Correlation between copy number variations of arm-level result and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1K072KF
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/C1K072KF
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 79 arm-level results and 12 molecular subtypes across 589 patients, 89 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

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

  • 11q gain cnv correlated to 'CN_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'.

  • 17q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_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 'METHLYATION_CNMF'.

  • 4p loss cnv correlated to 'CN_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 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10q loss cnv correlated to 'CN_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',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_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'.

  • 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 89 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%) 177 4.38e-17
(3.91e-14) 		4.38e-16
(3.9e-13) 		1.09e-46
(9.91e-44) 		5.48e-17
(4.88e-14) 		0.000181
(0.149) 		0.000158
(0.131) 		1.96e-17
(1.75e-14) 		2.26e-21
(2.02e-18) 		0.0481
(1.00) 		0.735
(1.00) 		1.22e-12
(1.07e-09) 		0.00352
(1.00)
13q gain 0 (0%) 270 8.56e-07
(0.000734) 		0.000164
(0.135) 		1.82e-39
(1.65e-36) 		5.7e-09
(4.96e-06) 		0.0331
(1.00) 		0.08
(1.00) 		3.26e-06
(0.00276) 		5.2e-07
(0.000447) 		0.000677
(0.546) 		0.705
(1.00) 		1.59e-07
(0.000138) 		0.0386
(1.00)
20p gain 0 (0%) 294 0.000145
(0.12) 		1.65e-07
(0.000142) 		1.38e-17
(1.23e-14) 		6.02e-06
(0.00509) 		0.00413
(1.00) 		0.0222
(1.00) 		1.96e-09
(1.71e-06) 		2.01e-09
(1.75e-06) 		0.281
(1.00) 		0.662
(1.00) 		1.8e-05
(0.0151) 		0.403
(1.00)
14q loss 0 (0%) 443 0.000142
(0.118) 		1.77e-06
(0.0015) 		1.07e-37
(9.7e-35) 		1.34e-07
(0.000116) 		0.0023
(1.00) 		0.00944
(1.00) 		2.87e-05
(0.0241) 		5.35e-06
(0.00453) 		0.105
(1.00) 		0.903
(1.00) 		4.9e-07
(0.000422) 		0.248
(1.00)
18p loss 0 (0%) 254 5.24e-13
(4.62e-10) 		1.58e-11
(1.39e-08) 		9.96e-49
(9.03e-46) 		7.74e-22
(6.95e-19) 		0.00974
(1.00) 		0.0109
(1.00) 		5.84e-14
(5.16e-11) 		8.02e-16
(7.12e-13) 		0.0333
(1.00) 		0.907
(1.00) 		2.21e-14
(1.96e-11) 		0.0128
(1.00)
18q loss 0 (0%) 228 1.36e-12
(1.19e-09) 		4.31e-12
(3.77e-09) 		6.64e-51
(6.03e-48) 		8.81e-23
(7.93e-20) 		0.0311
(1.00) 		0.0948
(1.00) 		2.55e-14
(2.25e-11) 		1.73e-14
(1.53e-11) 		0.00329
(1.00) 		0.518
(1.00) 		2.89e-13
(2.55e-10) 		0.0139
(1.00)
7p gain 0 (0%) 291 0.000828
(0.666) 		0.00122
(0.973) 		4.73e-22
(4.25e-19) 		1.84e-07
(0.000159) 		0.0316
(1.00) 		0.0203
(1.00) 		3.96e-07
(0.000341) 		5.51e-08
(4.79e-05) 		0.0129
(1.00) 		0.0701
(1.00) 		0.000106
(0.0885) 		0.631
(1.00)
17p loss 0 (0%) 333 0.000419
