0.309
(1.00) 		0.728
(1.00) 		0.563
(1.00) 		1.07e-05
(0.0116) 		0.0953
(1.00) 		0.365
(1.00) 		0.798
(1.00) 		0.64
(1.00) 		0.619
(1.00) 		0.206
(1.00) 		0.457
(1.00) 		0.876
(1.00) 		0.517
(1.00)
3q gain 0 (0%) 361 0.923
(1.00) 		0.708
(1.00) 		0.735
(1.00) 		0.284
(1.00) 		1.02e-09
(1.13e-06) 		0.00695
(1.00) 		0.447
(1.00) 		0.248
(1.00) 		0.352
(1.00) 		0.678
(1.00) 		0.387
(1.00) 		0.449
(1.00) 		0.114
(1.00) 		0.605
(1.00)
5p gain 0 (0%) 422 0.489
(1.00) 		0.992
(1.00) 		0.688
(1.00) 		0.485
(1.00) 		2.09e-07
(0.00023) 		0.428
(1.00) 		0.599
(1.00) 		0.196
(1.00) 		0.544
(1.00) 		0.905
(1.00) 		0.0767
(1.00) 		0.3
(1.00) 		0.137
(1.00) 		0.104
(1.00)
6p gain 0 (0%) 448 0.514
(1.00) 		0.2
(1.00) 		0.873
(1.00) 		0.0212
(1.00) 		1.19e-06
(0.0013) 		0.000736
(0.778) 		0.546
(1.00) 		0.744
(1.00) 		0.154
(1.00) 		0.619
(1.00) 		0.291
(1.00) 		0.147
(1.00) 		0.402
(1.00) 		0.169
(1.00)
7q gain 0 (0%) 416 0.103
(1.00) 		0.0763
(1.00) 		0.353
(1.00) 		0.357
(1.00) 		1.05e-05
(0.0114) 		0.00146
(1.00) 		0.266
(1.00) 		0.0944
(1.00) 		0.175
(1.00) 		0.173
(1.00) 		0.24
(1.00) 		0.492
(1.00) 		0.0486
(1.00) 		0.439
(1.00)
10p gain 0 (0%) 437 0.00844
(1.00) 		0.0435
(1.00) 		0.783
(1.00) 		0.00763
(1.00) 		2.95e-09
(3.27e-06) 		0.00154
(1.00) 		0.294
(1.00) 		0.454
(1.00) 		0.0126
(1.00) 		0.865
(1.00) 		0.507
(1.00) 		0.963
(1.00) 		0.121
(1.00) 		0.622
(1.00)
11q gain 0 (0%) 507 0.369
(1.00) 		0.634
(1.00) 		0.94
(1.00) 		0.0125
(1.00) 		7.92e-05
(0.0851) 		0.000751
(0.793) 		0.369
(1.00) 		0.451
(1.00) 		0.577
(1.00) 		0.221
(1.00) 		0.281
(1.00) 		0.436
(1.00) 		0.488
(1.00) 		0.403
(1.00)
13q gain 0 (0%) 528 0.0403
(1.00) 		0.0749
(1.00) 		0.889
(1.00) 		0.00174
(1.00) 		0.00588
(1.00) 		9.27e-05
(0.0993) 		0.829
(1.00) 		0.336
(1.00) 		0.451
(1.00) 		0.949
(1.00) 		0.289
(1.00) 		0.618
(1.00) 		0.943
(1.00) 		0.62
(1.00)
19p gain 0 (0%) 470 0.0163
(1.00) 		0.0253
(1.00) 		0.664
(1.00) 		0.192
(1.00) 		1.95e-08
(2.15e-05) 		0.000844
(0.887) 		0.0151
(1.00) 		0.235
(1.00) 		0.741
(1.00) 		0.822
(1.00) 		0.677
(1.00) 		0.311
(1.00) 		0.77
(1.00) 		0.0763
(1.00)
19q gain 0 (0%) 477 0.0125
(1.00) 		0.0455
(1.00) 		0.624
(1.00) 		0.16
(1.00) 		6.85e-07
(0.000752) 		0.00249
(1.00) 		0.0242
(1.00) 		0.266
(1.00) 		0.558
(1.00) 		0.525
(1.00) 		0.328
(1.00) 		0.217
(1.00) 		0.27
(1.00) 		0.0397
(1.00)
21q gain 0 (0%) 499 0.504
(1.00) 		0.198
(1.00) 		0.986
(1.00) 		0.906
(1.00) 		7.07e-06
(0.00769) 		0.000544
(0.577) 		0.29
(1.00) 		0.259
(1.00) 		0.371
(1.00) 		0.171
(1.00) 		0.231
(1.00) 		0.683
(1.00) 		0.176
(1.00) 		0.332
(1.00)
9q loss 0 (0%) 329 0.00257
(1.00) 		0.00162
(1.00) 		0.142
(1.00) 		0.00651
(1.00) 		1.51e-11
