Correlation between copy number variations of arm-level result and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1FQ9TK9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Ovarian Serous Cystadenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1FQ9TK9
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 12 molecular subtypes across 569 patients, 60 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' and 'METHLYATION_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 'MRNA_CHIERARCHICAL' and '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'.

  • 18p 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 'MRNA_CHIERARCHICAL',  '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' and 'METHLYATION_CNMF'.

  • 4q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  '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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 60 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
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
2p gain 0 (0%) 440 5.21e-09
(4.91e-06) 		1.03e-10
(9.71e-08) 		0.615
(1.00) 		1.31e-05
(0.0121) 		3.02e-11
(2.87e-08) 		3.13e-11
(2.97e-08) 		0.0363
(1.00) 		0.439
(1.00) 		8.7e-05
(0.0791) 		0.00457
(1.00) 		0.426
(1.00) 		0.209
(1.00)
12p gain 0 (0%) 361 7.56e-05
(0.0689) 		1.27e-05
(0.0117) 		0.306
(1.00) 		4.46e-05
(0.0408) 		4.27e-13
(4.07e-10) 		3.95e-09
(3.73e-06) 		0.362
(1.00) 		0.825
(1.00) 		1.46e-05
(0.0135) 		0.00033
(0.297) 		0.183
(1.00) 		0.194
(1.00)
20q gain 0 (0%) 296 1.94e-05
(0.0178) 		3.35e-13
(3.2e-10) 		0.497
(1.00) 		1.6e-06
(0.00149) 		3.3e-20
(3.17e-17) 		9.65e-17
(9.23e-14) 		0.456
(1.00) 		0.175
(1.00) 		0.0033
(1.00) 		0.395
(1.00) 		0.351
(1.00) 		0.877
(1.00)
2q gain 0 (0%) 466 1.53e-06
(0.00142) 		6.48e-07
(0.000606) 		0.648
(1.00) 		0.00255
(1.00) 		1.43e-08
(1.34e-05) 		2e-06
(0.00186) 		0.0338
(1.00) 		0.329
(1.00) 		0.00183
(1.00) 		0.00447
(1.00) 		0.535
(1.00) 		0.481
(1.00)
20p gain 0 (0%) 335 0.00174
(1.00) 		5.26e-07
(0.000493) 		0.207
(1.00) 		4.08e-06
(0.00379) 		3.87e-15
(3.7e-12) 		4.1e-12
(3.9e-09) 		0.322
(1.00) 		0.572
(1.00) 		0.00375
(1.00) 		0.144
(1.00) 		0.569
(1.00) 		1
(1.00)
5q loss 0 (0%) 397 0.000144
(0.131) 		2.22e-05
(0.0203) 		0.655
(1.00) 		0.00138
(1.00) 		0.000173
(0.157) 		1.7e-07
(0.00016) 		0.00843
(1.00) 		0.0604
(1.00) 		0.000664
(0.592) 		0.284
(1.00) 		0.533
(1.00) 		0.595
(1.00)
12q gain 0 (0%) 447 0.000834
(0.741) 		5.65e-06
(0.00524) 		0.533
(1.00) 		0.00204
(1.00) 		1.22e-14
(1.17e-11) 		9.49e-06
(0.00877) 		0.00933
(1.00) 		0.663
(1.00) 		0.000731
(0.65) 		0.00235
(1.00) 		0.102
(1.00) 		0.119
(1.00)
22q loss 0 (0%) 182 0.00012
(0.109) 		1.8e-05
(0.0166) 		0.056
(1.00) 		0.0363
(1.00) 		0.000176
(0.16) 		0.0095
(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)
6p gain 0 (0%) 448 0.492
(1.00) 		0.00412
(1.00) 		0.873
(1.00) 		0.0212
(1.00) 		1.19e-06
(0.00111) 		0.000238
(0.214) 		0.546
(1.00) 		0.744
(1.00) 		0.154
(1.00) 		0.619
(1.00) 		0.291
(1.00) 		0.147
(1.00)