(0.341) 		0.00223
(1.00) 		1.5e-23
(1.36e-20) 		6.11e-08
(5.31e-05) 		0.268
(1.00) 		0.473
(1.00) 		4.73e-05
(0.0396) 		2.78e-08
(2.42e-05) 		0.00953
(1.00) 		0.0128
(1.00) 		2.83e-06
(0.00241) 		0.351
(1.00)
7q gain 0 (0%) 327 0.00129
(1.00) 		0.00905
(1.00) 		1.7e-15
(1.5e-12) 		8.24e-06
(0.00695) 		0.301
(1.00) 		0.18
(1.00) 		2.53e-07
(0.000218) 		9.84e-07
(0.000842) 		0.0289
(1.00) 		0.25
(1.00) 		0.000343
(0.281) 		0.665
(1.00)
8p loss 0 (0%) 442 0.00406
(1.00) 		0.00186
(1.00) 		3.55e-26
(3.2e-23) 		0.000213
(0.174) 		0.0801
(1.00) 		0.0393
(1.00) 		0.0172
(1.00) 		1.73e-06
(0.00147) 		0.415
(1.00) 		0.494
(1.00) 		0.000945
(0.757) 		0.487
(1.00)
15q loss 0 (0%) 431 0.005
(1.00) 		0.00311
(1.00) 		1.86e-18
(1.67e-15) 		0.00803
(1.00) 		0.31
(1.00) 		0.832
(1.00) 		0.00341
(1.00) 		0.000139
(0.116) 		0.49
(1.00) 		0.523
(1.00) 		0.00028
(0.23) 		0.498
(1.00)
2q gain 0 (0%) 529 0.0178
(1.00) 		8.52e-05
(0.0711) 		0.000597
(0.484) 		1.35e-06
(0.00115) 		0.119
(1.00) 		0.806
(1.00) 		0.00469
(1.00) 		0.0128
(1.00) 		0.0966
(1.00) 		0.132
(1.00) 		0.846
(1.00) 		0.157
(1.00)
11p gain 0 (0%) 548 0.0615
(1.00) 		0.275
(1.00) 		9.4e-05
(0.0784) 		0.00014
(0.116) 		0.772
(1.00) 		0.764
(1.00) 		0.102
(1.00) 		0.00308
(1.00) 		0.574
(1.00) 		0.822
(1.00) 		0.0225
(1.00) 		0.0725
(1.00)
9q loss 0 (0%) 552 0.241
(1.00) 		0.0097
(1.00) 		0.000102
(0.0849) 		3.39e-05
(0.0284) 		0.531
(1.00) 		0.209
(1.00) 		0.0159
(1.00) 		0.00969
(1.00) 		0.0199
(1.00) 		0.894
(1.00) 		0.00313
(1.00) 		0.124
(1.00)
2p gain 0 (0%) 528 0.0608
(1.00) 		0.000322
(0.263) 		0.00401
(1.00) 		6.7e-05
(0.056) 		0.0441
(1.00) 		0.357
(1.00) 		0.000978
(0.782) 		0.00673
(1.00) 		0.103
(1.00) 		0.0365
(1.00) 		0.481
(1.00) 		0.00982
(1.00)
3q gain 0 (0%) 536 0.235
(1.00) 		0.0891
(1.00) 		5.4e-06
(0.00457) 		0.032
(1.00) 		0.347
(1.00) 		0.655
(1.00) 		0.118
(1.00) 		0.212
(1.00) 		0.0424
(1.00) 		0.435
(1.00) 		0.104
(1.00) 		0.398
(1.00)
6p gain 0 (0%) 509 0.185
(1.00) 		0.00295
(1.00) 		3.39e-07
(0.000292) 		0.226
(1.00) 		0.79
(1.00) 		0.12
(1.00) 		0.0206
(1.00) 		0.508
(1.00) 		0.807
(1.00) 		0.667
(1.00) 		0.406
(1.00) 		0.968
(1.00)
6q gain 0 (0%) 515 0.309
(1.00) 		0.0401
(1.00) 		1.09e-06
(0.000933) 		0.15
(1.00) 		0.363
(1.00) 		0.0418
(1.00) 		0.365
(1.00) 		0.296
(1.00) 		0.52
(1.00) 		0.758
(1.00) 		0.797
(1.00) 		0.449
(1.00)
8p gain 0 (0%) 478 0.963
(1.00) 		0.717
(1.00) 		1.14e-06
(0.000972) 		0.245
(1.00) 		0.248
(1.00) 		0.185
(1.00) 		0.533
(1.00) 		0.787
(1.00) 		0.517
(1.00) 		0.696
(1.00) 		0.228
(1.00) 		0.723
(1.00)
8q gain 0 (0%) 351 0.145
(1.00) 		0.0172
(1.00) 		1.19e-39
(1.07e-36) 		0.028
(1.00) 		0.13
(1.00) 		0.342
(1.00) 		0.000764
(0.615) 		0.0116
(1.00) 		0.266
(1.00) 		0.534
(1.00) 		0.0186
(1.00) 		0.46
(1.00)
11q gain 0 (0%) 548 0.0956
(1.00) 		0.0299
(1.00) 		6.12e-05
