Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1VM49KW
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/C1VM49KW
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 77 arm-level results and 12 molecular subtypes across 427 patients, 88 significant findings detected with Q value < 0.25.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 21q loss cnv correlated to 'CN_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 77 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 88 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
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
20q gain 0 (0%) 153 1.14e-12
(9.5e-10) 		4.97e-15
(4.21e-12) 		1.22e-44
(1.05e-41) 		2.01e-11
(1.67e-08) 		3.09e-05
(0.0248) 		1.58e-06
(0.00128) 		2.58e-14
(2.17e-11) 		1.39e-16
(1.19e-13) 		0.478
(1.00) 		0.000353
(0.273) 		1.57e-12
(1.31e-09) 		0.057
(1.00)
18p loss 0 (0%) 208 3.93e-13
(3.29e-10) 		3.83e-10
(3.17e-07) 		2.22e-47
(1.92e-44) 		8.46e-15
(7.16e-12) 		0.000275
(0.214) 		0.000381
(0.294) 		4.47e-15
(3.79e-12) 		1.38e-14
(1.17e-11) 		0.648
(1.00) 		0.0233
(1.00) 		3.92e-14
(3.3e-11) 		0.000892
(0.675)
13q gain 0 (0%) 210 1.06e-05
(0.00854) 		1.66e-05
(0.0134) 		2.2e-29
(1.89e-26) 		6.37e-05
(0.0506) 		0.00884
(1.00) 		0.0051
(1.00) 		1.49e-05
(0.012) 		2.24e-07
(0.000184) 		0.195
(1.00) 		0.212
(1.00) 		1.48e-07
(0.000122) 		0.813
(1.00)
17p loss 0 (0%) 255 3.77e-05
(0.03) 		5.37e-06
(0.00435) 		8.7e-22
(7.47e-19) 		4.78e-08
(3.93e-05) 		0.0623
(1.00) 		0.0552
(1.00) 		1.59e-07
(0.00013) 		2.11e-08
(1.74e-05) 		0.367
(1.00) 		0.152
(1.00) 		5.08e-09
(4.2e-06) 		0.0141
(1.00)
18q loss 0 (0%) 193 3.42e-13
(2.87e-10) 		8.79e-11
(7.3e-08) 		1.1e-44
(9.5e-42) 		6.41e-16
(5.46e-13) 		0.00368
(1.00) 		0.00138
(1.00) 		7.16e-15
(6.06e-12) 		9.08e-16
(7.73e-13) 		0.316
(1.00) 		0.0283
(1.00) 		2.5e-12
(2.08e-09) 		0.0455
(1.00)
14q loss 0 (0%) 331 3.18e-08
(2.62e-05) 		2.14e-06
(0.00174) 		1.43e-20
(1.23e-17) 		4.01e-06
(0.00326) 		0.00106
(0.799) 		0.0266
(1.00) 		1.94e-05
(0.0156) 		3.63e-05
(0.0289) 		0.268
(1.00) 		0.00596
(1.00) 		0.000593
(0.453) 		0.0478
(1.00)
7p gain 0 (0%) 221 0.00304
(1.00) 		0.00223
(1.00) 		1.01e-14
(8.48e-12) 		6.74e-05
(0.0534) 		0.0059
(1.00) 		0.0397
(1.00) 		1.25e-06
(0.00102) 		7.37e-06
(0.00596) 		0.654
(1.00) 		0.15
(1.00) 		5.95e-05
(0.0473) 		0.394
(1.00)
20p gain 0 (0%) 233 0.0017
(1.00) 		8.7e-07
(0.000712) 		6.89e-17
(5.89e-14) 		0.00287
(1.00) 		0.0112
(1.00) 		0.0371
(1.00) 		6.25e-07
(0.000512) 		2.29e-08
(1.89e-05) 		0.21
(1.00) 		0.00245
(1.00) 		7.97e-05
(0.063) 		0.881
(1.00)
7q gain 0 (0%) 247 0.0145
(1.00) 		0.013
(1.00) 		2.5e-09
(2.07e-06) 		0.00473
(1.00) 		0.105
(1.00) 		0.072
(1.00) 		0.000128
(0.101) 		8.91e-05
(0.0704) 		0.833
(1.00) 		0.242
(1.00) 		0.000563
(0.433) 		0.811
(1.00)
8p loss 0 (0%) 330 0.000332
(0.257) 		0.000581
(0.446) 		2.32e-16
(1.98e-13) 		0.000313
(0.243) 		0.0617
(1.00) 		0.0753
(1.00) 		0.0203
(1.00) 		0.000886
(0.671) 		0.19
(1.00) 		0.0319
(1.00) 		0.000113
(0.0894) 		0.275
(1.00)
8q gain 0 (0%) 260 0.73
(1.00) 		0.691
(1.00) 		1.32e-19
(1.13e-16) 		0.000243
(0.19) 		0.554
(1.00) 		0.0399
(1.00) 		0.0353