(1.68e-08) 		0.000827
(0.871) 		0.653
(1.00) 		0.881
(1.00) 		0.00276
(1.00) 		0.212
(1.00) 		0.109
(1.00) 		0.0309
(1.00) 		0.204
(1.00) 		0.0283
(1.00)
13q loss 0 (0%) 307 0.0689
(1.00) 		0.0409
(1.00) 		0.907
(1.00) 		0.0687
(1.00) 		0.000857
(0.9) 		4.36e-06
(0.00475) 		0.00299
(1.00) 		0.00436
(1.00) 		0.297
(1.00) 		0.985
(1.00) 		0.418
(1.00) 		0.896
(1.00) 		0.0881
(1.00) 		0.873
(1.00)
14q loss 0 (0%) 405 0.133
(1.00) 		0.0223
(1.00) 		0.875
(1.00) 		0.917
(1.00) 		0.000118
(0.126) 		0.0381
(1.00) 		0.966
(1.00) 		0.479
(1.00) 		0.0454
(1.00) 		0.557
(1.00) 		0.43
(1.00) 		0.356
(1.00) 		0.163
(1.00) 		0.422
(1.00)
1p gain 0 (0%) 465 0.0767
(1.00) 		0.0965
(1.00) 		0.0931
(1.00) 		0.436
(1.00) 		0.336
(1.00) 		0.839
(1.00) 		0.04
(1.00) 		0.333
(1.00) 		0.694
(1.00) 		0.344
(1.00) 		0.125
(1.00) 		0.714
(1.00) 		0.306
(1.00) 		0.457
(1.00)
3p gain 0 (0%) 460 0.39
(1.00) 		0.645
(1.00) 		0.102
(1.00) 		0.619
(1.00) 		0.00102
(1.00) 		0.902
(1.00) 		0.201
(1.00) 		0.464
(1.00) 		0.633
(1.00) 		0.889
(1.00) 		0.797
(1.00) 		0.618
(1.00) 		0.767
(1.00) 		0.678
(1.00)
4p gain 0 (0%) 538 0.887
(1.00) 		0.836
(1.00) 		0.0047
(1.00) 		0.688
(1.00) 		0.0876
(1.00) 		0.0559
(1.00) 		0.0149
(1.00) 		0.458
(1.00) 		0.953
(1.00) 		0.573
(1.00) 		0.272
(1.00) 		0.286
(1.00) 		0.389
(1.00) 		0.047
(1.00)
4q gain 0 (0%) 553 0.899
(1.00) 		0.652
(1.00) 		0.853
(1.00) 		0.938
(1.00) 		0.332
(1.00) 		0.0231
(1.00) 		0.0208
(1.00) 		0.257
(1.00) 		0.913
(1.00) 		0.585
(1.00) 		0.00385
(1.00) 		0.0479
(1.00) 		0.00262
(1.00) 		0.0163
(1.00)
5q gain 0 (0%) 535 0.0336
(1.00) 		0.103
(1.00) 		0.499
(1.00) 		0.356
(1.00) 		0.597
(1.00) 		0.396
(1.00) 		0.157
(1.00) 		0.58
(1.00) 		0.316
(1.00) 		0.658
(1.00) 		0.039
(1.00) 		0.422
(1.00) 		0.244
(1.00) 		0.102
(1.00)
8p gain 0 (0%) 483 0.303
(1.00) 		0.0142
(1.00) 		0.977
(1.00) 		0.0131
(1.00) 		0.264
(1.00) 		0.924
(1.00) 		0.83
(1.00) 		0.232
(1.00) 		0.547
(1.00) 		0.232
(1.00) 		0.579
(1.00) 		0.345
(1.00) 		0.971
(1.00) 		0.526
(1.00)
8q gain 0 (0%) 365 0.169
(1.00) 		0.0706
(1.00) 		0.128
(1.00) 		0.0883
(1.00) 		0.0087
(1.00) 		1
(1.00) 		0.786
(1.00) 		0.125
(1.00) 		0.00385
(1.00) 		0.38
(1.00) 		0.812
(1.00) 		0.795
(1.00) 		0.632
(1.00) 		0.773
(1.00)
9p gain 0 (0%) 508 0.0445
(1.00) 		0.594
(1.00) 		0.28
(1.00) 		0.319
(1.00) 		0.00446
(1.00) 		0.0235
(1.00) 		0.173
(1.00) 		0.596
(1.00) 		0.896
(1.00) 		0.587
(1.00) 		0.157
(1.00) 		0.748
(1.00) 		0.855
(1.00) 		0.696
(1.00)
9q gain 0 (0%) 542 0.452
(1.00) 		0.485
(1.00) 		0.104
(1.00) 		0.619
(1.00) 		0.0726
(1.00) 		0.224
(1.00) 		0.611
(1.00) 		0.208
(1.00) 		0.813
(1.00) 		0.0484
(1.00) 		0.829
(1.00) 		0.738