(0.0512) 		0.000489
(0.397) 		0.429
(1.00) 		0.651
(1.00) 		0.0135
(1.00) 		0.00126
(1.00) 		0.678
(1.00) 		0.21
(1.00) 		0.00232
(1.00) 		0.76
(1.00)
16p gain 0 (0%) 492 0.0702
(1.00) 		0.137
(1.00) 		1.41e-16
(1.25e-13) 		0.000928
(0.745) 		0.562
(1.00) 		0.0295
(1.00) 		0.0111
(1.00) 		0.00265
(1.00) 		0.428
(1.00) 		0.431
(1.00) 		0.0885
(1.00) 		0.771
(1.00)
16q gain 0 (0%) 492 0.0766
(1.00) 		0.13
(1.00) 		1.39e-18
(1.25e-15) 		0.00104
(0.834) 		0.582
(1.00) 		0.0182
(1.00) 		0.00658
(1.00) 		0.000669
(0.54) 		0.639
(1.00) 		0.904
(1.00) 		0.0105
(1.00) 		0.474
(1.00)
17q gain 0 (0%) 522 0.0504
(1.00) 		0.035
(1.00) 		0.000658
(0.532) 		0.00462
(1.00) 		0.666
(1.00) 		0.0837
(1.00) 		0.0018
(1.00) 		0.000209
(0.172) 		0.0656
(1.00) 		0.953
(1.00) 		0.783
(1.00) 		0.478
(1.00)
19p gain 0 (0%) 535 0.194
(1.00) 		0.146
(1.00) 		0.00012
(0.0996) 		0.0159
(1.00) 		0.279
(1.00) 		0.0285
(1.00) 		0.0423
(1.00) 		0.0262
(1.00) 		0.713
(1.00) 		0.356
(1.00) 		0.868
(1.00) 		0.849
(1.00)
1p loss 0 (0%) 520 0.194
(1.00) 		0.00358
(1.00) 		0.000397
(0.324) 		0.000115
(0.0956) 		0.954
(1.00) 		0.812
(1.00) 		0.00794
(1.00) 		0.159
(1.00) 		0.226
(1.00) 		0.202
(1.00) 		0.596
(1.00) 		0.145
(1.00)
4p loss 0 (0%) 462 0.176
(1.00) 		0.21
(1.00) 		1.81e-12
(1.58e-09) 		0.00105
(0.841) 		0.387
(1.00) 		0.889
(1.00) 		0.449
(1.00) 		0.0408
(1.00) 		0.0131
(1.00) 		0.675
(1.00) 		0.00445
(1.00) 		0.604
(1.00)
4q loss 0 (0%) 470 0.162
(1.00) 		0.132
(1.00) 		2.62e-13
(2.31e-10) 		0.000437
(0.356) 		0.487
(1.00) 		0.81
(1.00) 		0.511
(1.00) 		0.0851
(1.00) 		0.0134
(1.00) 		0.286
(1.00) 		0.0396
(1.00) 		0.105
(1.00)
5q loss 0 (0%) 528 0.0144
(1.00) 		0.0106
(1.00) 		4.48e-06
(0.0038) 		0.0614
(1.00) 		0.0601
(1.00) 		0.88
(1.00) 		0.0491
(1.00) 		0.019
(1.00) 		0.686
(1.00) 		0.188
(1.00) 		0.00952
(1.00) 		0.143
(1.00)
10q loss 0 (0%) 543 0.335
(1.00) 		0.419
(1.00) 		9.17e-06
(0.00772) 		0.135
(1.00) 		0.0216
(1.00) 		0.772
(1.00) 		0.0653
(1.00) 		0.0444
(1.00) 		0.547
(1.00) 		0.687
(1.00) 		0.122
(1.00) 		0.583
(1.00)
12p loss 0 (0%) 556 0.0938
(1.00) 		0.228
(1.00) 		5.26e-07
(0.000451) 		0.323
(1.00) 		0.829
(1.00) 		0.373
(1.00) 		0.507
(1.00) 		0.891
(1.00) 		0.863
(1.00) 		0.217
(1.00) 		0.175
(1.00) 		0.492
(1.00)
12q loss 0 (0%) 560 0.352
(1.00) 		0.0834
(1.00) 		6.35e-06
(0.00536) 		0.325
(1.00) 		0.784
(1.00) 		0.632
(1.00) 		0.185
(1.00) 		0.265
(1.00) 		0.904
(1.00) 		0.745
(1.00) 		0.43
(1.00) 		0.818
(1.00)
22q loss 0 (0%) 461 0.0148
(1.00) 		0.00606
(1.00) 		3.51e-11
(3.06e-08) 		0.0599
(1.00) 		0.336
(1.00) 		0.264
(1.00) 		0.0815
(1.00) 		0.00656
(1.00) 		0.183
(1.00) 		0.684
(1.00) 		0.00164
(1.00) 		0.361
(1.00)
1p gain 0 (0%) 574 0.408
(1.00) 		0.375
(1.00) 		0.835
(1.00) 		0.316
(1.00) 		0.368
(1.00) 		0.232
(1.00) 		0.742
(1.00) 		0.488
(1.00) 		0.52
(1.00) 		0.836
(1.00) 		0.487
(1.00) 		0.617