6q gain 0 (0%) 507 0.751
(1.00) 		0.00709
(1.00) 		0.896
(1.00) 		0.0396
(1.00) 		1.01e-05
(0.00936) 		6.58e-05
(0.0601) 		0.14
(1.00) 		0.857
(1.00) 		0.00314
(1.00) 		0.354
(1.00) 		0.93
(1.00) 		0.416
(1.00)
7p gain 0 (0%) 444 0.214
(1.00) 		0.151
(1.00) 		0.0456
(1.00) 		0.00843
(1.00) 		9.19e-08
(8.64e-05) 		1.05e-06
(0.000984) 		0.407
(1.00) 		0.158
(1.00) 		0.0836
(1.00) 		0.109
(1.00) 		0.944
(1.00) 		0.371
(1.00)
10p gain 0 (0%) 437 0.0106
(1.00) 		5.38e-05
(0.0492) 		0.783
(1.00) 		0.00763
(1.00) 		2.95e-09
(2.79e-06) 		0.00123
(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)
21q gain 0 (0%) 499 0.666
(1.00) 		0.0322
(1.00) 		0.986
(1.00) 		0.906
(1.00) 		7.07e-06
(0.00655) 		0.000186
(0.168) 		0.29
(1.00) 		0.259
(1.00) 		0.371
(1.00) 		0.171
(1.00) 		0.231
(1.00) 		0.683
(1.00)
15q loss 0 (0%) 349 0.00346
(1.00) 		0.00872
(1.00) 		0.000914
(0.81) 		0.0035
(1.00) 		7.17e-11
(6.8e-08) 		0.000185
(0.167) 		0.884
(1.00) 		0.885
(1.00) 		0.0245
(1.00) 		0.449
(1.00) 		0.00638
(1.00) 		0.375
(1.00)
1q gain 0 (0%) 408 0.521
(1.00) 		0.518
(1.00) 		0.728
(1.00) 		0.563
(1.00) 		1.07e-05
(0.00984) 		0.209
(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)
3q gain 0 (0%) 361 0.948
(1.00) 		0.00133
(1.00) 		0.735
(1.00) 		0.284
(1.00) 		1.02e-09
(9.62e-07) 		0.00325
(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)
5p gain 0 (0%) 422 0.641
(1.00) 		0.276
(1.00) 		0.688
(1.00) 		0.485
(1.00) 		2.09e-07
(0.000196) 		0.348
(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)
7q gain 0 (0%) 416 0.0877
(1.00) 		0.303
(1.00) 		0.353
(1.00) 		0.357
(1.00) 		1.05e-05
(0.00968) 		0.0005
(0.447) 		0.266
(1.00) 		0.0944
(1.00) 		0.175
(1.00) 		0.173
(1.00) 		0.24
(1.00) 		0.492
(1.00)
11q gain 0 (0%) 507 0.383
(1.00) 		0.776
(1.00) 		0.94
(1.00) 		0.0125
(1.00) 		7.92e-05
(0.0722) 		0.000679
(0.605) 		0.369
(1.00) 		0.451
(1.00) 		0.577
(1.00) 		0.221
(1.00) 		0.281
(1.00) 		0.436
(1.00)
13q gain 0 (0%) 528 0.0168
(1.00) 		0.221
(1.00) 		0.889
(1.00) 		0.00174
(1.00) 		0.00588
(1.00) 		0.000254
(0.229) 		0.829
(1.00) 		0.336
(1.00) 		0.451
(1.00) 		0.949
(1.00) 		0.289
(1.00) 		0.618
(1.00)
18p gain 0 (0%) 495 0.00725
(1.00) 		0.00119
(1.00) 		0.852
(1.00) 		0.157
(1.00) 		0.00147
(1.00) 		8.22e-05
(0.0748) 		0.00283
(1.00) 		0.0731
(1.00) 		0.527
(1.00) 		0.611
(1.00) 		0.271
(1.00) 		0.589
(1.00)
19p gain 0 (0%) 470 0.0238
(1.00) 		0.0208
(1.00) 		0.664
(1.00) 		0.192
(1.00) 		1.95e-08
(1.84e-05) 		0.000683
(0.607) 		0.0151
(1.00) 		0.235
(1.00) 		0.741
(1.00) 		0.822
(1.00) 		0.677
(1.00) 		0.311
(1.00)
19q gain 0 (0%) 477 0.0226
(1.00) 		0.047
(1.00) 		0.624
(1.00) 		0.16
(1.00) 		6.85e-07
(0.00064) 		0.000364
(0.327) 		0.0242
(1.00) 		0.266
(1.00) 		0.558
(1.00) 		0.525
(1.00) 		0.328
(1.00) 		0.217
(1.00)
4q loss 0 (0%) 267 0.0489
(1.00) 		0.021
(1.00) 		0.269
(1.00) 		0.0147
(1.00) 		0.0101
(1.00) 		0.763
(1.00) 		0.286
(1.00) 		0.0925
(1.00) 		0.47
(1.00) 		0.0357
(1.00) 		0.0471
(1.00) 		0.000253
(0.227)
9q loss 0 (0%) 329 0.00133