(1.00) 		0.569
(1.00) 		0.738
(1.00)
10q gain 0 (0%) 501 0.00947
(1.00) 		0.0255
(1.00) 		0.959
(1.00) 		0.0166
(1.00) 		0.0135
(1.00) 		0.0293
(1.00) 		0.283
(1.00) 		0.511
(1.00) 		0.08
(1.00) 		0.312
(1.00) 		0.38
(1.00) 		0.57
(1.00) 		0.706
(1.00) 		0.702
(1.00)
11p gain 0 (0%) 529 0.268
(1.00) 		0.239
(1.00) 		0.223
(1.00) 		0.34
(1.00) 		0.043
(1.00) 		0.0168
(1.00) 		0.0225
(1.00) 		0.00441
(1.00) 		0.0427
(1.00) 		0.284
(1.00) 		0.121
(1.00) 		0.183
(1.00) 		0.267
(1.00) 		0.163
(1.00)
14q gain 0 (0%) 535 0.00978
(1.00) 		0.0368
(1.00) 		0.348
(1.00) 		0.0546
(1.00) 		0.975
(1.00) 		0.2
(1.00) 		0.0644
(1.00) 		0.00978
(1.00) 		0.273
(1.00) 		0.0362
(1.00) 		0.46
(1.00) 		0.642
(1.00) 		0.554
(1.00) 		0.643
(1.00)
15q gain 0 (0%) 544 0.425
(1.00) 		0.412
(1.00) 		0.337
(1.00) 		0.459
(1.00) 		0.27
(1.00) 		0.662
(1.00) 		0.166
(1.00) 		0.824
(1.00) 		1
(1.00) 		1
(1.00) 		0.638
(1.00) 		0.54
(1.00) 		0.855
(1.00) 		0.542
(1.00)
16p gain 0 (0%) 538 0.0329
(1.00) 		0.0311
(1.00) 		0.919
(1.00) 		0.355
(1.00) 		0.149
(1.00) 		0.324
(1.00) 		0.675
(1.00) 		0.101
(1.00) 		1
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.513
(1.00) 		0.417
(1.00) 		0.61
(1.00)
16q gain 0 (0%) 553 0.0169
(1.00) 		0.253
(1.00) 		0.219
(1.00) 		0.491
(1.00) 		0.597
(1.00) 		0.0392
(1.00) 		0.512
(1.00) 		0.124
(1.00) 		0.119
(1.00) 		0.269
(1.00) 		0.128
(1.00) 		0.271
(1.00)
17p gain 0 (0%) 558 0.397
(1.00) 		0.361
(1.00) 		0.509
(1.00) 		0.27
(1.00) 		0.064
(1.00) 		0.435
(1.00) 		0.414
(1.00) 		0.795
(1.00) 		0.352
(1.00) 		0.632
(1.00) 		0.58
(1.00) 		0.365
(1.00) 		0.408
(1.00) 		0.368
(1.00)
17q gain 0 (0%) 546 0.788
(1.00) 		0.697
(1.00) 		0.271
(1.00) 		0.245
(1.00) 		0.0705
(1.00) 		0.339
(1.00) 		0.509
(1.00) 		0.922
(1.00) 		0.591
(1.00) 		0.683
(1.00) 		0.695
(1.00) 		0.466
(1.00) 		0.826
(1.00) 		0.47
(1.00)
18p gain 0 (0%) 495 0.0085
(1.00) 		0.00758
(1.00) 		0.852
(1.00) 		0.157
(1.00) 		0.00147
(1.00) 		0.000349
(0.371) 		0.00283
(1.00) 		0.0731
(1.00) 		0.527
(1.00) 		0.611
(1.00) 		0.271
(1.00) 		0.589
(1.00) 		0.0594
(1.00) 		0.675
(1.00)
18q gain 0 (0%) 528 0.294
(1.00) 		0.398
(1.00) 		0.531
(1.00) 		0.565
(1.00) 		0.042
(1.00) 		0.064
(1.00) 		0.206
(1.00) 		0.454
(1.00) 		0.614
(1.00) 		0.44
(1.00) 		0.136
(1.00) 		0.792
(1.00) 		0.0395
(1.00) 		0.791
(1.00)
22q gain 0 (0%) 560 0.32
(1.00) 		0.0983
(1.00) 		0.692
(1.00) 		0.641
(1.00) 		0.205
(1.00) 		0.84
(1.00) 		0.604
(1.00) 		0.701
(1.00) 		0.833
(1.00) 		1
(1.00) 		0.0433
(1.00) 		0.474
(1.00) 		0.00527
(1.00) 		0.324
(1.00)
Xq gain 0 (0%) 535 0.209
(1.00) 		0.298
(1.00) 		0.949
(1.00) 		0.603
(1.00) 		0.0139
(1.00) 		0.0892
(1.00) 		0.0904