(1.00)
1q gain 0 (0%) 508 0.601
(1.00) 		0.967
(1.00) 		0.0194
(1.00) 		0.744
(1.00) 		0.136
(1.00) 		0.179
(1.00) 		0.23
(1.00) 		0.247
(1.00) 		0.0715
(1.00) 		0.357
(1.00) 		0.0654
(1.00) 		0.243
(1.00)
3p gain 0 (0%) 553 0.133
(1.00) 		0.593
(1.00) 		0.00202
(1.00) 		0.225
(1.00) 		0.856
(1.00) 		0.77
(1.00) 		0.729
(1.00) 		0.44
(1.00) 		0.113
(1.00) 		0.0592
(1.00) 		0.307
(1.00) 		0.0634
(1.00)
4p gain 0 (0%) 582 0.418
(1.00) 		0.15
(1.00) 		0.375
(1.00) 		0.339
(1.00) 		0.207
(1.00) 		0.215
(1.00) 		0.133
(1.00) 		0.186
(1.00) 		0.0796
(1.00) 		0.252
(1.00)
4q gain 0 (0%) 581 0.707
(1.00) 		0.719
(1.00) 		0.238
(1.00) 		0.47
(1.00) 		0.598
(1.00) 		0.645
(1.00) 		0.402
(1.00) 		0.042
(1.00)
5p gain 0 (0%) 527 0.138
(1.00) 		0.661
(1.00) 		0.0026
(1.00) 		0.198
(1.00) 		0.509
(1.00) 		0.863
(1.00) 		0.208
(1.00) 		0.0301
(1.00) 		0.915
(1.00) 		0.881
(1.00) 		0.49
(1.00) 		0.954
(1.00)
5q gain 0 (0%) 554 0.527
(1.00) 		0.826
(1.00) 		0.00389
(1.00) 		0.06
(1.00) 		0.917
(1.00) 		0.574
(1.00) 		0.0641
(1.00) 		0.0123
(1.00) 		0.781
(1.00) 		0.262
(1.00) 		0.894
(1.00) 		0.957
(1.00)
9p gain 0 (0%) 508 0.503
(1.00) 		1
(1.00) 		0.0413
(1.00) 		0.601
(1.00) 		0.706
(1.00) 		0.204
(1.00) 		0.369
(1.00) 		0.196
(1.00) 		0.741
(1.00) 		0.64
(1.00) 		0.424
(1.00) 		0.778
(1.00)
9q gain 0 (0%) 524 0.385
(1.00) 		0.854
(1.00) 		0.114
(1.00) 		0.639
(1.00) 		0.582
(1.00) 		0.0336
(1.00) 		1
(1.00) 		0.748
(1.00) 		0.187
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.59
(1.00)
10p gain 0 (0%) 561 0.196
(1.00) 		0.628
(1.00) 		0.0453
(1.00) 		0.0073
(1.00) 		0.474
(1.00) 		0.857
(1.00) 		0.498
(1.00) 		0.39
(1.00) 		0.446
(1.00) 		0.689
(1.00) 		0.0504
(1.00) 		0.526
(1.00)
10q gain 0 (0%) 575 0.887
(1.00) 		0.277
(1.00) 		0.359
(1.00) 		0.0181
(1.00) 		0.377
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.332
(1.00) 		0.529
(1.00) 		0.596
(1.00) 		0.257
(1.00) 		0.456
(1.00)
12p gain 0 (0%) 495 0.521
(1.00) 		0.796
(1.00) 		0.0654
(1.00) 		0.00831
(1.00) 		0.624
(1.00) 		0.17
(1.00) 		0.724
(1.00) 		0.0919
(1.00) 		0.0648
(1.00) 		0.147
(1.00) 		0.00189
(1.00) 		0.0128
(1.00)
12q gain 0 (0%) 508 0.422
(1.00) 		0.903
(1.00) 		0.022
(1.00) 		0.00119
(0.946) 		0.793
(1.00) 		0.246
(1.00) 		0.458
(1.00) 		0.0431
(1.00) 		0.0585
(1.00) 		0.0914
(1.00) 		0.000631
(0.51) 		0.00325
(1.00)
14q gain 0 (0%) 568 0.519
(1.00) 		0.251
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.92
(1.00) 		0.408
(1.00) 		0.178
(1.00) 		0.215
(1.00) 		0.676
(1.00) 		0.807
(1.00) 		0.745
(1.00) 		0.435
(1.00)
15q gain 0 (0%) 582 0.487
(1.00) 		0.876
(1.00) 		0.222
(1.00) 		0.131
(1.00) 		0.74
(1.00) 		0.453
(1.00) 		0.868
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.476
(1.00)
17p gain 0 (0%) 577 0.78
(1.00) 		0.00703
(1.00) 		0.75
(1.00) 		0.697
(1.00) 		0.514
(1.00) 		0.607
(1.00) 		0.666