(1.00) 		0.0331
(1.00) 		0.151
(1.00) 		0.631
(1.00) 		0.0129
(1.00) 		0.452
(1.00)
11p gain 0 (0%) 407 0.138
(1.00) 		0.00139
(1.00) 		6.93e-05
(0.0549) 		0.000171
(0.135) 		0.548
(1.00) 		0.804
(1.00) 		0.682
(1.00) 		0.367
(1.00) 		0.947
(1.00) 		0.767
(1.00) 		0.317
(1.00) 		0.246
(1.00)
11q gain 0 (0%) 403 0.0214
(1.00) 		0.00277
(1.00) 		4.5e-06
(0.00365) 		0.000296
(0.231) 		0.334
(1.00) 		0.808
(1.00) 		0.166
(1.00) 		0.0347
(1.00) 		0.659
(1.00) 		0.18
(1.00) 		0.0336
(1.00) 		0.247
(1.00)
4p loss 0 (0%) 339 0.00271
(1.00) 		0.0199
(1.00) 		1.25e-13
(1.05e-10) 		0.00255
(1.00) 		0.317
(1.00) 		0.708
(1.00) 		0.000306
(0.238) 		0.00059
(0.452) 		0.13
(1.00) 		0.382
(1.00) 		0.0145
(1.00) 		0.08
(1.00)
11p loss 0 (0%) 405 0.445
(1.00) 		0.068
(1.00) 		0.000254
(0.198) 		0.000226
(0.177) 		0.417
(1.00) 		0.317
(1.00) 		0.00441
(1.00) 		0.00486
(1.00) 		0.0463
(1.00) 		0.274
(1.00) 		0.00409
(1.00) 		0.0369
(1.00)
11q loss 0 (0%) 399 0.288
(1.00) 		0.0386
(1.00) 		9.01e-05
(0.0711) 		1.34e-06
(0.00109) 		0.58
(1.00) 		0.6
(1.00) 		0.176
(1.00) 		0.0378
(1.00) 		0.0842
(1.00) 		0.534
(1.00) 		0.221
(1.00) 		0.564
(1.00)
15q loss 0 (0%) 326 0.0108
(1.00) 		0.00275
(1.00) 		5.43e-18
(4.65e-15) 		0.00453
(1.00) 		0.0467
(1.00) 		0.393
(1.00) 		0.00172
(1.00) 		2.14e-05
(0.0172) 		0.279
(1.00) 		0.00974
(1.00) 		0.0041
(1.00) 		0.463
(1.00)
22q loss 0 (0%) 340 0.00032
(0.249) 		0.000581
(0.446) 		7.06e-13
(5.91e-10) 		0.0343
(1.00) 		0.206
(1.00) 		0.138
(1.00) 		0.000983
(0.742) 		0.00124
(0.929) 		0.289
(1.00) 		0.113
(1.00) 		0.0111
(1.00) 		0.267
(1.00)
8p gain 0 (0%) 342 0.691
(1.00) 		0.357
(1.00) 		8.03e-13
(6.72e-10) 		0.0519
(1.00) 		0.0669
(1.00) 		0.161
(1.00) 		0.446
(1.00) 		0.06
(1.00) 		0.63
(1.00) 		0.193
(1.00) 		0.436
(1.00) 		0.851
(1.00)
16p gain 0 (0%) 360 0.00749
(1.00) 		0.000804
(0.611) 		9.25e-15
(7.81e-12) 		0.118
(1.00) 		0.724
(1.00) 		0.0329
(1.00) 		0.0383
(1.00) 		0.0301
(1.00) 		0.0805
(1.00) 		0.0183
(1.00) 		0.085
(1.00) 		0.956
(1.00)
16q gain 0 (0%) 361 0.00602
(1.00) 		0.00116
(0.873) 		1.41e-15
(1.2e-12) 		0.13
(1.00) 		0.847
(1.00) 		0.0199
(1.00) 		0.0383
(1.00) 		0.0301
(1.00) 		0.164
(1.00) 		0.0149
(1.00) 		0.00874
(1.00) 		0.676
(1.00)
1p loss 0 (0%) 376 0.00283
(1.00) 		0.000972
(0.735) 		3.55e-05
(0.0284) 		0.00492
(1.00) 		0.458
(1.00) 		0.698
(1.00) 		0.152
(1.00) 		0.333
(1.00) 		0.498
(1.00) 		0.0747
(1.00) 		0.269
(1.00) 		0.0199
(1.00)
4q loss 0 (0%) 354 0.00361
(1.00) 		0.0107
(1.00) 		3.56e-11
(2.96e-08) 		0.0014
(1.00) 		0.118
(1.00) 		0.427
(1.00) 		0.000392
(0.303) 		0.00293
(1.00) 		0.00533
(1.00) 		0.0297
(1.00) 		0.0388
(1.00) 		0.0792
(1.00)
5q loss 0 (0%) 388 0.0599
(1.00) 		0.00757
(1.00) 		1.79e-05
(0.0144) 		0.201
(1.00) 		0.00779
(1.00) 		0.242
(1.00) 		0.00163
(1.00) 		0.0103
(1.00) 		0.659
(1.00) 		0.537
(1.00) 		0.0287
(1.00) 		0.475
(1.00)
9p loss 0 (0%) 400 0.81
(1.00) 		0.123
(1.00) 		0.000254
(0.198) 		0.0578
(1.00) 		0.163
(1.00) 		0.33
(1.00) 		0.0535
(1.00) 		0.0451
(1.00) 		0.34
(1.00) 		0.902
(1.00) 		0.105
(1.00) 		0.0454
(1.00)
9q loss 0 (0%) 401 0.308
(1.00) 		0.139
(1.00) 		3.58e-05
(0.0286) 		0.000593
(0.453) 		0.235