(1.00) 		0.328
(1.00) 		0.393
(1.00) 		0.5
(1.00) 		0.203
(1.00) 		0.767
(1.00) 		0.0216
(1.00) 		0.769
(1.00)
1p loss 0 (0%) 534 0.00438
(1.00) 		0.0215
(1.00) 		0.284
(1.00) 		0.49
(1.00) 		0.779
(1.00) 		0.178
(1.00) 		0.503
(1.00) 		0.514
(1.00) 		0.736
(1.00) 		0.361
(1.00) 		1
(1.00) 		1
(1.00) 		0.245
(1.00) 		1
(1.00)
1q loss 0 (0%) 547 0.0176
(1.00) 		0.0154
(1.00) 		0.00412
(1.00) 		0.347
(1.00) 		0.337
(1.00) 		0.46
(1.00) 		0.648
(1.00) 		0.189
(1.00) 		0.796
(1.00) 		0.0964
(1.00) 		0.329
(1.00) 		0.843
(1.00) 		0.36
(1.00) 		1
(1.00)
2p loss 0 (0%) 543 0.787
(1.00) 		0.787
(1.00) 		0.905
(1.00) 		0.181
(1.00) 		0.572
(1.00) 		0.698
(1.00) 		0.332
(1.00) 		0.585
(1.00) 		0.178
(1.00) 		0.29
(1.00) 		0.833
(1.00) 		0.229
(1.00) 		0.606
(1.00) 		0.871
(1.00)
2q loss 0 (0%) 539 0.836
(1.00) 		0.501
(1.00) 		0.816
(1.00) 		0.0858
(1.00) 		0.53
(1.00) 		0.276
(1.00) 		0.287
(1.00) 		0.668
(1.00) 		0.546
(1.00) 		0.243
(1.00) 		0.676
(1.00) 		0.109
(1.00) 		0.518
(1.00) 		0.491
(1.00)
3p loss 0 (0%) 508 0.0487
(1.00) 		0.0959
(1.00) 		0.925
(1.00) 		0.0476
(1.00) 		0.00469
(1.00) 		0.184
(1.00) 		0.87
(1.00) 		0.25
(1.00) 		0.0181
(1.00) 		0.458
(1.00) 		0.194
(1.00) 		0.534
(1.00) 		0.761
(1.00) 		0.453
(1.00)
3q loss 0 (0%) 546 0.179
(1.00) 		0.196
(1.00) 		0.964
(1.00) 		0.182
(1.00) 		0.198
(1.00) 		0.396
(1.00) 		0.592
(1.00) 		0.606
(1.00) 		0.0803
(1.00) 		0.276
(1.00) 		0.489
(1.00) 		0.684
(1.00) 		0.948
(1.00) 		0.683
(1.00)
4p loss 0 (0%) 307 0.159
(1.00) 		0.416
(1.00) 		0.516
(1.00) 		0.0236
(1.00) 		0.0312
(1.00) 		0.977
(1.00) 		0.155
(1.00) 		0.177
(1.00) 		0.152
(1.00) 		0.292
(1.00) 		0.0344
(1.00) 		0.0104
(1.00) 		0.0528
(1.00) 		0.0168
(1.00)
4q loss 0 (0%) 267 0.0829
(1.00) 		0.265
(1.00) 		0.269
(1.00) 		0.0147
(1.00) 		0.0101
(1.00) 		0.767
(1.00) 		0.286
(1.00) 		0.0925
(1.00) 		0.47
(1.00) 		0.0357
(1.00) 		0.0471
(1.00) 		0.000253
(0.269) 		0.0413
(1.00) 		0.00082
(0.864)
5p loss 0 (0%) 484 0.405
(1.00) 		0.216
(1.00) 		0.188
(1.00) 		0.162
(1.00) 		0.0129
(1.00) 		0.0144
(1.00) 		0.204
(1.00) 		0.156
(1.00) 		0.000407
(0.431) 		0.562
(1.00) 		0.919
(1.00) 		0.699
(1.00) 		0.942
(1.00) 		0.7
(1.00)
6p loss 0 (0%) 443 0.792
(1.00) 		0.442
(1.00) 		0.716
(1.00) 		0.794
(1.00) 		0.19
(1.00) 		0.125
(1.00) 		0.212
(1.00) 		0.407
(1.00) 		0.48
(1.00) 		0.797
(1.00) 		0.18
(1.00) 		1
(1.00) 		0.0841
(1.00) 		1
(1.00)
6q loss 0 (0%) 371 0.98
(1.00) 		0.542
(1.00) 		0.829
(1.00) 		0.844
(1.00) 		0.079
(1.00) 		0.0322
(1.00) 		0.0986
(1.00) 		0.653
(1.00) 		0.124
(1.00) 		0.194
(1.00) 		0.211
(1.00) 		0.812
(1.00) 		0.264
(1.00) 		0.891
(1.00)
7p loss 0 (0%) 478 0.903
(1.00) 		0.299