(1.00) 		0.024
(1.00) 		0.69
(1.00) 		0.904
(1.00) 		1
(1.00) 		0.616
(1.00)
18p gain 0 (0%) 568 0.207
(1.00) 		0.0592
(1.00) 		0.000354
(0.289) 		0.00644
(1.00) 		0.64
(1.00) 		0.897
(1.00) 		0.68
(1.00) 		0.363
(1.00) 		0.486
(1.00) 		0.404
(1.00) 		0.579
(1.00) 		0.854
(1.00)
18q gain 0 (0%) 577 0.0334
(1.00) 		0.00359
(1.00) 		0.77
(1.00) 		0.468
(1.00) 		0.223
(1.00) 		0.356
(1.00) 		0.135
(1.00) 		0.179
(1.00) 		0.194
(1.00) 		1
(1.00)
19q gain 0 (0%) 525 0.0157
(1.00) 		0.0412
(1.00) 		0.00394
(1.00) 		0.0622
(1.00) 		0.0266
(1.00) 		0.0302
(1.00) 		0.208
(1.00) 		0.0957
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.803
(1.00) 		0.221
(1.00)
21q gain 0 (0%) 569 0.456
(1.00) 		0.715
(1.00) 		0.0571
(1.00) 		0.3
(1.00) 		0.305
(1.00) 		0.133
(1.00) 		0.465
(1.00) 		0.933
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.782
(1.00) 		0.764
(1.00)
22q gain 0 (0%) 582 0.691
(1.00) 		0.00703
(1.00) 		0.39
(1.00) 		0.47
(1.00) 		0.926
(1.00) 		0.47
(1.00) 		0.299
(1.00) 		0.109
(1.00) 		0.491
(1.00) 		0.398
(1.00)
Xq gain 0 (0%) 572 0.178
(1.00) 		0.446
(1.00) 		0.0319
(1.00) 		0.392
(1.00) 		0.147
(1.00) 		0.22
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.268
(1.00) 		0.918
(1.00) 		0.398
(1.00) 		0.821
(1.00)
1q loss 0 (0%) 564 0.559
(1.00) 		0.0258
(1.00) 		0.189
(1.00) 		0.0356
(1.00) 		0.747
(1.00) 		0.949
(1.00) 		0.116
(1.00) 		0.46
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.403
(1.00)
2p loss 0 (0%) 578 1
(1.00) 		0.739
(1.00) 		0.101
(1.00) 		0.0432
(1.00) 		0.803
(1.00) 		0.0353
(1.00) 		0.0234
(1.00)
2q loss 0 (0%) 581 0.74
(1.00) 		0.614
(1.00) 		0.586
(1.00) 		0.123
(1.00) 		0.299
(1.00) 		0.0609
(1.00) 		0.0147
(1.00)
3p loss 0 (0%) 551 1
(1.00) 		0.292
(1.00) 		0.362
(1.00) 		0.817
(1.00) 		0.78
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.379
(1.00) 		0.852
(1.00) 		0.74
(1.00) 		0.617
(1.00)
3q loss 0 (0%) 570 0.45
(1.00) 		0.0138
(1.00) 		0.078
(1.00) 		0.0697
(1.00) 		0.0599
(1.00) 		0.462
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.897
(1.00) 		0.924
(1.00) 		0.762
(1.00) 		0.714
(1.00)
5p loss 0 (0%) 555 0.269
(1.00) 		0.45
(1.00) 		0.00057
(0.463) 		0.0302
(1.00) 		0.386
(1.00) 		0.449
(1.00) 		0.134
(1.00) 		0.0586
(1.00) 		0.938
(1.00) 		0.291
(1.00) 		0.619
(1.00) 		0.212
(1.00)
6p loss 0 (0%) 570 0.132
(1.00) 		0.186
(1.00) 		0.643
(1.00) 		0.356
(1.00) 		0.392
(1.00) 		0.641
(1.00) 		0.401
(1.00) 		0.287
(1.00) 		0.646
(1.00) 		0.735
(1.00) 		0.394
(1.00) 		0.584
(1.00)
6q loss 0 (0%) 555 0.784
(1.00) 		0.621
(1.00) 		0.663
(1.00) 		0.886
(1.00) 		0.219
(1.00) 		0.145
(1.00) 		0.798
(1.00) 		0.842
(1.00) 		0.616
(1.00) 		0.155
(1.00) 		0.725
(1.00) 		0.973
(1.00)
7q loss 0 (0%) 586 0.399
(1.00) 		0.844
(1.00) 		1
(1.00) 		0.781
(1.00) 		1
(1.00)
8q loss 0 (0%) 578 0.815
(1.00) 		0.869
(1.00) 		0.317
(1.00) 		0.58
