Correlation between copy number variations of arm-level result and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1WD3XXP
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/C1WD3XXP
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 570 patients, 54 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',  'MIR_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' and 'METHLYATION_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

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

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

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_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'.

  • 9p loss cnv correlated to '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'.

  • 17q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • 22q loss cnv correlated to 'MRNA_CNMF' 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, 54 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 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 Fisher's exact test
2p gain 0 (0%) 440 2.56e-09
(2.83e-06) 		4.88e-09
(5.39e-06) 		0.612
(1.00) 		6.24e-07
(0.000685) 		7.24e-11
(8.05e-08) 		8.05e-11
(8.93e-08) 		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) 		0.752
(1.00) 		0.384
(1.00)
2q gain 0 (0%) 466 7.16e-07
(0.000785) 		6.2e-06
(0.00677) 		0.38
(1.00) 		0.000188
(0.2) 		3.04e-08
(3.35e-05) 		1.06e-05
(0.0116) 		0.0338
(1.00) 		0.329
(1.00) 		0.00183
(1.00) 		0.00447
(1.00) 		0.535
(1.00) 		0.481
(1.00) 		0.403
(1.00) 		0.193
(1.00)
12p gain 0 (0%) 361 2.48e-05
(0.0268) 		2.01e-05
(0.0217) 		0.402
(1.00) 		0.00122
(1.00) 		6.57e-14
(7.32e-11) 		3.88e-09
(4.29e-06) 		0.362
(1.00) 		0.825
(1.00) 		1.46e-05
(0.0159) 		0.00033
(0.35) 		0.183
(1.00) 		0.194
(1.00) 		0.279
(1.00) 		0.103
(1.00)
20q gain 0 (0%) 296 1.32e-05
(0.0143) 		9.72e-06
(0.0106) 		0.477
(1.00) 		0.00423
(1.00) 		1.57e-20
(1.76e-17) 		3.04e-15
(3.4e-12) 		0.456
(1.00) 		0.175
(1.00) 		0.0033
(1.00) 		0.395
(1.00) 		0.351
(1.00) 		0.877
(1.00) 		0.828
(1.00) 		0.212
(1.00)
12q gain 0 (0%) 447 0.000247
(0.262) 		7.92e-06
(0.00862) 		0.825
(1.00) 		0.000767
(0.807) 		6.43e-15
(7.17e-12) 		2.84e-06
(0.00311) 		0.00933
(1.00) 		0.663
(1.00) 		0.000731
(0.77) 		0.00235
(1.00) 		0.102
(1.00) 		0.119
(1.00) 		0.196
(1.00) 		0.122
(1.00)
5q loss 0 (0%) 397 0.000108
(0.116) 		0.00202
(1.00) 		0.625
(1.00) 		0.00532
(1.00) 		4.39e-05
(0.0472) 		1.41e-07
(0.000155) 		0.00599
(1.00) 		0.041
(1.00) 		0.000664
(0.7) 		0.284
(1.00) 		0.507
(1.00) 		0.525
(1.00) 		0.225
(1.00) 		0.24
(1.00)
6q gain 0 (0%) 508 0.717
(1.00) 		0.139
(1.00) 		0.694
(1.00) 		0.0469
(1.00) 		1.19e-05
(0.0129) 		0.000117
(0.126) 		0.14
(1.00) 		0.857
(1.00) 		0.00314
(1.00) 		0.354
(1.00) 		0.93
(1.00) 		0.416
(1.00) 		0.927
(1.00) 		0.0237
(1.00)
7p gain 0 (0%) 443 0.205
(1.00) 		0.205
(1.00) 		0.208
(1.00) 		0.382
(1.00) 		3.54e-08
(3.9e-05) 		1.32e-05
(0.0143) 		0.486
(1.00) 		0.126
(1.00) 		0.0836
(1.00) 		0.109
(1.00) 		0.893
(1.00) 		0.412
(1.00) 		0.359