(1.00) 		0.000371
(0.332) 		0.142
(1.00) 		0.00651
(1.00) 		1.51e-11
(1.44e-08) 		0.00232
(1.00) 		0.653
(1.00) 		0.881
(1.00) 		0.00276
(1.00) 		0.212
(1.00) 		0.109
(1.00) 		0.0309
(1.00)
13q loss 0 (0%) 307 0.12
(1.00) 		0.74
(1.00) 		0.907
(1.00) 		0.0687
(1.00) 		0.000857
(0.76) 		1.26e-06
(0.00118) 		0.00299
(1.00) 		0.00436
(1.00) 		0.297
(1.00) 		0.985
(1.00) 		0.418
(1.00) 		0.896
(1.00)
14q loss 0 (0%) 405 0.0842
(1.00) 		0.16
(1.00) 		0.875
(1.00) 		0.917
(1.00) 		0.000118
(0.107) 		0.0256
(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)
1p gain 0 (0%) 465 0.0537
(1.00) 		0.337
(1.00) 		0.0931
(1.00) 		0.436
(1.00) 		0.336
(1.00) 		0.898
(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)
3p gain 0 (0%) 460 0.407
(1.00) 		0.118
(1.00) 		0.102
(1.00) 		0.619
(1.00) 		0.00102
(0.902) 		0.893
(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)
4p gain 0 (0%) 538 0.888
(1.00) 		0.499
(1.00) 		0.0047
(1.00) 		0.688
(1.00) 		0.0876
(1.00) 		0.051
(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)
4q gain 0 (0%) 553 0.948
(1.00) 		0.805
(1.00) 		0.853
(1.00) 		0.938
(1.00) 		0.332
(1.00) 		0.0214
(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)
5q gain 0 (0%) 535 0.0365
(1.00) 		0.118
(1.00) 		0.499
(1.00) 		0.356
(1.00) 		0.597
(1.00) 		0.416
(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)
8p gain 0 (0%) 483 0.355
(1.00) 		0.125
(1.00) 		0.977
(1.00) 		0.0131
(1.00) 		0.264
(1.00) 		0.956
(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)
8q gain 0 (0%) 365 0.184
(1.00) 		0.417
(1.00) 		0.128
(1.00) 		0.0883
(1.00) 		0.0087
(1.00) 		0.975
(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)
9p gain 0 (0%) 508 0.0325
(1.00) 		0.505
(1.00) 		0.28
(1.00) 		0.319
(1.00) 		0.00446
(1.00) 		0.0217
(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)
9q gain 0 (0%) 542 0.397
(1.00) 		0.275
(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)
10q gain 0 (0%) 501 0.0085
(1.00) 		0.00254
(1.00) 		0.959
(1.00) 		0.0166
(1.00) 		0.0135
(1.00) 		0.0297
(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)
11p gain 0 (0%) 529 0.244
(1.00) 		0.404
(1.00) 		0.223
(1.00) 		0.34
(1.00) 		0.043
(1.00) 		0.016
(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)
14q gain 0 (0%) 535 0.011
(1.00) 		0.0521
(1.00) 		0.348
(1.00) 		0.0546
(1.00) 		0.975
(1.00) 		0.188
(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)
15q gain 0 (0%) 544 0.382
(1.00) 		0.64
(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)
16p gain 0 (0%) 538 0.0368
(1.00) 		0.0224
(1.00) 		0.919
(1.00) 		0.355
(1.00) 		0.149
(1.00) 		0.148
(1.00) 		0.675
(1.00) 		0.101
(1.00) 		1
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.513
(1.00)
16q gain 0 (0%) 553 0.0183
(1.00) 		0.000961
(0.85) 		0.219
(1.00) 		0.491
(1.00) 		0.597
(1.00) 		0.042
(1.00) 		0.512
(1.00) 		0.124
(1.00) 		0.119
(1.00) 		0.269
(1.00)
17p gain 0 (0%) 558 0.433
(1.00) 		0.129
(1.00) 		0.509
(1.00) 		0.27
(1.00) 		0.064
(1.00) 		0.434