(1.00) 		0.33
(1.00) 		0.00361
(1.00) 		0.00775
(1.00) 		0.0935
(1.00) 		0.279
(1.00) 		0.00669
(1.00) 		0.0788
(1.00)
12p loss 0 (0%) 406 0.0792
(1.00) 		0.123
(1.00) 		1.73e-05
(0.0139) 		0.223
(1.00) 		0.419
(1.00) 		0.922
(1.00) 		0.13
(1.00) 		0.00977
(1.00) 		0.43
(1.00) 		0.228
(1.00) 		0.288
(1.00) 		0.205
(1.00)
12q loss 0 (0%) 407 0.208
(1.00) 		0.139
(1.00) 		5.79e-06
(0.00468) 		0.0938
(1.00) 		0.829
(1.00) 		0.88
(1.00) 		0.0149
(1.00) 		0.0617
(1.00) 		0.36
(1.00) 		0.145
(1.00) 		0.0752
(1.00) 		0.205
(1.00)
17q loss 0 (0%) 390 0.0918
(1.00) 		0.227
(1.00) 		0.000174
(0.137) 		0.079
(1.00) 		0.531
(1.00) 		0.428
(1.00) 		0.00247
(1.00) 		0.0245
(1.00) 		0.783
(1.00) 		0.456
(1.00) 		0.0229
(1.00) 		0.0788
(1.00)
21q loss 0 (0%) 351 0.0141
(1.00) 		0.00227
(1.00) 		1.44e-06
(0.00117) 		0.591
(1.00) 		0.393
(1.00) 		0.572
(1.00) 		0.0301
(1.00) 		0.0719
(1.00) 		0.0566
(1.00) 		0.403
(1.00) 		0.217
(1.00) 		0.137
(1.00)
1p gain 0 (0%) 416 0.288
(1.00) 		0.698
(1.00) 		0.178
(1.00) 		0.384
(1.00) 		0.768
(1.00) 		0.244
(1.00) 		0.598
(1.00) 		0.733
(1.00) 		1
(1.00) 		1
(1.00)
1q gain 0 (0%) 378 0.0405
(1.00) 		0.536
(1.00) 		0.0682
(1.00) 		0.199
(1.00) 		0.282
(1.00) 		0.0481
(1.00) 		0.224
(1.00) 		0.291
(1.00) 		0.697
(1.00) 		0.71
(1.00) 		0.15
(1.00) 		0.444
(1.00)
2p gain 0 (0%) 386 0.124
(1.00) 		0.0746
(1.00) 		0.0173
(1.00) 		0.00921
(1.00) 		0.0278
(1.00) 		0.393
(1.00) 		0.00227
(1.00) 		0.08
(1.00) 		0.234
(1.00) 		0.488
(1.00) 		0.107
(1.00) 		0.00799
(1.00)
2q gain 0 (0%) 388 0.0737
(1.00) 		0.051
(1.00) 		0.00652
(1.00) 		0.00165
(1.00) 		0.0464
(1.00) 		0.45
(1.00) 		0.0291
(1.00) 		0.141
(1.00) 		0.275
(1.00) 		0.41
(1.00) 		0.113
(1.00) 		0.121
(1.00)
3p gain 0 (0%) 407 0.298
(1.00) 		0.43
(1.00) 		0.158
(1.00) 		0.388
(1.00) 		0.364
(1.00) 		0.721
(1.00) 		0.844
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.714
(1.00) 		0.756
(1.00) 		0.621
(1.00)
3q gain 0 (0%) 397 0.375
(1.00) 		0.164
(1.00) 		0.00472
(1.00) 		0.234
(1.00) 		0.536
(1.00) 		0.752
(1.00) 		0.131
(1.00) 		0.629
(1.00) 		0.436
(1.00) 		0.746
(1.00) 		0.907
(1.00) 		0.265
(1.00)
4p gain 0 (0%) 424 0.244
(1.00) 		0.185
(1.00)
4q gain 0 (0%) 422 0.251
(1.00) 		0.79
(1.00) 		0.527
(1.00) 		0.543
(1.00)
5p gain 0 (0%) 387 0.218
(1.00) 		0.0988
(1.00) 		0.00203
(1.00) 		0.12
(1.00) 		0.662
(1.00) 		0.971
(1.00) 		0.428
(1.00) 		0.76
(1.00) 		0.575
(1.00) 		0.637
(1.00) 		0.0748
(1.00) 		0.882
(1.00)
5q gain 0 (0%) 405 0.545
(1.00) 		0.631
(1.00) 		0.0555
(1.00) 		0.19
(1.00) 		0.533
(1.00) 		0.293
(1.00) 		0.686
(1.00) 		0.25
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.261
(1.00) 		0.733
(1.00)
6p gain 0 (0%) 374 0.589
(1.00) 		0.0136
(1.00) 		0.000613
(0.467) 		0.373
(1.00) 		0.568
(1.00) 		0.443
(1.00) 		0.25
(1.00) 		0.106
(1.00) 		0.414
(1.00) 		0.515
(1.00) 		0.454
(1.00) 		0.897
(1.00)
6q gain 0 (0%) 380 0.348
(1.00) 		0.0274
(1.00) 		0.00437
(1.00) 		0.228
(1.00) 		0.484
(1.00) 		0.433
(1.00) 		0.466
(1.00) 		0.743
(1.00) 		0.359
(1.00) 		0.59
(1.00) 		0.115
(1.00) 		0.549
(1.00)
9p gain 0 (0%) 379 0.00645
(1.00) 		0.192
(1.00) 		0.152
(1.00) 		0.291
(1.00) 		0.0679
(1.00) 		0.179