(1.00) 		0.219
(1.00)
10p gain 0 (0%) 438 0.0109
(1.00) 		0.0248
(1.00) 		0.723
(1.00) 		0.0462
(1.00) 		2.41e-09
(2.68e-06) 		0.000159
(0.17) 		0.294
(1.00) 		0.454
(1.00) 		0.0126
(1.00) 		0.865
(1.00) 		0.507
(1.00) 		0.963
(1.00) 		0.399
(1.00) 		0.0734
(1.00)
20p gain 0 (0%) 335 0.0022
(1.00) 		0.00133
(1.00) 		0.114
(1.00) 		0.00291
(1.00) 		2.05e-15
(2.29e-12) 		2.76e-11
(3.07e-08) 		0.322
(1.00) 		0.572
(1.00) 		0.00375
(1.00) 		0.144
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.961
(1.00) 		0.333
(1.00)
15q loss 0 (0%) 350 0.00146
(1.00) 		0.0121
(1.00) 		0.000942
(0.99) 		0.000377
(0.399) 		1.11e-10
(1.23e-07) 		2.47e-05
(0.0267) 		0.884
(1.00) 		0.885
(1.00) 		0.0245
(1.00) 		0.449
(1.00) 		0.00504
(1.00) 		0.387
(1.00) 		0.035
(1.00) 		0.00343
(1.00)
17q loss 0 (0%) 238 0.0114
(1.00) 		0.000207
(0.22) 		0.00471
(1.00) 		0.47
(1.00) 		0.698
(1.00) 		0.258
(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) 		4.78e-05
(0.0514) 		0.259
(1.00)
22q loss 0 (0%) 182 4.38e-05
(0.0472) 		0.000237
(0.252) 		0.115
(1.00) 		0.000404
(0.428) 		0.000156
(0.167) 		0.00166
(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) 		0.00325
(1.00) 		0.318
(1.00)
1q gain 0 (0%) 408 0.497
(1.00) 		0.36
(1.00) 		0.618
(1.00) 		0.158
(1.00) 		7.45e-06
(0.00812) 		0.057
(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) 		0.167
(1.00) 		0.228
(1.00)
3q gain 0 (0%) 362 0.936
(1.00) 		0.698
(1.00) 		0.617
(1.00) 		0.803
(1.00) 		5.99e-09
(6.62e-06) 		0.00128
(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) 		0.0652
(1.00) 		0.638
(1.00)
5p gain 0 (0%) 424 0.741
(1.00) 		0.906
(1.00) 		0.694
(1.00) 		0.336
(1.00) 		4.44e-07
(0.000488) 		0.383
(1.00) 		0.589
(1.00) 		0.155
(1.00) 		0.544
(1.00) 		0.905
(1.00) 		0.0563
(1.00) 		0.242
(1.00) 		0.128
(1.00) 		0.14
(1.00)
6p gain 0 (0%) 448 0.453
(1.00) 		0.0829
(1.00) 		0.841
(1.00) 		0.106
(1.00) 		1.44e-06
(0.00158) 		0.00246
(1.00) 		0.546
(1.00) 		0.744
(1.00) 		0.154
(1.00) 		0.619
(1.00) 		0.291
(1.00) 		0.147
(1.00) 		0.416
(1.00) 		0.0924
(1.00)
7q gain 0 (0%) 415 0.0795
(1.00) 		0.075
(1.00) 		0.593
(1.00) 		0.224
(1.00) 		4.33e-06
(0.00473) 		0.00221
(1.00) 		0.316
(1.00) 		0.0757
(1.00) 		0.175
(1.00) 		0.173
(1.00) 		0.209
(1.00) 		0.572
(1.00) 		0.0719
(1.00) 		0.562
(1.00)
11q gain 0 (0%) 508 0.616
(1.00) 		0.299
(1.00) 		0.83
(1.00) 		0.661
(1.00) 		1.94e-05
(0.021) 		0.00153
(1.00) 		0.369
(1.00) 		0.451
(1.00) 		0.577
(1.00) 		0.221
(1.00) 		0.281
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.691
(1.00)
18p gain 0 (0%) 496 0.0288
(1.00) 		0.0117
(1.00) 		0.897
(1.00) 		0.12
(1.00) 		0.00707
(1.00) 		0.000217
(0.231) 		0.00283
(1.00) 		0.0731
(1.00) 		0.527
(1.00) 		0.611
(1.00) 		0.271
(1.00) 		0.589
(1.00) 		0.26
(1.00) 		0.406
(1.00)
19p gain 0 (0%) 471 0.0176
(1.00) 		0.0562
(1.00) 		0.808
(1.00) 		0.371
(1.00) 		7.71e-08
(8.49e-05) 		0.00136
(1.00) 		0.0151
(1.00) 		0.235
(1.00) 		0.741
(1.00) 		0.822
(1.00) 		0.677
(1.00) 		0.311
(1.00) 		0.573
(1.00) 		0.93
(1.00)