(1.00) 		0.0287
(1.00) 		0.658
(1.00) 		0.836
(1.00) 		0.818
(1.00) 		0.314
(1.00) 		0.148
(1.00) 		0.836
(1.00) 		0.086
(1.00)
9p loss 0 (0%) 550 0.911
(1.00) 		0.286
(1.00) 		0.00161
(1.00) 		0.00203
(1.00) 		0.32
(1.00) 		0.147
(1.00) 		0.0938
(1.00) 		0.109
(1.00) 		0.0556
(1.00) 		0.631
(1.00) 		0.0183
(1.00) 		0.0778
(1.00)
10p loss 0 (0%) 548 0.72
(1.00) 		0.49
(1.00) 		0.00316
(1.00) 		0.415
(1.00) 		0.0958
(1.00) 		0.682
(1.00) 		0.305
(1.00) 		0.0545
(1.00) 		0.0957
(1.00) 		0.307
(1.00) 		0.716
(1.00) 		1
(1.00)
11p loss 0 (0%) 547 0.73
(1.00) 		0.336
(1.00) 		0.0292
(1.00) 		0.222
(1.00) 		0.289
(1.00) 		0.174
(1.00) 		0.17
(1.00) 		0.356
(1.00) 		0.328
(1.00) 		0.159
(1.00) 		0.246
(1.00) 		0.912
(1.00)
11q loss 0 (0%) 537 0.827
(1.00) 		0.464
(1.00) 		0.00376
(1.00) 		0.0634
(1.00) 		0.781
(1.00) 		0.292
(1.00) 		0.333
(1.00) 		0.737
(1.00) 		0.233
(1.00) 		0.095
(1.00) 		0.201
(1.00) 		0.949
(1.00)
13q loss 0 (0%) 576 0.297
(1.00) 		0.282
(1.00) 		0.146
(1.00) 		0.169
(1.00) 		0.27
(1.00) 		0.108
(1.00) 		0.245
(1.00) 		0.0571
(1.00) 		0.801
(1.00) 		0.566
(1.00) 		0.046
(1.00) 		0.307
(1.00)
16p loss 0 (0%) 573 0.266
(1.00) 		0.184
(1.00) 		0.46
(1.00) 		0.169
(1.00) 		0.644
(1.00) 		0.646
(1.00) 		0.302
(1.00) 		0.254
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.669
(1.00) 		0.172
(1.00)
16q loss 0 (0%) 571 0.0284
(1.00) 		0.243
(1.00) 		0.0617
(1.00) 		0.385
(1.00) 		0.655
(1.00) 		0.748
(1.00) 		0.181
(1.00) 		0.138
(1.00) 		0.0951
(1.00) 		0.724
(1.00) 		0.331
(1.00) 		0.235
(1.00)
17q loss 0 (0%) 540 0.844
(1.00) 		0.487
(1.00) 		0.00546
(1.00) 		0.666
(1.00) 		0.342
(1.00) 		0.454
(1.00) 		0.057
(1.00) 		0.0711
(1.00) 		0.412
(1.00) 		0.911
(1.00) 		0.0812
(1.00) 		0.155
(1.00)
19p loss 0 (0%) 568 0.74
(1.00) 		0.431
(1.00) 		0.000849
(0.682) 		0.0247
(1.00) 		0.614
(1.00) 		0.705
(1.00) 		0.00414
(1.00) 		0.0837
(1.00) 		0.059
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.171
(1.00)
19q loss 0 (0%) 572 0.74
(1.00) 		0.431
(1.00) 		0.00227
(1.00) 		0.186
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.00358
(1.00) 		0.136
(1.00) 		0.268
(1.00) 		0.707
(1.00) 		0.0691
(1.00) 		0.319
(1.00)
20p loss 0 (0%) 540 0.0412
(1.00) 		0.184
(1.00) 		0.000603
(0.489) 		0.163
(1.00) 		0.402
(1.00) 		0.581
(1.00) 		0.633
(1.00) 		0.123
(1.00) 		0.666
(1.00) 		0.938
(1.00) 		0.412
(1.00) 		0.697
(1.00)
20q loss 0 (0%) 586 0.647
(1.00)
21q loss 0 (0%) 470 0.376
(1.00) 		0.517
(1.00) 		0.00133
(1.00) 		0.0741
(1.00) 		0.31
(1.00) 		0.31
(1.00) 		0.0449
(1.00) 		0.0549
(1.00) 		0.0759
(1.00) 		0.686
(1.00) 		0.124
(1.00) 		0.708
(1.00)
Xq loss 0 (0%) 577 0.765
(1.00) 		1
(1.00) 		0.237
(1.00) 		0.671
(1.00) 		0.017
(1.00) 		0.345
(1.00) 		0.63
(1.00) 		0.526
(1.00) 		0.393
(1.00) 		0.205
(1.00) 		0.289
(1.00) 		0.109
(1.00)
'2p gain' versus 'METHLYATION_CNMF'