(1.00) 		0.52
(1.00) 		0.835
(1.00) 		0.731
(1.00) 		0.436
(1.00) 		0.888
(1.00) 		0.614
(1.00)
9q gain 0 (0%) 387 0.011
(1.00) 		0.073
(1.00) 		0.27
(1.00) 		0.0936
(1.00) 		0.0195
(1.00) 		0.034
(1.00) 		0.294
(1.00) 		0.589
(1.00) 		0.0402
(1.00) 		0.0369
(1.00) 		0.757
(1.00) 		0.038
(1.00)
10p gain 0 (0%) 408 0.691
(1.00) 		0.52
(1.00) 		0.152
(1.00) 		0.023
(1.00) 		0.184
(1.00) 		0.727
(1.00) 		0.695
(1.00) 		0.433
(1.00) 		0.448
(1.00) 		0.515
(1.00) 		0.0029
(1.00) 		0.749
(1.00)
10q gain 0 (0%) 416 0.288
(1.00) 		0.0139
(1.00) 		0.377
(1.00) 		0.498
(1.00) 		0.832
(1.00) 		0.362
(1.00) 		0.167
(1.00) 		0.217
(1.00) 		0.0973
(1.00) 		0.764
(1.00)
12p gain 0 (0%) 361 0.267
(1.00) 		0.382
(1.00) 		0.000544
(0.418) 		0.00505
(1.00) 		0.85
(1.00) 		0.813
(1.00) 		0.665
(1.00) 		0.659
(1.00) 		0.0499
(1.00) 		0.135
(1.00) 		0.0332
(1.00) 		0.248
(1.00)
12q gain 0 (0%) 366 0.341
(1.00) 		0.542
(1.00) 		0.000451
(0.348) 		0.000767
(0.583) 		0.779
(1.00) 		0.669
(1.00) 		0.678
(1.00) 		0.816
(1.00) 		0.00606
(1.00) 		0.115
(1.00) 		0.036
(1.00) 		0.243
(1.00)
14q gain 0 (0%) 411 0.482
(1.00) 		0.443
(1.00) 		0.14
(1.00) 		0.203
(1.00) 		0.285
(1.00) 		0.309
(1.00) 		0.0646
(1.00) 		0.00978
(1.00) 		1
(1.00) 		0.659
(1.00) 		1
(1.00) 		0.65
(1.00)
15q gain 0 (0%) 422 0.109
(1.00) 		0.685
(1.00) 		0.058
(1.00) 		0.0333
(1.00) 		0.66
(1.00) 		0.694
(1.00) 		0.485
(1.00) 		0.44
(1.00) 		0.394
(1.00) 		0.302
(1.00)
17p gain 0 (0%) 417 1
(1.00) 		0.812
(1.00) 		0.603
(1.00) 		0.182
(1.00) 		0.0718
(1.00) 		0.131
(1.00) 		0.568
(1.00) 		0.595
(1.00) 		0.629
(1.00) 		1
(1.00)
17q gain 0 (0%) 381 0.0292
(1.00) 		0.0495
(1.00) 		0.0027
(1.00) 		0.00511
(1.00) 		0.91
(1.00) 		0.226
(1.00) 		0.00317
(1.00) 		0.00961
(1.00) 		0.0379
(1.00) 		0.854
(1.00) 		0.124
(1.00) 		0.221
(1.00)
18p gain 0 (0%) 412 0.144
(1.00) 		0.635
(1.00) 		0.00145
(1.00) 		0.0119
(1.00) 		0.721
(1.00) 		0.968
(1.00) 		0.216
(1.00) 		0.262
(1.00) 		0.13
(1.00) 		0.155
(1.00) 		0.805
(1.00) 		0.66
(1.00)
18q gain 0 (0%) 418 0.0117
(1.00) 		0.019
(1.00) 		0.502
(1.00) 		0.158
(1.00) 		0.0708
(1.00) 		0.147
(1.00) 		0.285
(1.00) 		0.158
(1.00) 		0.45
(1.00) 		0.627
(1.00)
19p gain 0 (0%) 391 0.0563
(1.00) 		0.208
(1.00) 		0.0209
(1.00) 		0.0354
(1.00) 		0.177
(1.00) 		0.0782
(1.00) 		0.213
(1.00) 		0.396
(1.00) 		0.699
(1.00) 		0.758
(1.00) 		0.257
(1.00) 		0.132
(1.00)
19q gain 0 (0%) 383 0.0476
(1.00) 		0.0537
(1.00) 		0.176
(1.00) 		0.102
(1.00) 		0.0555
(1.00) 		0.0129
(1.00) 		0.114
(1.00) 		0.234
(1.00) 		0.904
(1.00) 		0.751
(1.00) 		0.664
(1.00) 		0.356
(1.00)
21q gain 0 (0%) 414 0.17
(1.00) 		0.195
(1.00) 		0.434
(1.00) 		0.203
(1.00) 		0.306
(1.00) 		0.275
(1.00) 		0.587
(1.00) 		0.909
(1.00) 		0.848
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.853
(1.00)
Xq gain 0 (0%) 415 0.0659
(1.00) 		0.777
(1.00) 		0.00394
(1.00) 		0.203
(1.00) 		0.132
(1.00) 		0.426
(1.00) 		0.637
(1.00) 		1
(1.00) 		0.568
(1.00) 		0.342
(1.00) 		0.183
(1.00) 		0.853
(1.00)
1q loss 0 (0%) 409 0.356
(1.00) 		0.135
(1.00) 		0.135
(1.00) 		0.295
(1.00) 		0.373
(1.00) 		0.791
(1.00) 		0.148
(1.00) 		0.403
(1.00) 		0.89
(1.00) 		0.802