19q gain 0 (0%) 479 0.00981
(1.00) 		0.117
(1.00) 		0.768
(1.00) 		0.101
(1.00) 		1.24e-06
(0.00136) 		0.00147
(1.00) 		0.0152
(1.00) 		0.197
(1.00) 		0.558
(1.00) 		0.525
(1.00) 		0.235
(1.00) 		0.187
(1.00) 		0.221
(1.00) 		0.502
(1.00)
21q gain 0 (0%) 500 0.374
(1.00) 		0.231
(1.00) 		0.5
(1.00) 		0.646
(1.00) 		2.2e-05
(0.0238) 		0.000289
(0.307) 		0.29
(1.00) 		0.259
(1.00) 		0.371
(1.00) 		0.171
(1.00) 		0.231
(1.00) 		0.683
(1.00) 		0.345
(1.00) 		0.512
(1.00)
9p loss 0 (0%) 358 0.00315
(1.00) 		0.00165
(1.00) 		0.739
(1.00) 		0.00965
(1.00) 		0.0157
(1.00) 		0.000218
(0.232) 		0.674
(1.00) 		0.976
(1.00) 		0.567
(1.00) 		0.134
(1.00) 		0.0402
(1.00) 		0.331
(1.00) 		0.0494
(1.00) 		0.425
(1.00)
9q loss 0 (0%) 329 0.00215
(1.00) 		0.00548
(1.00) 		0.185
(1.00) 		0.00339
(1.00) 		3.3e-12
(3.67e-09) 		0.00267
(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) 		0.1
(1.00) 		0.00919
(1.00)
13q loss 0 (0%) 307 0.0649
(1.00) 		0.0448
(1.00) 		0.649
(1.00) 		0.52
(1.00) 		0.00119
(1.00) 		3.22e-06
(0.00352) 		0.0021
(1.00) 		0.00341
(1.00) 		0.297
(1.00) 		0.985
(1.00) 		0.388
(1.00) 		0.897
(1.00) 		0.256
(1.00) 		0.83
(1.00)
14q loss 0 (0%) 406 0.0841
(1.00) 		0.0675
(1.00) 		0.874
(1.00) 		0.698
(1.00) 		8.1e-05
(0.087) 		0.00807
(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) 		0.689
(1.00) 		0.562
(1.00)
1p gain 0 (0%) 465 0.163
(1.00) 		0.313
(1.00) 		0.12
(1.00) 		0.801
(1.00) 		0.197
(1.00) 		0.848
(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) 		0.0287
(1.00) 		1
(1.00)
3p gain 0 (0%) 461 0.363
(1.00) 		0.643
(1.00) 		0.156
(1.00) 		0.464
(1.00) 		0.00189
(1.00) 		0.444
(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) 		0.799
(1.00) 		0.307
(1.00)
4p gain 0 (0%) 539 0.838
(1.00) 		0.861
(1.00) 		0.0052
(1.00) 		0.391
(1.00) 		0.0904
(1.00) 		0.1
(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) 		0.179
(1.00) 		0.113
(1.00)
4q gain 0 (0%) 554 0.948
(1.00) 		0.618
(1.00) 		0.686
(1.00) 		0.901
(1.00) 		0.35
(1.00) 		0.0373
(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) 		0.00157
(1.00) 		0.0626
(1.00)
5q gain 0 (0%) 536 0.0417
(1.00) 		0.115
(1.00) 		0.919
(1.00) 		0.265
(1.00) 		0.598
(1.00) 		0.346
(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) 		0.177
(1.00) 		0.421
(1.00)
8p gain 0 (0%) 484 0.205
(1.00) 		0.0868
(1.00) 		0.954
(1.00) 		0.138
(1.00) 		0.277
(1.00) 		0.719
(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) 		0.889
(1.00) 		0.3
(1.00)
8q gain 0 (0%) 366 0.0565
(1.00) 		0.154
(1.00) 		0.0728
(1.00) 		0.615
(1.00) 		0.0167
(1.00) 		0.981
(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) 		0.428
(1.00) 		0.801
(1.00)
9p gain 0 (0%) 507 0.0169
(1.00) 		0.305
(1.00) 		0.318
(1.00) 		0.659
(1.00) 		0.0105
(1.00) 		0.00953
(1.00) 		0.184
(1.00) 		0.688
(1.00) 		0.896
(1.00) 		0.587
(1.00) 		0.157
(1.00) 		0.748
(1.00) 		0.734
(1.00) 		0.293
(1.00)
9q gain 0 (0%) 541 0.499
(1.00) 		0.705
(1.00) 		0.26
(1.00) 		0.23
(1.00) 		0.283
(1.00) 		0.234
(1.00) 		0.519
(1.00) 		0.208