(1.00) 		0.184
(1.00) 		0.304
(1.00) 		0.0746
(1.00) 		0.143
(1.00) 		0.382
(1.00) 		0.767
(1.00) 		0.944
(1.00) 		0.0347
(1.00) 		0.0259
(1.00) 		0.718
(1.00) 		0.189
(1.00) 		0.612
(1.00)
7q loss 0 (0%) 521 0.839
(1.00) 		0.677
(1.00) 		0.431
(1.00) 		0.652
(1.00) 		0.267
(1.00) 		0.0238
(1.00) 		0.349
(1.00) 		0.756
(1.00) 		0.579
(1.00) 		0.22
(1.00) 		0.0537
(1.00) 		0.837
(1.00) 		0.0557
(1.00) 		1
(1.00)
8p loss 0 (0%) 334 0.731
(1.00) 		0.79
(1.00) 		0.454
(1.00) 		0.86
(1.00) 		0.00151
(1.00) 		0.0426
(1.00) 		0.199
(1.00) 		0.351
(1.00) 		0.34
(1.00) 		0.914
(1.00) 		0.471
(1.00) 		0.191
(1.00) 		0.834
(1.00) 		0.215
(1.00)
8q loss 0 (0%) 506 0.0707
(1.00) 		0.365
(1.00) 		0.201
(1.00) 		0.369
(1.00) 		0.00207
(1.00) 		0.0729
(1.00) 		0.0766
(1.00) 		0.485
(1.00) 		0.0393
(1.00) 		0.044
(1.00) 		0.789
(1.00) 		0.38
(1.00) 		0.959
(1.00) 		0.38
(1.00)
9p loss 0 (0%) 357 0.00217
(1.00) 		0.00753
(1.00) 		0.737
(1.00) 		0.0603
(1.00) 		0.0297
(1.00) 		0.000554
(0.587) 		0.674
(1.00) 		0.976
(1.00) 		0.567
(1.00) 		0.134
(1.00) 		0.0402
(1.00) 		0.331
(1.00) 		0.236
(1.00) 		0.287
(1.00)
10p loss 0 (0%) 502 0.499
(1.00) 		0.86
(1.00) 		0.328
(1.00) 		0.806
(1.00) 		0.895
(1.00) 		0.532
(1.00) 		0.193
(1.00) 		0.205
(1.00) 		0.964
(1.00) 		0.659
(1.00) 		0.109
(1.00) 		0.613
(1.00) 		0.539
(1.00) 		0.451
(1.00)
10q loss 0 (0%) 479 0.764
(1.00) 		0.218
(1.00) 		0.0994
(1.00) 		0.799
(1.00) 		0.118
(1.00) 		0.376
(1.00) 		0.259
(1.00) 		0.227
(1.00) 		0.763
(1.00) 		0.26
(1.00) 		0.298
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.826
(1.00)
11p loss 0 (0%) 423 0.0105
(1.00) 		0.00253
(1.00) 		0.0964
(1.00) 		0.262
(1.00) 		0.0816
(1.00) 		0.00978
(1.00) 		0.558
(1.00) 		0.133
(1.00) 		0.0213
(1.00) 		0.687
(1.00) 		0.787
(1.00) 		0.809
(1.00) 		0.101
(1.00) 		0.321
(1.00)
11q loss 0 (0%) 461 0.14
(1.00) 		0.0567
(1.00) 		0.0135
(1.00) 		0.258
(1.00) 		0.187
(1.00) 		0.0624
(1.00) 		0.822
(1.00) 		0.0791
(1.00) 		0.0733
(1.00) 		0.797
(1.00) 		0.295
(1.00) 		0.137
(1.00) 		0.0653
(1.00) 		0.169
(1.00)
12p loss 0 (0%) 518 0.383
(1.00) 		0.193
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.00812
(1.00) 		0.416
(1.00) 		0.971
(1.00) 		0.0597
(1.00) 		0.296
(1.00) 		0.44
(1.00) 		0.591
(1.00) 		0.277
(1.00) 		0.453
(1.00) 		0.228
(1.00)
12q loss 0 (0%) 493 0.153
(1.00) 		0.0109
(1.00) 		0.389
(1.00) 		0.277
(1.00) 		0.00274
(1.00) 		0.148
(1.00) 		0.839
(1.00) 		0.266
(1.00) 		0.149
(1.00) 		0.0162
(1.00) 		0.421
(1.00) 		0.335
(1.00) 		0.57
(1.00) 		0.0672
(1.00)
16p loss 0 (0%) 298 0.889
(1.00) 		0.846
(1.00) 		0.196
(1.00) 		0.677
(1.00) 		0.0275
(1.00) 		0.0603
(1.00) 		0.964
(1.00) 		0.931