(1.00) 		0.434
(1.00) 		0.327
(1.00)
2p loss 0 (0%) 422 0.898
(1.00) 		0.315
(1.00) 		0.065
(1.00) 		0.391
(1.00) 		0.288
(1.00)
2q loss 0 (0%) 421 1
(1.00) 		0.156
(1.00) 		0.316
(1.00) 		0.204
(1.00) 		0.245
(1.00) 		0.181
(1.00) 		0.216
(1.00)
3p loss 0 (0%) 397 0.413
(1.00) 		0.187
(1.00) 		0.000479
(0.369) 		0.33
(1.00) 		0.312
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.15
(1.00) 		0.413
(1.00) 		0.649
(1.00) 		0.123
(1.00) 		0.402
(1.00)
3q loss 0 (0%) 413 0.745
(1.00) 		0.631
(1.00) 		0.278
(1.00) 		1
(1.00) 		0.0163
(1.00) 		0.187
(1.00) 		0.152
(1.00) 		0.635
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.175
(1.00)
5p loss 0 (0%) 403 0.406
(1.00) 		0.118
(1.00) 		0.00112
(0.841) 		0.0827
(1.00) 		0.487
(1.00) 		0.745
(1.00) 		0.0623
(1.00) 		0.0378
(1.00) 		0.832
(1.00) 		0.916
(1.00) 		0.156
(1.00) 		0.402
(1.00)
6p loss 0 (0%) 415 0.456
(1.00) 		0.247
(1.00) 		0.0684
(1.00) 		1
(1.00) 		0.403
(1.00) 		0.942
(1.00) 		0.642
(1.00) 		0.167
(1.00) 		0.652
(1.00) 		0.262
(1.00) 		1
(1.00) 		0.302
(1.00)
6q loss 0 (0%) 406 0.915
(1.00) 		0.789
(1.00) 		0.157
(1.00) 		0.837
(1.00) 		0.528
(1.00) 		0.871
(1.00) 		0.944
(1.00) 		0.394
(1.00) 		0.614
(1.00) 		0.602
(1.00) 		0.694
(1.00) 		0.787
(1.00)
8q loss 0 (0%) 417 0.274
(1.00) 		0.386
(1.00) 		0.0121
(1.00) 		0.577
(1.00) 		0.075
(1.00) 		0.331
(1.00) 		1
(1.00) 		1
(1.00) 		0.0634
(1.00) 		0.371
(1.00) 		1
(1.00) 		0.689
(1.00)
10p loss 0 (0%) 402 0.7
(1.00) 		0.673
(1.00) 		0.0314
(1.00) 		0.813
(1.00) 		0.226
(1.00) 		0.962
(1.00) 		0.461
(1.00) 		0.117
(1.00) 		0.271
(1.00) 		0.329
(1.00) 		0.722
(1.00) 		1
(1.00)
10q loss 0 (0%) 401 0.597
(1.00) 		0.711
(1.00) 		0.00476
(1.00) 		0.661
(1.00) 		0.143
(1.00) 		1
(1.00) 		0.24
(1.00) 		0.0194
(1.00) 		0.675
(1.00) 		0.921
(1.00) 		0.392
(1.00) 		0.564
(1.00)
13q loss 0 (0%) 420 0.312
(1.00) 		0.265
(1.00) 		0.0144
(1.00) 		0.0931
(1.00) 		0.211
(1.00) 		0.624
(1.00) 		0.554
(1.00) 		0.309
(1.00) 		0.394
(1.00) 		0.0464
(1.00)
16p loss 0 (0%) 417 0.274
(1.00) 		0.554
(1.00) 		0.9
(1.00) 		0.0159
(1.00) 		0.927
(1.00) 		0.904
(1.00) 		0.85
(1.00) 		0.531
(1.00) 		1
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.499
(1.00)
16q loss 0 (0%) 419 0.519
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.185
(1.00) 		0.254
(1.00) 		0.493
(1.00) 		0.181
(1.00) 		0.216
(1.00)
19p loss 0 (0%) 411 1
(1.00) 		0.32
(1.00) 		0.031
(1.00) 		0.0289
(1.00) 		0.551
(1.00) 		0.183
(1.00) 		0.000822
(0.624) 		0.0244
(1.00) 		0.471
(1.00) 		0.598
(1.00) 		0.358
(1.00) 		0.0369
(1.00)
19q loss 0 (0%) 414 0.924
(1.00) 		0.381
(1.00) 		0.133
(1.00) 		0.131
(1.00) 		0.864
(1.00) 		0.363
(1.00) 		0.00999
(1.00) 		0.0341
(1.00) 		0.49
(1.00) 		0.6
(1.00) 		0.135
(1.00) 		0.0638
(1.00)
20p loss 0 (0%) 390 0.0508
(1.00) 		0.0544
(1.00) 		0.0013
(0.975) 		0.0838
(1.00) 		0.758
(1.00) 		0.327
(1.00) 		0.472
(1.00) 		0.0476
(1.00) 		0.789
(1.00) 		0.568
(1.00) 		0.322
(1.00) 		0.236
(1.00)
20q loss 0 (0%) 424 0.164
(1.00)
Xq loss 0 (0%) 422 0.82
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.821
(1.00) 		0.716
(1.00) 		0.525
(1.00) 		0.641
(1.00) 		1
(1.00)
'7p gain' versus 'CN_CNMF'