(1.00) 		0.813
(1.00) 		0.0484
(1.00) 		0.749
(1.00) 		0.871
(1.00) 		0.769
(1.00) 		0.897
(1.00)
10q gain 0 (0%) 502 0.00969
(1.00) 		0.025
(1.00) 		0.785
(1.00) 		0.0311
(1.00) 		0.0152
(1.00) 		0.0106
(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) 		0.753
(1.00) 		0.25
(1.00)
11p gain 0 (0%) 530 0.393
(1.00) 		0.157
(1.00) 		0.282
(1.00) 		0.271
(1.00) 		0.0142
(1.00) 		0.0314
(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) 		0.306
(1.00) 		0.33
(1.00)
13q gain 0 (0%) 529 0.0627
(1.00) 		0.0259
(1.00) 		0.932
(1.00) 		0.00645
(1.00) 		0.000616
(0.65) 		0.000597
(0.631) 		0.701
(1.00) 		0.361
(1.00) 		0.451
(1.00) 		0.949
(1.00) 		0.194
(1.00) 		0.536
(1.00) 		0.676
(1.00) 		0.368
(1.00)
14q gain 0 (0%) 536 0.0119
(1.00) 		0.0403
(1.00) 		0.619
(1.00) 		0.0055
(1.00) 		0.95
(1.00) 		0.145
(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) 		0.463
(1.00) 		0.643
(1.00)
15q gain 0 (0%) 545 0.319
(1.00) 		0.151
(1.00) 		0.369
(1.00) 		0.628
(1.00) 		0.278
(1.00) 		0.597
(1.00) 		0.166
(1.00) 		0.824
(1.00) 		1
(1.00) 		1
(1.00) 		0.638
(1.00) 		0.54
(1.00) 		0.769
(1.00) 		0.332
(1.00)
16p gain 0 (0%) 540 0.0633
(1.00) 		0.0565
(1.00) 		0.971
(1.00) 		0.402
(1.00) 		0.167
(1.00) 		0.152
(1.00) 		0.675
(1.00) 		0.101
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.72
(1.00) 		0.878
(1.00) 		0.581
(1.00)
16q gain 0 (0%) 554 0.0133
(1.00) 		0.225
(1.00) 		0.286
(1.00) 		0.0938
(1.00) 		0.903
(1.00) 		0.061
(1.00) 		0.512
(1.00) 		0.124
(1.00) 		0.119
(1.00) 		0.269
(1.00) 		0.119
(1.00) 		0.0759
(1.00)
17p gain 0 (0%) 558 0.264
(1.00) 		0.201
(1.00) 		0.221
(1.00) 		0.645
(1.00) 		0.0431
(1.00) 		0.407
(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) 		0.343
(1.00) 		0.11
(1.00)
17q gain 0 (0%) 546 0.893
(1.00) 		0.708
(1.00) 		0.136
(1.00) 		0.221
(1.00) 		0.0516
(1.00) 		0.306
(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) 		0.83
(1.00) 		0.235
(1.00)
18q gain 0 (0%) 529 0.439
(1.00) 		0.426
(1.00) 		0.678
(1.00) 		0.418
(1.00) 		0.0892
(1.00) 		0.0444
(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) 		0.137
(1.00) 		0.597
(1.00)
22q gain 0 (0%) 561 0.382
(1.00) 		0.0979
(1.00) 		0.527
(1.00) 		0.4
(1.00) 		0.205
(1.00) 		0.918
(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) 		0.0832
(1.00) 		0.506
(1.00)
Xq gain 0 (0%) 535 0.133
(1.00) 		0.19
(1.00) 		0.95
(1.00) 		0.19
(1.00) 		0.00898
(1.00) 		0.0495
(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) 		0.00203
(1.00) 		0.606
(1.00)
1p loss 0 (0%) 535 0.00452
(1.00) 		0.041
(1.00) 		0.164
(1.00) 		0.401
(1.00) 		0.951
(1.00) 		0.209
(1.00) 		0.503
(1.00) 		0.514
(1.00) 		0.736
(1.00) 		0.361
(1.00) 		1
(1.00) 		1
(1.00) 		0.129
(1.00) 		0.818
(1.00)
1q loss 0 (0%) 548 0.0183
(1.00) 		0.0226
(1.00) 		0.00944
(1.00) 		0.106
(1.00) 		0.227
(1.00) 		0.559
(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) 		0.449
(1.00) 		0.629
(1.00)
2p loss 0 (0%) 544 0.667
(1.00) 		0.519
(1.00) 		0.935
(1.00) 		0.0398
(1.00) 		0.357
(1.00) 		0.937