(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)
17q gain 0 (0%) 546 0.729
(1.00) 		0.285
(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)
18q gain 0 (0%) 528 0.25
(1.00) 		0.615
(1.00) 		0.531
(1.00) 		0.565
(1.00) 		0.042
(1.00) 		0.0213
(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)
22q gain 0 (0%) 560 0.379
(1.00) 		0.833
(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)
Xq gain 0 (0%) 535 0.194
(1.00) 		0.0261
(1.00) 		0.949
(1.00) 		0.603
(1.00) 		0.0139
(1.00) 		0.105
(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)
1p loss 0 (0%) 534 0.00443
(1.00) 		0.0112
(1.00) 		0.284
(1.00) 		0.49
(1.00) 		0.779
(1.00) 		0.218
(1.00) 		0.503
(1.00) 		0.514
(1.00) 		0.736
(1.00) 		0.361
(1.00) 		1
(1.00) 		1
(1.00)
1q loss 0 (0%) 547 0.018
(1.00) 		0.00428
(1.00) 		0.00412
(1.00) 		0.347
(1.00) 		0.337
(1.00) 		0.497
(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)
2p loss 0 (0%) 543 0.761
(1.00) 		0.871
(1.00) 		0.905
(1.00) 		0.181
(1.00) 		0.572
(1.00) 		0.383
(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)
2q loss 0 (0%) 539 0.789
(1.00) 		0.53
(1.00) 		0.816
(1.00) 		0.0858
(1.00) 		0.53
(1.00) 		0.139
(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)
3p loss 0 (0%) 508 0.0592
(1.00) 		0.0121
(1.00) 		0.925
(1.00) 		0.0476
(1.00) 		0.00469
(1.00) 		0.118
(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)
3q loss 0 (0%) 546 0.239
(1.00) 		0.0866
(1.00) 		0.964
(1.00) 		0.182
(1.00) 		0.198
(1.00) 		0.198
(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)
4p loss 0 (0%) 307 0.0989
(1.00) 		0.0801
(1.00) 		0.516
(1.00) 		0.0236
(1.00) 		0.0312
(1.00) 		0.889
(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)
5p loss 0 (0%) 484 0.378
(1.00) 		0.088
(1.00) 		0.188
(1.00) 		0.162
(1.00) 		0.0129
(1.00) 		0.0047
(1.00) 		0.204
(1.00) 		0.156
(1.00) 		0.000407
(0.364) 		0.562
(1.00) 		0.919
(1.00) 		0.699
(1.00)
6p loss 0 (0%) 443 0.923
(1.00) 		0.0524
(1.00) 		0.716
(1.00) 		0.794
(1.00) 		0.19
(1.00) 		0.0511
(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)
6q loss 0 (0%) 371 0.96
(1.00) 		0.0238
(1.00) 		0.829
(1.00) 		0.844
(1.00) 		0.079
(1.00) 		0.0202
(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)
7p loss 0 (0%) 478 0.614
(1.00) 		0.246
(1.00) 		0.184
(1.00) 		0.304
(1.00) 		0.0746
(1.00) 		0.146
(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)
7q loss 0 (0%) 521 0.337
(1.00) 		0.855
(1.00) 		0.431
(1.00) 		0.652
(1.00) 		0.267
(1.00) 		0.0267
(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)
8p loss 0 (0%) 334 0.756
(1.00) 		0.571
(1.00) 		0.454
(1.00) 		0.86
(1.00) 		0.00151
(1.00) 		0.0744
(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)
8q loss 0 (0%) 506 0.0697
(1.00) 		0.035
(1.00) 		0.201
(1.00) 		0.369
(1.00) 		0.00207
(1.00) 		0.0675
(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)
9p loss 0 (0%) 357 0.000585
(0.523) 		0.00456
(1.00) 		0.737
(1.00) 		0.0603
(1.00) 		0.0297
(1.00) 		0.00103
(0.913) 		0.674
(1.00) 		0.976
(1.00) 		0.567