P value = 1.01e-14 (Fisher's exact test), Q value = 8.5e-12

Table S1.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
7P GAIN CNV 123 54 29
7P GAIN WILD-TYPE 61 142 18

Figure S1.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 6.74e-05 (Fisher's exact test), Q value = 0.053

Table S2.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
7P GAIN CNV 76 40 24
7P GAIN WILD-TYPE 38 48 44

Figure S2.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.001

Table S3.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
7P GAIN CNV 22 49 26 14
7P GAIN WILD-TYPE 21 21 31 47

Figure S3.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.37e-06 (Fisher's exact test), Q value = 0.006

Table S4.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
7P GAIN CNV 45 20 46
7P GAIN WILD-TYPE 35 57 28

Figure S4.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.95e-05 (Fisher's exact test), Q value = 0.047

Table S5.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
7P GAIN CNV 53 25 31
7P GAIN WILD-TYPE 26 53 32

Figure S5.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.5e-09 (Fisher's exact test), Q value = 2.1e-06

Table S6.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
7Q GAIN CNV 103 51 26
7Q GAIN WILD-TYPE 81 145 21

Figure S6.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.1

Table S7.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
7Q GAIN CNV 18 42 24 13
7Q GAIN WILD-TYPE 25 28 33 48

Figure S7.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.91e-05 (Fisher's exact test), Q value = 0.07

Table S8.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
7Q GAIN CNV 37 18 42
7Q GAIN WILD-TYPE 43 59 32

Figure S8.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 8.03e-13 (Fisher's exact test), Q value = 6.7e-10

Table S9.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
8P GAIN CNV 26 28 31
8P GAIN WILD-TYPE 158 168 16

Figure S9.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.32e-19 (Fisher's exact test), Q value = 1.1e-16

Table S10.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
8Q GAIN CNV 82 42 43
8Q GAIN WILD-TYPE 102 154 4

Figure S10.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.000243 (Fisher's exact test), Q value = 0.19

Table S11.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
8Q GAIN CNV 63 29 19
8Q GAIN WILD-TYPE 51 59 49

Figure S11.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 6.93e-05 (Fisher's exact test), Q value = 0.055

Table S12.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
11P GAIN CNV 18 2 0
11P GAIN WILD-TYPE 166 194 47

Figure S12.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
11P GAIN CNV 13 0 1
11P GAIN WILD-TYPE 101 88 67

Figure S13.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 4.5e-06 (Fisher's exact test), Q value = 0.0037

Table S14.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
11Q GAIN CNV 21 1 2
11Q GAIN WILD-TYPE 163 195 45

Figure S14.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.23

Table S15.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
11Q GAIN CNV 13 1 0
11Q GAIN WILD-TYPE 101 87 68

Figure S15.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0085

Table S16.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
13Q GAIN CNV 10 45 9 13
13Q GAIN WILD-TYPE 25 16 20 8

Figure S16.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.013

Table S17.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
13Q GAIN CNV 35 10 32
13Q GAIN WILD-TYPE 21 33 15

Figure S17.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 2.2e-29 (Fisher's exact test), Q value = 1.9e-26

Table S18.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
13Q GAIN CNV 147 45 25
13Q GAIN WILD-TYPE 37 151 22

Figure S18.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 6.37e-05 (Fisher's exact test), Q value = 0.051

Table S19.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
13Q GAIN CNV 76 34 28
13Q GAIN WILD-TYPE 38 54 40

Figure S19.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.012

Table S20.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
13Q GAIN CNV 22 46 27 14
13Q GAIN WILD-TYPE 21 24 30 47

Figure S20.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.24e-07 (Fisher's exact test), Q value = 0.00018

Table S21.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
13Q GAIN CNV 46 17 46
13Q GAIN WILD-TYPE 34 60 28

Figure S21.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.48e-07 (Fisher's exact test), Q value = 0.00012

Table S22.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
13Q GAIN CNV 57 22 35
13Q GAIN WILD-TYPE 22 56 28

Figure S22.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 9.25e-15 (Fisher's exact test), Q value = 7.8e-12

Table S23.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
16P GAIN CNV 57 5 5
16P GAIN WILD-TYPE 127 191 42

Figure S23.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1.41e-15 (Fisher's exact test), Q value = 1.2e-12

Table S24.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
16Q GAIN CNV 57 4 5
16Q GAIN WILD-TYPE 127 192 42

Figure S24.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.7e-07 (Fisher's exact test), Q value = 0.00071

Table S25.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20P GAIN CNV 36 7 29
20P GAIN WILD-TYPE 20 36 18

Figure S25.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 6.89e-17 (Fisher's exact test), Q value = 5.9e-14

Table S26.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
20P GAIN CNV 121 46 27
20P GAIN WILD-TYPE 63 150 20

Figure S26.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 6.25e-07 (Fisher's exact test), Q value = 0.00051

Table S27.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
20P GAIN CNV 20 41 24 8
20P GAIN WILD-TYPE 23 29 33 53

Figure S27.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.29e-08 (Fisher's exact test), Q value = 1.9e-05

Table S28.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
20P GAIN CNV 41 11 41
20P GAIN WILD-TYPE 39 66 33

Figure S28.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.97e-05 (Fisher's exact test), Q value = 0.063

Table S29.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
20P GAIN CNV 44 18 30
20P GAIN WILD-TYPE 35 60 33

Figure S29.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1.14e-12 (Fisher's exact test), Q value = 9.5e-10

Table S30.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
20Q GAIN CNV 9 57 14 18
20Q GAIN WILD-TYPE 26 4 15 3

Figure S30.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.97e-15 (Fisher's exact test), Q value = 4.2e-12

Table S31.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20Q GAIN CNV 48 8 42
20Q GAIN WILD-TYPE 8 35 5

Figure S31.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.22e-44 (Fisher's exact test), Q value = 1.1e-41

Table S32.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
20Q GAIN CNV 173 59 42
20Q GAIN WILD-TYPE 11 137 5

Figure S32.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 2.01e-11 (Fisher's exact test), Q value = 1.7e-08

Table S33.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
20Q GAIN CNV 98 37 35
20Q GAIN WILD-TYPE 16 51 33

Figure S33.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.025

Table S34.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 127 26 94
20Q GAIN CNV 57 89 19 40
20Q GAIN WILD-TYPE 21 38 7 54