(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) 		0.485
(1.00) 		0.897
(1.00)
2q loss 0 (0%) 540 0.765
(1.00) 		0.583
(1.00) 		0.943
(1.00) 		0.0412
(1.00) 		0.515
(1.00) 		0.372
(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) 		0.598
(1.00) 		0.497
(1.00)
3p loss 0 (0%) 509 0.075
(1.00) 		0.0554
(1.00) 		0.895
(1.00) 		0.618
(1.00) 		0.00178
(1.00) 		0.0538
(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) 		0.83
(1.00) 		0.0641
(1.00)
3q loss 0 (0%) 547 0.267
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.0931
(1.00) 		0.279
(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) 		1
(1.00) 		0.382
(1.00)
4p loss 0 (0%) 306 0.189
(1.00) 		0.6
(1.00) 		0.473
(1.00) 		0.785
(1.00) 		0.0107
(1.00) 		0.932
(1.00) 		0.145
(1.00) 		0.243
(1.00) 		0.152
(1.00) 		0.292
(1.00) 		0.0486
(1.00) 		0.0135
(1.00) 		0.0211
(1.00) 		0.0146
(1.00)
4q loss 0 (0%) 267 0.0794
(1.00) 		0.37
(1.00) 		0.404
(1.00) 		0.229
(1.00) 		0.00225
(1.00) 		0.754
(1.00) 		0.286
(1.00) 		0.0925
(1.00) 		0.47
(1.00) 		0.0357
(1.00) 		0.0471
(1.00) 		0.000253
(0.268) 		0.00552
(1.00) 		0.00346
(1.00)
5p loss 0 (0%) 483 0.345
(1.00) 		0.249
(1.00) 		0.352
(1.00) 		0.248
(1.00) 		0.0121
(1.00) 		0.0123
(1.00) 		0.161
(1.00) 		0.0995
(1.00) 		0.000407
(0.43) 		0.562
(1.00) 		0.894
(1.00) 		0.558
(1.00) 		0.827
(1.00) 		0.0811
(1.00)
6p loss 0 (0%) 444 0.991
(1.00) 		0.257
(1.00) 		0.64
(1.00) 		0.598
(1.00) 		0.233
(1.00) 		0.194
(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) 		0.0331
(1.00) 		0.811
(1.00)
6q loss 0 (0%) 372 0.96
(1.00) 		0.381
(1.00) 		0.928
(1.00) 		0.385
(1.00) 		0.108
(1.00) 		0.119
(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) 		0.0757
(1.00) 		0.707
(1.00)
7p loss 0 (0%) 479 0.914
(1.00) 		0.259
(1.00) 		0.361
(1.00) 		0.353
(1.00) 		0.0816
(1.00) 		0.105
(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) 		0.259
(1.00) 		0.458
(1.00)
7q loss 0 (0%) 522 0.778
(1.00) 		0.414
(1.00) 		0.488
(1.00) 		0.611
(1.00) 		0.272
(1.00) 		0.0288
(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) 		0.115
(1.00) 		1
(1.00)
8p loss 0 (0%) 334 0.715
(1.00) 		0.669
(1.00) 		0.963
(1.00) 		0.521
(1.00) 		0.0041
(1.00) 		0.122
(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) 		0.968
(1.00) 		0.263
(1.00)
8q loss 0 (0%) 506 0.0465
(1.00) 		0.473
(1.00) 		0.289
(1.00) 		0.134
(1.00) 		0.00697
(1.00) 		0.113
(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) 		0.866
(1.00) 		0.599
(1.00)
10p loss 0 (0%) 503 0.413
(1.00) 		0.696
(1.00) 		0.269
(1.00) 		0.757
(1.00) 		0.778
(1.00) 		0.882
(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) 		0.0783
(1.00) 		0.432
(1.00)
10q loss 0 (0%) 479 0.538
(1.00) 		0.112
(1.00) 		0.0867
(1.00) 		0.924
(1.00) 		0.247
(1.00) 		0.438
(1.00) 		0.259
(1.00) 		0.227
(1.00) 		0.763
(1.00) 		0.26
(1.00) 		0.248
(1.00) 		0.222
(1.00) 		0.543
(1.00) 		0.733
(1.00)
11p loss 0 (0%) 424 0.0203
(1.00) 		0.00752
(1.00) 		0.0826
(1.00) 		0.263
(1.00) 		0.0633
(1.00) 		0.00175