P value = 6.7e-05 (Fisher's exact test), Q value = 0.056

Table S1.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
2P GAIN CNV 31 8 3
2P GAIN WILD-TYPE 125 108 88

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.52e-05 (Fisher's exact test), Q value = 0.071

Table S2.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
2Q GAIN CNV 7 1 0 10
2Q GAIN WILD-TYPE 35 49 63 50

Figure S2.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1.35e-06 (Fisher's exact test), Q value = 0.0012

Table S3.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
2Q GAIN CNV 31 7 1
2Q GAIN WILD-TYPE 125 109 90

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 5.4e-06 (Fisher's exact test), Q value = 0.0046

Table S4.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
3Q GAIN CNV 32 7 13 1
3Q GAIN WILD-TYPE 154 234 134 14

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 3.39e-07 (Fisher's exact test), Q value = 0.00029

Table S5.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
6P GAIN CNV 47 15 16 2
6P GAIN WILD-TYPE 139 226 131 13

Figure S5.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00093

Table S6.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
6Q GAIN CNV 43 13 16 2
6Q GAIN WILD-TYPE 143 228 131 13

Figure S6.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 4.73e-22 (Fisher's exact test), Q value = 4.2e-19

Table S7.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
7P GAIN CNV 136 65 87 10
7P GAIN WILD-TYPE 50 176 60 5

Figure S7.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1.84e-07 (Fisher's exact test), Q value = 0.00016

Table S8.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
7P GAIN CNV 111 53 35
7P GAIN WILD-TYPE 45 63 56

Figure S8.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.96e-07 (Fisher's exact test), Q value = 0.00034

Table S9.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
7P GAIN CNV 56 72 40
7P GAIN WILD-TYPE 39 31 76

Figure S9.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.51e-08 (Fisher's exact test), Q value = 4.8e-05

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
7P GAIN CNV 60 60 48
7P GAIN WILD-TYPE 24 34 88

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.088

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
7P GAIN CNV 65 41 52
7P GAIN WILD-TYPE 35 68 33

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1.7e-15 (Fisher's exact test), Q value = 1.5e-12

Table S12.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
7Q GAIN CNV 117 60 75 10
7Q GAIN WILD-TYPE 69 181 72 5

Figure S12.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 8.24e-06 (Fisher's exact test), Q value = 0.0069

Table S13.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
7Q GAIN CNV 95 48 28
7Q GAIN WILD-TYPE 61 68 63

Figure S13.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 2.53e-07 (Fisher's exact test), Q value = 0.00022

Table S14.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
7Q GAIN CNV 47 66 32
7Q GAIN WILD-TYPE 48 37 84

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.84e-07 (Fisher's exact test), Q value = 0.00084

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
7Q GAIN CNV 49 56 40
7Q GAIN WILD-TYPE 35 38 96

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00097

Table S16.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
8P GAIN CNV 23 35 45 8
8P GAIN WILD-TYPE 163 206 102 7

Figure S16.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.19e-39 (Fisher's exact test), Q value = 1.1e-36

Table S17.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
8Q GAIN CNV 63 43 124 8
8Q GAIN WILD-TYPE 123 198 23 7

Figure S17.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 9.4e-05 (Fisher's exact test), Q value = 0.078

Table S18.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
11P GAIN CNV 24 5 12 0
11P GAIN WILD-TYPE 162 236 135 15

Figure S18.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
11P GAIN CNV 22 2 3
11P GAIN WILD-TYPE 134 114 88

Figure S19.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.051

Table S20.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
11Q GAIN CNV 22 4 14 1
11Q GAIN WILD-TYPE 164 237 133 14

Figure S20.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 8.56e-07 (Fisher's exact test), Q value = 0.00073

Table S21.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
13Q GAIN CNV 12 44 48 15
13Q GAIN WILD-TYPE 31 18 21 26

Figure S21.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.14

Table S22.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
13Q GAIN CNV 27 33 20 39
13Q GAIN WILD-TYPE 15 17 43 21

Figure S22.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1.82e-39 (Fisher's exact test), Q value = 1.6e-36

Table S23.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
13Q GAIN CNV 166 65 81 7
13Q GAIN WILD-TYPE 20 176 66 8

Figure S23.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 5.7e-09 (Fisher's exact test), Q value = 5e-06

Table S24.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
13Q GAIN CNV 114 46 39
13Q GAIN WILD-TYPE 42 70 52

Figure S24.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.0028

Table S25.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
13Q GAIN CNV 51 72 42
13Q GAIN WILD-TYPE 44 31 74

Figure S25.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.2e-07 (Fisher's exact test), Q value = 0.00045

Table S26.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
13Q GAIN CNV 54 63 48
13Q GAIN WILD-TYPE 30 31 88

Figure S26.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.59e-07 (Fisher's exact test), Q value = 0.00014

Table S27.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
13Q GAIN CNV 72 39 55
13Q GAIN WILD-TYPE 28 70 30

Figure S27.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1.41e-16 (Fisher's exact test), Q value = 1.3e-13

Table S28.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
16P GAIN CNV 61 7 27 2
16P GAIN WILD-TYPE 125 234 120 13

Figure S28.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1.39e-18 (Fisher's exact test), Q value = 1.2e-15

Table S29.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
16Q GAIN CNV 64 6 25 2
16Q GAIN WILD-TYPE 122 235 122 13

Figure S29.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000209 (Fisher's exact test), Q value = 0.17

Table S30.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
17Q GAIN CNV 10 22 7
17Q GAIN WILD-TYPE 74 72 129

Figure S30.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.1

Table S31.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
19P GAIN CNV 28 8 17 1
19P GAIN WILD-TYPE 158 233 130 14