(1.00) 		0.353
(1.00) 		0.611
(1.00) 		0.271
(1.00) 		0.561
(1.00) 		0.656
(1.00) 		0.562
(1.00)
16q loss 0 (0%) 209 0.859
(1.00) 		0.798
(1.00) 		0.041
(1.00) 		0.362
(1.00) 		0.0263
(1.00) 		0.0574
(1.00) 		0.733
(1.00) 		0.973
(1.00) 		0.492
(1.00) 		0.812
(1.00) 		0.269
(1.00) 		0.0826
(1.00) 		0.0919
(1.00) 		0.0742
(1.00)
17p loss 0 (0%) 140 0.199
(1.00) 		0.00704
(1.00) 		0.891
(1.00) 		0.545
(1.00) 		0.243
(1.00) 		0.0315
(1.00) 		0.525
(1.00) 		0.178
(1.00) 		0.295
(1.00) 		0.119
(1.00) 		0.339
(1.00) 		0.418
(1.00) 		0.384
(1.00) 		0.624
(1.00)
17q loss 0 (0%) 237 0.0351
(1.00) 		0.00175
(1.00) 		0.0246
(1.00) 		0.663
(1.00) 		0.597
(1.00) 		0.156
(1.00) 		0.188
(1.00) 		0.127
(1.00) 		0.128
(1.00) 		0.109
(1.00) 		0.00734
(1.00) 		0.288
(1.00) 		0.00489
(1.00) 		0.374
(1.00)
18p loss 0 (0%) 382 0.684
(1.00) 		0.894
(1.00) 		0.33
(1.00) 		0.413
(1.00) 		0.216
(1.00) 		0.0109
(1.00) 		0.941
(1.00) 		0.24
(1.00) 		0.018
(1.00) 		0.206
(1.00) 		0.881
(1.00) 		0.917
(1.00) 		0.705
(1.00) 		0.388
(1.00)
18q loss 0 (0%) 333 0.135
(1.00) 		0.211
(1.00) 		0.7
(1.00) 		0.608
(1.00) 		0.845
(1.00) 		0.402
(1.00) 		0.963
(1.00) 		0.14
(1.00) 		0.00285
(1.00) 		0.103
(1.00) 		0.669
(1.00) 		0.467
(1.00) 		0.468
(1.00) 		0.325
(1.00)
19p loss 0 (0%) 424 0.566
(1.00) 		0.125
(1.00) 		0.152
(1.00) 		0.225
(1.00) 		0.179
(1.00) 		0.0916
(1.00) 		0.027
(1.00) 		0.108
(1.00) 		0.466
(1.00) 		0.71
(1.00) 		0.907
(1.00) 		0.778
(1.00) 		0.617
(1.00) 		0.965
(1.00)
19q loss 0 (0%) 424 0.131
(1.00) 		0.0333
(1.00) 		0.315
(1.00) 		0.296
(1.00) 		0.278
(1.00) 		0.619
(1.00) 		0.0706
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.201
(1.00) 		0.313
(1.00) 		0.279
(1.00) 		0.774
(1.00)
20p loss 0 (0%) 531 0.309
(1.00) 		0.335
(1.00) 		0.625
(1.00) 		0.361
(1.00) 		0.172
(1.00) 		0.163
(1.00) 		0.657
(1.00) 		0.447
(1.00) 		0.0208
(1.00) 		0.0759
(1.00) 		0.0116
(1.00) 		0.891
(1.00) 		0.0551
(1.00) 		0.688
(1.00)
20q loss 0 (0%) 547 0.45
(1.00) 		0.959
(1.00) 		0.276
(1.00) 		0.737
(1.00) 		0.518
(1.00) 		0.708
(1.00) 		0.352
(1.00) 		0.269
(1.00) 		0.245
(1.00) 		0.625
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.566
(1.00)
21q loss 0 (0%) 418 0.347
(1.00) 		0.145
(1.00) 		0.31
(1.00) 		0.0634
(1.00) 		0.793
(1.00) 		0.0376
(1.00) 		0.286
(1.00) 		0.387
(1.00) 		0.46
(1.00) 		0.563
(1.00) 		0.464
(1.00) 		0.966
(1.00) 		0.191
(1.00) 		1
(1.00)
Xq loss 0 (0%) 468 0.121
(1.00) 		0.256
(1.00) 		0.0363
(1.00) 		0.15
(1.00) 		0.0851
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.295
(1.00) 		0.822
(1.00) 		0.975
(1.00) 		0.384
(1.00) 		0.842
(1.00) 		0.404
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.012