(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) 		0.0692
(1.00) 		0.402
(1.00)
11q loss 0 (0%) 463 0.169
(1.00) 		0.168
(1.00) 		0.00554
(1.00) 		0.0751
(1.00) 		0.094
(1.00) 		0.0251
(1.00) 		0.845
(1.00) 		0.0995
(1.00) 		0.0733
(1.00) 		0.797
(1.00) 		0.282
(1.00) 		0.156
(1.00) 		0.0419
(1.00) 		0.0339
(1.00)
12p loss 0 (0%) 519 0.465
(1.00) 		0.219
(1.00) 		0.964
(1.00) 		0.834
(1.00) 		0.00776
(1.00) 		0.247
(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) 		0.354
(1.00) 		0.602
(1.00)
12q loss 0 (0%) 494 0.094
(1.00) 		0.0174
(1.00) 		0.798
(1.00) 		0.558
(1.00) 		0.00279
(1.00) 		0.146
(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) 		0.365
(1.00) 		0.579
(1.00)
16p loss 0 (0%) 299 0.941
(1.00) 		0.835
(1.00) 		0.355
(1.00) 		0.976
(1.00) 		0.0508
(1.00) 		0.0824
(1.00) 		0.888
(1.00) 		0.931
(1.00) 		0.367
(1.00) 		0.72
(1.00) 		0.228
(1.00) 		0.591
(1.00) 		0.477
(1.00) 		0.239
(1.00)
16q loss 0 (0%) 208 0.98
(1.00) 		0.568
(1.00) 		0.174
(1.00) 		0.408
(1.00) 		0.0159
(1.00) 		0.121
(1.00) 		0.733
(1.00) 		0.973
(1.00) 		0.492
(1.00) 		0.812
(1.00) 		0.318
(1.00) 		0.117
(1.00) 		0.142
(1.00) 		0.195
(1.00)
17p loss 0 (0%) 141 0.171
(1.00) 		0.00405
(1.00) 		0.699
(1.00) 		0.389
(1.00) 		0.271
(1.00) 		0.0311
(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) 		0.162
(1.00) 		0.712
(1.00)
18p loss 0 (0%) 383 0.581
(1.00) 		0.913
(1.00) 		0.245
(1.00) 		0.688
(1.00) 		0.186
(1.00) 		0.0243
(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) 		0.696
(1.00) 		0.565
(1.00)
18q loss 0 (0%) 334 0.0688
(1.00) 		0.26
(1.00) 		0.524
(1.00) 		0.472
(1.00) 		0.759
(1.00) 		0.512
(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) 		0.573
(1.00) 		0.168
(1.00)
19p loss 0 (0%) 423 0.787
(1.00) 		0.173
(1.00) 		0.203
(1.00) 		0.131
(1.00) 		0.112
(1.00) 		0.0756
(1.00) 		0.0177
(1.00) 		0.12
(1.00) 		0.466
(1.00) 		0.71
(1.00) 		0.972
(1.00) 		0.755
(1.00) 		0.923
(1.00) 		1
(1.00)
19q loss 0 (0%) 424 0.33
(1.00) 		0.119
(1.00) 		0.215
(1.00) 		0.389
(1.00) 		0.159
(1.00) 		0.626
(1.00) 		0.0454
(1.00) 		0.393
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.206
(1.00) 		0.358
(1.00) 		0.352
(1.00) 		0.356
(1.00)
20p loss 0 (0%) 532 0.322
(1.00) 		0.542
(1.00) 		0.414
(1.00) 		0.345
(1.00) 		0.157
(1.00) 		0.463
(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) 		0.0387
(1.00) 		0.765
(1.00)
20q loss 0 (0%) 548 0.689
(1.00) 		0.959
(1.00) 		0.16
(1.00) 		0.886
(1.00) 		0.48
(1.00) 		0.891
(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) 		0.33
(1.00) 		0.737
(1.00)
21q loss 0 (0%) 418 0.257
(1.00) 		0.157
(1.00) 		0.248
(1.00) 		0.0346
(1.00) 		0.607
(1.00) 		0.0135
(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) 		0.0298
(1.00) 		0.672
(1.00)
Xq loss 0 (0%) 469 0.0862
(1.00) 		0.336
(1.00) 		0.0147
(1.00) 		0.027
(1.00) 		0.168
(1.00) 		0.138
(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) 		0.57
(1.00) 		0.483
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 7.45e-06 (Fisher's exact test), Q value = 0.0081