Figure S34.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0013

Table S35.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
20Q GAIN CNV 11 21 50 123
20Q GAIN WILD-TYPE 15 35 13 57

Figure S35.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 2.58e-14 (Fisher's exact test), Q value = 2.2e-11

Table S36.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
20Q GAIN CNV 25 62 37 13
20Q GAIN WILD-TYPE 18 8 20 48

Figure S36.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-16 (Fisher's exact test), Q value = 1.2e-13

Table S37.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
20Q GAIN CNV 63 16 58
20Q GAIN WILD-TYPE 17 61 16

Figure S37.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.57e-12 (Fisher's exact test), Q value = 1.3e-09

Table S38.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
20Q GAIN CNV 69 25 43
20Q GAIN WILD-TYPE 10 53 20

Figure S38.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 3.55e-05 (Fisher's exact test), Q value = 0.028

Table S39.  Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
1P LOSS CNV 37 11 3
1P LOSS WILD-TYPE 147 185 44

Figure S39.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.25e-13 (Fisher's exact test), Q value = 1.1e-10

Table S40.  Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
4P LOSS CNV 69 13 6
4P LOSS WILD-TYPE 115 183 41

Figure S40.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000306 (Fisher's exact test), Q value = 0.24

Table S41.  Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
4P LOSS CNV 10 24 7 4
4P LOSS WILD-TYPE 33 46 50 57

Figure S41.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 3.56e-11 (Fisher's exact test), Q value = 3e-08

Table S42.  Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
4Q LOSS CNV 58 12 3
4Q LOSS WILD-TYPE 126 184 44

Figure S42.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.79e-05 (Fisher's exact test), Q value = 0.014

Table S43.  Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
5Q LOSS CNV 28 5 6
5Q LOSS WILD-TYPE 156 191 41

Figure S43.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 2.32e-16 (Fisher's exact test), Q value = 2e-13

Table S44.  Gene #52: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
8P LOSS CNV 77 13 7
8P LOSS WILD-TYPE 107 183 40

Figure S44.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.000313 (Fisher's exact test), Q value = 0.24

Table S45.  Gene #52: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
8P LOSS CNV 37 10 9
8P LOSS WILD-TYPE 77 78 59

Figure S45.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.089

Table S46.  Gene #52: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
8P LOSS CNV 25 5 16
8P LOSS WILD-TYPE 54 73 47

Figure S46.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.2

Table S47.  Gene #54: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
9P LOSS CNV 19 3 5
9P LOSS WILD-TYPE 165 193 42

Figure S47.  Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 3.58e-05 (Fisher's exact test), Q value = 0.029

Table S48.  Gene #55: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
9Q LOSS CNV 21 2 3
9Q LOSS WILD-TYPE 163 194 44

Figure S48.  Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.2

Table S49.  Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
11P LOSS CNV 18 2 2
11P LOSS WILD-TYPE 166 194 45

Figure S49.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.000226 (Fisher's exact test), Q value = 0.18

Table S50.  Gene #58: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
11P LOSS CNV 11 0 0
11P LOSS WILD-TYPE 103 88 68

Figure S50.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 9.01e-05 (Fisher's exact test), Q value = 0.071

Table S51.  Gene #59: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
11Q LOSS CNV 22 3 3
11Q LOSS WILD-TYPE 162 193 44

Figure S51.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.0011

Table S52.  Gene #59: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
11Q LOSS CNV 16 0 0
11Q LOSS WILD-TYPE 98 88 68

Figure S52.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.014

Table S53.  Gene #60: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
12P LOSS CNV 19 1 1
12P LOSS WILD-TYPE 165 195 46

Figure S53.  Get High-res Image Gene #60: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 5.79e-06 (Fisher's exact test), Q value = 0.0047

Table S54.  Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
12Q LOSS CNV 19 1 0
12Q LOSS WILD-TYPE 165 195 47

Figure S54.  Get High-res Image Gene #61: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 3.18e-08 (Fisher's exact test), Q value = 2.6e-05

Table S55.  Gene #63: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
14Q LOSS CNV 2 31 1 8
14Q LOSS WILD-TYPE 33 30 28 13

Figure S55.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0017

Table S56.  Gene #63: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
14Q LOSS CNV 21 1 20
14Q LOSS WILD-TYPE 35 42 27

Figure S56.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.43e-20 (Fisher's exact test), Q value = 1.2e-17

Table S57.  Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
14Q LOSS CNV 81 10 5
14Q LOSS WILD-TYPE 103 186 42

Figure S57.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 4.01e-06 (Fisher's exact test), Q value = 0.0033

Table S58.  Gene #63: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
14Q LOSS CNV 38 7 7
14Q LOSS WILD-TYPE 76 81 61

Figure S58.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.016

Table S59.  Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
14Q LOSS CNV 8 26 7 3
14Q LOSS WILD-TYPE 35 44 50 58

Figure S59.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.63e-05 (Fisher's exact test), Q value = 0.029

Table S60.  Gene #63: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
14Q LOSS CNV 21 3 20
14Q LOSS WILD-TYPE 59 74 54

Figure S60.  Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 5.43e-18 (Fisher's exact test), Q value = 4.7e-15

Table S61.  Gene #64: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
15Q LOSS CNV 81 13 7
15Q LOSS WILD-TYPE 103 183 40

Figure S61.  Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.017

Table S62.  Gene #64: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
15Q LOSS CNV 21 3 21
15Q LOSS WILD-TYPE 59 74 53

Figure S62.  Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 3.77e-05 (Fisher's exact test), Q value = 0.03

Table S63.  Gene #67: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
17P LOSS CNV 7 38 7 12
17P LOSS WILD-TYPE 28 23 22 9