(1.00) 		0.134
(1.00) 		0.0402
(1.00) 		0.331
(1.00)
10p loss 0 (0%) 502 0.436
(1.00) 		0.623
(1.00) 		0.328
(1.00) 		0.806
(1.00) 		0.895
(1.00) 		0.695
(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)
10q loss 0 (0%) 479 0.642
(1.00) 		0.38
(1.00) 		0.0994
(1.00) 		0.799
(1.00) 		0.118
(1.00) 		0.591
(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)
11p loss 0 (0%) 423 0.00609
(1.00) 		0.00524
(1.00) 		0.0964
(1.00) 		0.262
(1.00) 		0.0816
(1.00) 		0.00802
(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)
11q loss 0 (0%) 461 0.135
(1.00) 		0.392
(1.00) 		0.0135
(1.00) 		0.258
(1.00) 		0.187
(1.00) 		0.103
(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)
12p loss 0 (0%) 518 0.294
(1.00) 		0.0891
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.00812
(1.00) 		0.242
(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)
12q loss 0 (0%) 493 0.192
(1.00) 		0.00199
(1.00) 		0.389
(1.00) 		0.277
(1.00) 		0.00274
(1.00) 		0.0942
(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)
16p loss 0 (0%) 298 0.912
(1.00) 		0.969
(1.00) 		0.196
(1.00) 		0.677
(1.00) 		0.0275
(1.00) 		0.105
(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)
16q loss 0 (0%) 209 0.918
(1.00) 		0.887
(1.00) 		0.041
(1.00) 		0.362
(1.00) 		0.0263
(1.00) 		0.0886
(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)
17p loss 0 (0%) 140 0.188
(1.00) 		0.0406
(1.00) 		0.891
(1.00) 		0.545
(1.00) 		0.243
(1.00) 		0.0463
(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)
17q loss 0 (0%) 237 0.011
(1.00) 		0.00449
(1.00) 		0.0246
(1.00) 		0.663
(1.00) 		0.597
(1.00) 		0.186
(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)
18p loss 0 (0%) 382 0.767
(1.00) 		0.932
(1.00) 		0.33
(1.00) 		0.413
(1.00) 		0.216
(1.00) 		0.0128
(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)
18q loss 0 (0%) 333 0.202
(1.00) 		0.753
(1.00) 		0.7
(1.00) 		0.608
(1.00) 		0.845
(1.00) 		0.453
(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)
19p loss 0 (0%) 424 0.532
(1.00) 		0.809
(1.00) 		0.152
(1.00) 		0.225
(1.00) 		0.179
(1.00) 		0.0996
(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)
19q loss 0 (0%) 424 0.126
(1.00) 		0.448
(1.00) 		0.315
(1.00) 		0.296
(1.00) 		0.278
(1.00) 		0.723
(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)
20p loss 0 (0%) 531 0.304
(1.00) 		0.529
(1.00) 		0.625
(1.00) 		0.361
(1.00) 		0.172
(1.00) 		0.0962
(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)
20q loss 0 (0%) 547 0.717
(1.00) 		0.188
(1.00) 		0.276
(1.00) 		0.737
(1.00) 		0.518
(1.00) 		0.737
(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)
21q loss 0 (0%) 418 0.343
(1.00) 		0.248
(1.00) 		0.31
(1.00) 		0.0634
(1.00) 		0.793
(1.00) 		0.0515
(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)
Xq loss 0 (0%) 468 0.0795
(1.00) 		0.161
(1.00) 		0.0363
(1.00) 		0.15
(1.00) 		0.0851
(1.00) 		0.316
(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)
'1q gain' versus 'CN_CNMF'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0098