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
1Q GAIN CNV 38 42 82
1Q GAIN WILD-TYPE 127 163 118

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

'2p gain' versus 'MRNA_CNMF'

P value = 2.56e-09 (Fisher's exact test), Q value = 2.8e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 209 133
2P GAIN CNV 77 22 27
2P GAIN WILD-TYPE 139 187 106

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.88e-09 (Fisher's exact test), Q value = 5.4e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 195 128
2P GAIN CNV 28 72 26
2P GAIN WILD-TYPE 207 123 102

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

'2p gain' versus 'MIR_CHIERARCHICAL'

P value = 6.24e-07 (Fisher's exact test), Q value = 0.00069

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 220 157
2P GAIN CNV 64 29 33
2P GAIN WILD-TYPE 115 191 124

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

'2p gain' versus 'CN_CNMF'

P value = 7.24e-11 (Fisher's exact test), Q value = 8e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
2P GAIN CNV 22 29 79
2P GAIN WILD-TYPE 143 176 121

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 8.05e-11 (Fisher's exact test), Q value = 8.9e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
2P GAIN CNV 72 34 24
2P GAIN WILD-TYPE 110 134 195

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 = 7.16e-07 (Fisher's exact test), Q value = 0.00079

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 209 133
2Q GAIN CNV 62 20 18
2Q GAIN WILD-TYPE 154 189 115

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

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.2e-06 (Fisher's exact test), Q value = 0.0068

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 195 128
2Q GAIN CNV 25 56 19
2Q GAIN WILD-TYPE 210 139 109

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

'2q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 220 157
2Q GAIN CNV 49 25 26
2Q GAIN WILD-TYPE 130 195 131

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

'2q gain' versus 'CN_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 3.4e-05

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
2Q GAIN CNV 17 24 63
2Q GAIN WILD-TYPE 148 181 137

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.012

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
2Q GAIN CNV 54 25 25
2Q GAIN WILD-TYPE 128 143 194

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 5.99e-09 (Fisher's exact test), Q value = 6.6e-06

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
3Q GAIN CNV 39 63 106
3Q GAIN WILD-TYPE 126 142 94

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 4.44e-07 (Fisher's exact test), Q value = 0.00049

Table S14.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
5P GAIN CNV 18 64 64
5P GAIN WILD-TYPE 147 141 136

Figure S14.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.0016

Table S15.  Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
6P GAIN CNV 15 46 61
6P GAIN WILD-TYPE 150 159 139

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.013

Table S16.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
6Q GAIN CNV 5 21 36
6Q GAIN WILD-TYPE 160 184 164

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

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
6Q GAIN CNV 35 10 17
6Q GAIN WILD-TYPE 147 158 202

Figure S17.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3.54e-08 (Fisher's exact test), Q value = 3.9e-05

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
7P GAIN CNV 24 30 73
7P GAIN WILD-TYPE 141 175 127

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

'7p gain' versus 'METHLYATION_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
7P GAIN CNV 63 26 38
7P GAIN WILD-TYPE 119 142 181

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 4.33e-06 (Fisher's exact test), Q value = 0.0047

Table S20.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
7Q GAIN CNV 33 42 80
7Q GAIN WILD-TYPE 132 163 120

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

'10p gain' versus 'CN_CNMF'

P value = 2.41e-09 (Fisher's exact test), Q value = 2.7e-06

Table S21.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
10P GAIN CNV 19 37 76
10P GAIN WILD-TYPE 146 168 124

Figure S21.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.17

Table S22.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
10P GAIN CNV 62 33 37
10P GAIN WILD-TYPE 120 135 182

Figure S22.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.021

Table S23.  Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
11Q GAIN CNV 4 32 26
11Q GAIN WILD-TYPE 161 173 174

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

'12p gain' versus 'MRNA_CNMF'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 209 133
12P GAIN CNV 104 58 41
12P GAIN WILD-TYPE 112 151 92

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

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.022

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 195 128
12P GAIN CNV 66 96 41
12P GAIN WILD-TYPE 169 99 87

Figure S25.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 6.57e-14 (Fisher's exact test), Q value = 7.3e-11

Table S26.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
12P GAIN CNV 37 56 116
12P GAIN WILD-TYPE 128 149 84

Figure S26.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3.88e-09 (Fisher's exact test), Q value = 4.3e-06

Table S27.  Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
12P GAIN CNV 99 56 54
12P GAIN WILD-TYPE 83 112 165

Figure S27.  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 S28.  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 S28.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNA_CHIERARCHICAL'

P value = 7.92e-06 (Fisher's exact test), Q value = 0.0086

Table S29.  Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 195 128
12Q GAIN CNV 36 64 18
12Q GAIN WILD-TYPE 199 131 110

Figure S29.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 6.43e-15 (Fisher's exact test), Q value = 7.2e-12

Table S30.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
12Q GAIN CNV 24 18 81
12Q GAIN WILD-TYPE 141 187 119