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
1Q GAIN CNV 38 42 81
1Q GAIN WILD-TYPE 128 162 118

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 3.7e-09 (Fisher's exact test), Q value = 4.1e-06

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
2P GAIN CNV 76 23 26
2P GAIN WILD-TYPE 139 193 100

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.75e-08 (Fisher's exact test), Q value = 1.9e-05

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
2P GAIN CNV 26 74 25
2P GAIN WILD-TYPE 102 136 194

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'MIR_CHIERARCHICAL'

P value = 1.31e-05 (Chi-square test), Q value = 0.014

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
2P GAIN CNV 11 17 24 20 12 41
2P GAIN WILD-TYPE 54 98 101 79 45 53

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 3.02e-11 (Fisher's exact test), Q value = 3.4e-08

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
2P GAIN CNV 22 28 79
2P GAIN WILD-TYPE 144 176 120

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 8.24e-12 (Fisher's exact test), Q value = 9.2e-09

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2P GAIN CNV 71 34 24
2P GAIN WILD-TYPE 101 141 197

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 8.7e-05 (Fisher's exact test), Q value = 0.093

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
2P GAIN CNV 18 8 36
2P GAIN WILD-TYPE 82 59 55

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNA_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.0014

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
2Q GAIN CNV 61 21 17
2Q GAIN WILD-TYPE 154 195 109

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.25e-06 (Fisher's exact test), Q value = 0.0057

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
2Q GAIN CNV 20 58 21
2Q GAIN WILD-TYPE 108 152 198

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1.43e-08 (Fisher's exact test), Q value = 1.6e-05

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
2Q GAIN CNV 17 23 63
2Q GAIN WILD-TYPE 149 181 136

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 2.57e-06 (Fisher's exact test), Q value = 0.0028

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2Q GAIN CNV 53 25 25
2Q GAIN WILD-TYPE 119 150 196

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1.02e-09 (Fisher's exact test), Q value = 1.1e-06

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
3Q GAIN CNV 38 63 107
3Q GAIN WILD-TYPE 128 141 92

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00023

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
5P GAIN CNV 18 63 66
5P GAIN WILD-TYPE 148 141 133

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.0013

Table S14.  Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
6P GAIN CNV 15 45 61
6P GAIN WILD-TYPE 151 159 138

Figure S14.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.011

Table S15.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
6Q GAIN CNV 5 21 36
6Q GAIN WILD-TYPE 161 183 163

Figure S15.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 7.2e-05 (Fisher's exact test), Q value = 0.077

Table S16.  Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
6Q GAIN CNV 34 10 18
6Q GAIN WILD-TYPE 138 165 203

Figure S16.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 9.19e-08 (Fisher's exact test), Q value = 1e-04

Table S17.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
7P GAIN CNV 26 28 71
7P GAIN WILD-TYPE 140 176 128

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 4.53e-06 (Fisher's exact test), Q value = 0.0049

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
7P GAIN CNV 61 27 37
7P GAIN WILD-TYPE 111 148 184

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.011

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
7Q GAIN CNV 35 40 78
7Q GAIN WILD-TYPE 131 164 121

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 2.95e-09 (Fisher's exact test), Q value = 3.3e-06

Table S20.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
10P GAIN CNV 20 36 76
10P GAIN WILD-TYPE 146 168 123

Figure S20.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 7.92e-05 (Fisher's exact test), Q value = 0.085

Table S21.  Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
11Q GAIN CNV 5 32 25
11Q GAIN WILD-TYPE 161 172 174

Figure S21.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.035

Table S22.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
12P GAIN CNV 103 60 39
12P GAIN WILD-TYPE 112 156 87

Figure S22.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.012

Table S23.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
12P GAIN CNV 41 102 59
12P GAIN WILD-TYPE 87 108 160

Figure S23.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'MIR_CHIERARCHICAL'

P value = 4.46e-05 (Chi-square test), Q value = 0.048

Table S24.  Gene #23: '12p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
12P GAIN CNV 21 31 42 28 25 54
12P GAIN WILD-TYPE 44 84 83 71 32 40

Figure S24.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 4.27e-13 (Fisher's exact test), Q value = 4.8e-10

Table S25.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
12P GAIN CNV 38 56 114
12P GAIN WILD-TYPE 128 148 85

Figure S25.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1.24e-07 (Fisher's exact test), Q value = 0.00014

Table S26.  Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
12P GAIN CNV 92 58 58
12P GAIN WILD-TYPE 80 117 163

Figure S26.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.016

Table S27.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
12P GAIN CNV 23 20 50
12P GAIN WILD-TYPE 77 47 41

Figure S27.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.66e-06 (Fisher's exact test), Q value = 0.0094

Table S28.  Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
12Q GAIN CNV 19 67 31
12Q GAIN WILD-TYPE 109 143 188

Figure S28.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1.22e-14 (Fisher's exact test), Q value = 1.4e-11