Figure S63.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.37e-06 (Fisher's exact test), Q value = 0.0044

Table S64.  Gene #67: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
17P LOSS CNV 30 6 28
17P LOSS WILD-TYPE 26 37 19

Figure S64.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 8.7e-22 (Fisher's exact test), Q value = 7.5e-19

Table S65.  Gene #67: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
17P LOSS CNV 115 31 26
17P LOSS WILD-TYPE 69 165 21

Figure S65.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 4.78e-08 (Fisher's exact test), Q value = 3.9e-05

Table S66.  Gene #67: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
17P LOSS CNV 67 19 19
17P LOSS WILD-TYPE 47 69 49

Figure S66.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.59e-07 (Fisher's exact test), Q value = 0.00013

Table S67.  Gene #67: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
17P LOSS CNV 18 43 20 8
17P LOSS WILD-TYPE 25 27 37 53

Figure S67.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.11e-08 (Fisher's exact test), Q value = 1.7e-05

Table S68.  Gene #67: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
17P LOSS CNV 34 11 44
17P LOSS WILD-TYPE 46 66 30

Figure S68.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.08e-09 (Fisher's exact test), Q value = 4.2e-06

Table S69.  Gene #67: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
17P LOSS CNV 51 14 20
17P LOSS WILD-TYPE 28 64 43

Figure S69.  Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.000174 (Fisher's exact test), Q value = 0.14

Table S70.  Gene #68: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
17Q LOSS CNV 27 6 4
17Q LOSS WILD-TYPE 157 190 43

Figure S70.  Get High-res Image Gene #68: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 3.93e-13 (Fisher's exact test), Q value = 3.3e-10

Table S71.  Gene #69: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18P LOSS CNV 6 51 6 15
18P LOSS WILD-TYPE 29 10 23 6

Figure S71.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.83e-10 (Fisher's exact test), Q value = 3.2e-07

Table S72.  Gene #69: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18P LOSS CNV 35 6 37
18P LOSS WILD-TYPE 21 37 10

Figure S72.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 2.22e-47 (Fisher's exact test), Q value = 1.9e-44

Table S73.  Gene #69: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
18P LOSS CNV 161 32 26
18P LOSS WILD-TYPE 23 164 21

Figure S73.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 8.46e-15 (Fisher's exact test), Q value = 7.2e-12

Table S74.  Gene #69: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
18P LOSS CNV 90 24 24
18P LOSS WILD-TYPE 24 64 44

Figure S74.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.000275 (Fisher's exact test), Q value = 0.21

Table S75.  Gene #69: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 127 26 94
18P LOSS CNV 44 74 14 29
18P LOSS WILD-TYPE 34 53 12 65

Figure S75.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 4.47e-15 (Fisher's exact test), Q value = 3.8e-12

Table S76.  Gene #69: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
18P LOSS CNV 19 58 27 8
18P LOSS WILD-TYPE 24 12 30 53

Figure S76.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-14 (Fisher's exact test), Q value = 1.2e-11

Table S77.  Gene #69: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
18P LOSS CNV 50 10 52
18P LOSS WILD-TYPE 30 67 22

Figure S77.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.92e-14 (Fisher's exact test), Q value = 3.3e-11

Table S78.  Gene #69: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
18P LOSS CNV 61 13 32
18P LOSS WILD-TYPE 18 65 31

Figure S78.  Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 3.42e-13 (Fisher's exact test), Q value = 2.9e-10

Table S79.  Gene #70: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18Q LOSS CNV 6 52 7 15
18Q LOSS WILD-TYPE 29 9 22 6

Figure S79.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.79e-11 (Fisher's exact test), Q value = 7.3e-08

Table S80.  Gene #70: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18Q LOSS CNV 36 6 38
18Q LOSS WILD-TYPE 20 37 9

Figure S80.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1.1e-44 (Fisher's exact test), Q value = 9.5e-42

Table S81.  Gene #70: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
18Q LOSS CNV 164 40 30
18Q LOSS WILD-TYPE 20 156 17

Figure S81.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 6.41e-16 (Fisher's exact test), Q value = 5.5e-13

Table S82.  Gene #70: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
18Q LOSS CNV 96 29 25
18Q LOSS WILD-TYPE 18 59 43

Figure S82.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 7.16e-15 (Fisher's exact test), Q value = 6.1e-12

Table S83.  Gene #70: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 70 57 61
18Q LOSS CNV 23 61 28 11
18Q LOSS WILD-TYPE 20 9 29 50

Figure S83.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.08e-16 (Fisher's exact test), Q value = 7.7e-13

Table S84.  Gene #70: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 77 74
18Q LOSS CNV 51 13 59
18Q LOSS WILD-TYPE 29 64 15

Figure S84.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.5e-12 (Fisher's exact test), Q value = 2.1e-09

Table S85.  Gene #70: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
18Q LOSS CNV 63 18 35
18Q LOSS WILD-TYPE 16 60 28

Figure S85.  Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.0012

Table S86.  Gene #75: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
21Q LOSS CNV 53 18 5
21Q LOSS WILD-TYPE 131 178 42

Figure S86.  Get High-res Image Gene #75: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.25

Table S87.  Gene #76: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
22Q LOSS CNV 2 24 3 6
22Q LOSS WILD-TYPE 33 37 26 15

Figure S87.  Get High-res Image Gene #76: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.06e-13 (Fisher's exact test), Q value = 5.9e-10

Table S88.  Gene #76: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 184 196 47
22Q LOSS CNV 68 15 4
22Q LOSS WILD-TYPE 116 181 43

Figure S88.  Get High-res Image Gene #76: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 427

  • Number of significantly arm-level cnvs = 77

  • 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

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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