Figure S30.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0031

Table S31.  Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
12Q GAIN CNV 63 28 32
12Q GAIN WILD-TYPE 119 140 187

Figure S31.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.000217 (Fisher's exact test), Q value = 0.23

Table S32.  Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
18P GAIN CNV 39 12 23
18P GAIN WILD-TYPE 143 156 196

Figure S32.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 7.71e-08 (Fisher's exact test), Q value = 8.5e-05

Table S33.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
19P GAIN CNV 16 23 60
19P GAIN WILD-TYPE 149 182 140

Figure S33.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

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

Table S34.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
19Q GAIN CNV 14 23 54
19Q GAIN WILD-TYPE 151 182 146

Figure S34.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 2.05e-15 (Fisher's exact test), Q value = 2.3e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
20P GAIN CNV 42 65 128
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 = 2.76e-11 (Fisher's exact test), Q value = 3.1e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
20P GAIN CNV 113 58 64
20P GAIN WILD-TYPE 69 110 155

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

'20q gain' versus 'MRNA_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 209 133
20Q GAIN CNV 128 76 64
20Q GAIN WILD-TYPE 88 133 69

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

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.72e-06 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 195 128
20Q GAIN CNV 89 119 60
20Q GAIN WILD-TYPE 146 76 68

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

'20q gain' versus 'CN_CNMF'

P value = 1.57e-20 (Fisher's exact test), Q value = 1.8e-17

Table S39.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
20Q GAIN CNV 45 81 148
20Q GAIN WILD-TYPE 120 124 52

Figure S39.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 3.04e-15 (Fisher's exact test), Q value = 3.4e-12

Table S40.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
20Q GAIN CNV 132 68 74
20Q GAIN WILD-TYPE 50 100 145

Figure S40.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 2.2e-05 (Fisher's exact test), Q value = 0.024

Table S41.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
21Q GAIN CNV 10 18 42
21Q GAIN WILD-TYPE 155 187 158

Figure S41.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'MRNA_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.12

Table S42.  Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 209 133
5Q LOSS CNV 88 54 28
5Q LOSS WILD-TYPE 128 155 105

Figure S42.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 4.39e-05 (Fisher's exact test), Q value = 0.047

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
5Q LOSS CNV 36 53 84
5Q LOSS WILD-TYPE 129 152 116

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

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.41e-07 (Fisher's exact test), Q value = 0.00015

Table S44.  Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
5Q LOSS CNV 84 34 55
5Q LOSS WILD-TYPE 98 134 164

Figure S44.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.23

Table S45.  Gene #57: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
9P LOSS CNV 77 76 59
9P LOSS WILD-TYPE 105 92 160

Figure S45.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 3.3e-12 (Fisher's exact test), Q value = 3.7e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
9Q LOSS CNV 61 56 124
9Q LOSS WILD-TYPE 104 149 76

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

'13q loss' versus 'METHLYATION_CNMF'

P value = 3.22e-06 (Fisher's exact test), Q value = 0.0035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
13Q LOSS CNV 85 53 125
13Q LOSS WILD-TYPE 97 115 94

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

'14q loss' versus 'CN_CNMF'

P value = 8.1e-05 (Fisher's exact test), Q value = 0.087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
14Q LOSS CNV 40 44 80
14Q LOSS WILD-TYPE 125 161 120

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

'15q loss' versus 'CN_CNMF'

P value = 1.11e-10 (Fisher's exact test), Q value = 1.2e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
15Q LOSS CNV 47 58 115
15Q LOSS WILD-TYPE 118 147 85

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

'15q loss' versus 'METHLYATION_CNMF'

P value = 2.47e-05 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 168 219
15Q LOSS CNV 95 50 75
15Q LOSS WILD-TYPE 87 118 144

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

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000207 (Fisher's exact test), Q value = 0.22

Table S51.  Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 195 128
17Q LOSS CNV 159 105 60
17Q LOSS WILD-TYPE 76 90 68

Figure S51.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.051

Table S52.  Gene #71: '17q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 195 157
17Q LOSS CNV 37 127 100
17Q LOSS WILD-TYPE 58 68 57

Figure S52.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.047

Table S53.  Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 209 133
22Q LOSS CNV 170 126 82
22Q LOSS WILD-TYPE 46 83 51

Figure S53.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.000156 (Fisher's exact test), Q value = 0.17

Table S54.  Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 205 200
22Q LOSS CNV 102 128 158
22Q LOSS WILD-TYPE 63 77 42

Figure S54.  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 = 570

  • 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

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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] 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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