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 = 5.21e-09 (Fisher's exact test), Q value = 4.9e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
2P GAIN CNV 76 23 26
2P GAIN WILD-TYPE 139 190 103

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.03e-10 (Fisher's exact test), Q value = 9.7e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
2P GAIN CNV 34 77 14
2P GAIN WILD-TYPE 199 122 111

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 = 0.012

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 = 2.9e-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 = 3.13e-11 (Fisher's exact test), Q value = 3e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
2P GAIN CNV 70 34 25
2P GAIN WILD-TYPE 101 142 196

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 = 0.079

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 = 1.53e-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 215 213 129
2Q GAIN CNV 61 21 17
2Q GAIN WILD-TYPE 154 192 112

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

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.48e-07 (Fisher's exact test), Q value = 0.00061

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
2Q GAIN CNV 26 59 14
2Q GAIN WILD-TYPE 207 140 111

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 = 1.3e-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 = 2e-06 (Fisher's exact test), Q value = 0.0019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
2Q GAIN CNV 53 25 25
2Q GAIN WILD-TYPE 118 151 196

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 = 9.6e-07

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 = 2e-04

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 = 0.0011

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'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.000238 (Fisher's exact test), Q value = 0.21

Table S15.  Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
6P GAIN CNV 55 27 39
6P GAIN WILD-TYPE 116 149 182

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0094

Table S16.  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 S16.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 6.58e-05 (Fisher's exact test), Q value = 0.06

Table S17.  Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
6Q GAIN CNV 34 10 18
6Q GAIN WILD-TYPE 137 166 203

Figure S17.  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 = 8.6e-05

Table S18.  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 S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00098

Table S19.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
7P GAIN CNV 62 26 37
7P GAIN WILD-TYPE 109 150 184

Figure S19.  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 = 0.0097

Table S20.  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 S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.38e-05 (Fisher's exact test), Q value = 0.049

Table S21.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
10P GAIN CNV 54 64 14
10P GAIN WILD-TYPE 179 135 111

Figure S21.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 2.95e-09 (Fisher's exact test), Q value = 2.8e-06

Table S22.  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 S22.  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 = 0.072

Table S23.  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 S23.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 7.56e-05 (Fisher's exact test), Q value = 0.069

Table S24.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
12P GAIN CNV 102 60 40
12P GAIN WILD-TYPE 113 153 89

Figure S24.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.012

Table S25.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
12P GAIN CNV 70 98 34
12P GAIN WILD-TYPE 163 101 91

Figure S25.  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 = 0.041

Table S26.  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 S26.  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 = 4.1e-10

Table S27.  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 S27.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3.95e-09 (Fisher's exact test), Q value = 3.7e-06

Table S28.  Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
12P GAIN CNV 95 56 57
12P GAIN WILD-TYPE 76 120 164