Table S29.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
12Q GAIN CNV 24 18 80
12Q GAIN WILD-TYPE 142 186 119

Figure S29.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 4e-06 (Fisher's exact test), Q value = 0.0044

Table S30.  Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
12Q GAIN CNV 60 28 34
12Q GAIN WILD-TYPE 112 147 187

Figure S30.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 9.27e-05 (Fisher's exact test), Q value = 0.099

Table S31.  Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
13Q GAIN CNV 23 13 5
13Q GAIN WILD-TYPE 149 162 216

Figure S31.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1.95e-08 (Fisher's exact test), Q value = 2.2e-05

Table S32.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
19P GAIN CNV 17 21 61
19P GAIN WILD-TYPE 149 183 138

Figure S32.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 6.85e-07 (Fisher's exact test), Q value = 0.00075

Table S33.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
19Q GAIN CNV 15 22 55
19Q GAIN WILD-TYPE 151 182 144

Figure S33.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 4.08e-06 (Chi-square test), Q value = 0.0045

Table S34.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
20P GAIN CNV 24 41 37 36 30 60
20P GAIN WILD-TYPE 41 74 88 63 27 34

Figure S34.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 3.87e-15 (Fisher's exact test), Q value = 4.3e-12

Table S35.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
20P GAIN CNV 43 64 127
20P GAIN WILD-TYPE 123 140 72

Figure S35.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.68e-10 (Fisher's exact test), Q value = 4.1e-07

Table S36.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20P GAIN CNV 106 62 66
20P GAIN WILD-TYPE 66 113 155

Figure S36.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.011

Table S37.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
20Q GAIN CNV 127 78 62
20Q GAIN WILD-TYPE 88 138 64

Figure S37.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.09e-05 (Fisher's exact test), Q value = 0.097

Table S38.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
20Q GAIN CNV 59 124 84
20Q GAIN WILD-TYPE 69 86 135

Figure S38.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 1.6e-06 (Chi-square test), Q value = 0.0018

Table S39.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
20Q GAIN CNV 26 47 48 43 34 68
20Q GAIN WILD-TYPE 39 68 77 56 23 26

Figure S39.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3.3e-20 (Fisher's exact test), Q value = 3.7e-17

Table S40.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
20Q GAIN CNV 46 80 147
20Q GAIN WILD-TYPE 120 124 52

Figure S40.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 2.09e-14 (Fisher's exact test), Q value = 2.3e-11

Table S41.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20Q GAIN CNV 125 72 76
20Q GAIN WILD-TYPE 47 103 145

Figure S41.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 7.07e-06 (Fisher's exact test), Q value = 0.0077

Table S42.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
21Q GAIN CNV 10 17 43
21Q GAIN WILD-TYPE 156 187 156

Figure S42.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'MRNA_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
5Q LOSS CNV 87 56 26
5Q LOSS WILD-TYPE 128 160 100

Figure S43.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.19

Table S44.  Gene #50: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
5Q LOSS CNV 38 52 82
5Q LOSS WILD-TYPE 128 152 117

Figure S44.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.51e-07 (Fisher's exact test), Q value = 0.00017

Table S45.  Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
5Q LOSS CNV 80 35 57
5Q LOSS WILD-TYPE 92 140 164

Figure S45.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.51e-11 (Fisher's exact test), Q value = 1.7e-08

Table S46.  Gene #58: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
9Q LOSS CNV 62 56 122
9Q LOSS WILD-TYPE 104 148 77

Figure S46.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 4.36e-06 (Fisher's exact test), Q value = 0.0048

Table S47.  Gene #65: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
13Q LOSS CNV 78 57 127
13Q LOSS WILD-TYPE 94 118 94

Figure S47.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.13

Table S48.  Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
14Q LOSS CNV 42 43 79
14Q LOSS WILD-TYPE 124 161 120

Figure S48.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 7.17e-11 (Fisher's exact test), Q value = 8e-08

Table S49.  Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
15Q LOSS CNV 48 57 115
15Q LOSS WILD-TYPE 118 147 84

Figure S49.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 7.7e-05 (Fisher's exact test), Q value = 0.083

Table S50.  Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
15Q LOSS CNV 89 52 79
15Q LOSS WILD-TYPE 83 123 142

Figure S50.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 4.52e-05 (Fisher's exact test), Q value = 0.049

Table S51.  Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
22Q LOSS CNV 169 129 79
22Q LOSS WILD-TYPE 46 87 47

Figure S51.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.14

Table S52.  Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
22Q LOSS CNV 75 164 138
22Q LOSS WILD-TYPE 53 46 81

Figure S52.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 0.000176 (Fisher's exact test), Q value = 0.19

Table S53.  Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 204 199
22Q LOSS CNV 103 127 157
22Q LOSS WILD-TYPE 63 77 42

Figure S53.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 569

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 14

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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