Figure S28.  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 = 0.013

Table S29.  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 S29.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.65e-06 (Fisher's exact test), Q value = 0.0052

Table S30.  Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
12Q GAIN CNV 34 65 18
12Q GAIN WILD-TYPE 199 134 107

Figure S30.  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 = 1.2e-11

Table S31.  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 S31.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 9.49e-06 (Fisher's exact test), Q value = 0.0088

Table S32.  Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
12Q GAIN CNV 59 28 35
12Q GAIN WILD-TYPE 112 148 186

Figure S32.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.23

Table S33.  Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
13Q GAIN CNV 23 12 6
13Q GAIN WILD-TYPE 148 164 215

Figure S33.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 8.22e-05 (Fisher's exact test), Q value = 0.075

Table S34.  Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
18P GAIN CNV 38 12 24
18P GAIN WILD-TYPE 133 164 197

Figure S34.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1.95e-08 (Fisher's exact test), Q value = 1.8e-05

Table S35.  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 S35.  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 = 0.00064

Table S36.  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 S36.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.26e-07 (Fisher's exact test), Q value = 0.00049

Table S37.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
20P GAIN CNV 90 108 31
20P GAIN WILD-TYPE 143 91 94

Figure S37.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 4.08e-06 (Chi-square test), Q value = 0.0038

Table S38.  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 S38.  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 = 3.7e-12

Table S39.  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 S39.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 4.1e-12 (Fisher's exact test), Q value = 3.9e-09

Table S40.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
20P GAIN CNV 109 61 64
20P GAIN WILD-TYPE 62 115 157

Figure S40.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.018

Table S41.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
20Q GAIN CNV 127 78 62
20Q GAIN WILD-TYPE 88 135 67

Figure S41.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.35e-13 (Fisher's exact test), Q value = 3.2e-10

Table S42.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
20Q GAIN CNV 110 129 28
20Q GAIN WILD-TYPE 123 70 97

Figure S42.  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 = 0.0015

Table S43.  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 S43.  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 = 3.2e-17

Table S44.  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 S44.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 9.65e-17 (Fisher's exact test), Q value = 9.2e-14

Table S45.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
20Q GAIN CNV 128 70 75
20Q GAIN WILD-TYPE 43 106 146

Figure S45.  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 = 0.0065

Table S46.  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 S46.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.17

Table S47.  Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
21Q GAIN CNV 36 12 22
21Q GAIN WILD-TYPE 135 164 199

Figure S47.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000253 (Fisher's exact test), Q value = 0.23

Table S48.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 281 161
4Q LOSS CNV 0 133 101
4Q LOSS WILD-TYPE 5 148 60

Figure S48.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.13

Table S49.  Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
5Q LOSS CNV 87 55 27
5Q LOSS WILD-TYPE 128 158 102

Figure S49.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.02

Table S50.  Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
5Q LOSS CNV 51 84 34
5Q LOSS WILD-TYPE 182 115 91

Figure S50.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.16

Table S51.  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 S51.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.7e-07 (Fisher's exact test), Q value = 0.00016

Table S52.  Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
5Q LOSS CNV 79 34 59
5Q LOSS WILD-TYPE 92 142 162

Figure S52.  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 = 1.4e-08

Table S53.  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 S53.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.0012

Table S54.  Gene #65: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
13Q LOSS CNV 78 56 128
13Q LOSS WILD-TYPE 93 120 93

Figure S54.  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 = 0.11

Table S55.  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 S55.  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 = 6.8e-08

Table S56.  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 S56.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 176 221
15Q LOSS CNV 87 52 81
15Q LOSS WILD-TYPE 84 124 140

Figure S57.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.11

Table S58.  Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
22Q LOSS CNV 168 129 80
22Q LOSS WILD-TYPE 47 84 49

Figure S58.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.017

Table S59.  Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
22Q LOSS CNV 134 156 87
22Q LOSS WILD-TYPE 99 43 38

Figure S59.  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 = 0.16

Table S60.  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 S60.  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 = 12

  • 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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