Figure S31.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.12

Table S32.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20P GAIN CNV 13 38 47 16
20P GAIN WILD-TYPE 30 24 22 25

Figure S32.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.65e-07 (Fisher's exact test), Q value = 0.00014

Table S33.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20P GAIN CNV 32 30 15 37
20P GAIN WILD-TYPE 10 20 48 23

Figure S33.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1.38e-17 (Fisher's exact test), Q value = 1.2e-14

Table S34.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
20P GAIN CNV 128 75 77 15
20P GAIN WILD-TYPE 58 166 70 0

Figure S34.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 6.02e-06 (Fisher's exact test), Q value = 0.0051

Table S35.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
20P GAIN CNV 99 42 36
20P GAIN WILD-TYPE 57 74 55

Figure S35.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1.96e-09 (Fisher's exact test), Q value = 1.7e-06

Table S36.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
20P GAIN CNV 47 71 31
20P GAIN WILD-TYPE 48 32 85

Figure S36.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-09 (Fisher's exact test), Q value = 1.8e-06

Table S37.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
20P GAIN CNV 47 64 38
20P GAIN WILD-TYPE 37 30 98

Figure S37.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.015

Table S38.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
20P GAIN CNV 61 34 48
20P GAIN WILD-TYPE 39 75 37

Figure S38.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 4.38e-17 (Fisher's exact test), Q value = 3.9e-14

Table S39.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20Q GAIN CNV 14 60 62 20
20Q GAIN WILD-TYPE 29 2 7 21

Figure S39.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.38e-16 (Fisher's exact test), Q value = 3.9e-13

Table S40.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20Q GAIN CNV 38 42 20 56
20Q GAIN WILD-TYPE 4 8 43 4

Figure S40.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.09e-46 (Fisher's exact test), Q value = 9.9e-44

Table S41.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
20Q GAIN CNV 182 95 120 15
20Q GAIN WILD-TYPE 4 146 27 0

Figure S41.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.48e-17 (Fisher's exact test), Q value = 4.9e-14

Table S42.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
20Q GAIN CNV 143 56 51
20Q GAIN WILD-TYPE 13 60 40

Figure S42.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 97 178 39 137
20Q GAIN CNV 73 136 30 75
20Q GAIN WILD-TYPE 24 42 9 62

Figure S43.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.13

Table S44.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 248 92 35
20Q GAIN CNV 61 184 50 19
20Q GAIN WILD-TYPE 15 64 42 16

Figure S44.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.96e-17 (Fisher's exact test), Q value = 1.8e-14

Table S45.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
20Q GAIN CNV 71 94 44
20Q GAIN WILD-TYPE 24 9 72

Figure S45.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-21 (Fisher's exact test), Q value = 2e-18

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
20Q GAIN CNV 73 85 51
20Q GAIN WILD-TYPE 11 9 85

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.22e-12 (Fisher's exact test), Q value = 1.1e-09

Table S47.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
20Q GAIN CNV 87 47 69
20Q GAIN WILD-TYPE 13 62 16

Figure S47.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.096

Table S48.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
1P LOSS CNV 29 4 6
1P LOSS WILD-TYPE 127 112 85

Figure S48.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.81e-12 (Fisher's exact test), Q value = 1.6e-09

Table S49.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
4P LOSS CNV 70 22 28 7
4P LOSS WILD-TYPE 116 219 119 8

Figure S49.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 2.62e-13 (Fisher's exact test), Q value = 2.3e-10

Table S50.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
4Q LOSS CNV 67 17 29 6
4Q LOSS WILD-TYPE 119 224 118 9

Figure S50.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 4.48e-06 (Fisher's exact test), Q value = 0.0038

Table S51.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
5Q LOSS CNV 24 8 27 2
5Q LOSS WILD-TYPE 162 233 120 13

Figure S51.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 3.55e-26 (Fisher's exact test), Q value = 3.2e-23

Table S52.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
8P LOSS CNV 80 11 56 0
8P LOSS WILD-TYPE 106 230 91 15

Figure S52.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.000213 (Fisher's exact test), Q value = 0.17

Table S53.  Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
8P LOSS CNV 52 16 15
8P LOSS WILD-TYPE 104 100 76

Figure S53.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.73e-06 (Fisher's exact test), Q value = 0.0015

Table S54.  Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
8P LOSS CNV 32 24 13
8P LOSS WILD-TYPE 52 70 123

Figure S54.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.085

Table S55.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
9Q LOSS CNV 24 5 8 0
9Q LOSS WILD-TYPE 162 236 139 15

Figure S55.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.028

Table S56.  Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
9Q LOSS CNV 20 1 2
9Q LOSS WILD-TYPE 136 115 89

Figure S56.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 9.17e-06 (Fisher's exact test), Q value = 0.0077

Table S57.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
10Q LOSS CNV 17 6 18 5
10Q LOSS WILD-TYPE 169 235 129 10

Figure S57.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 5.26e-07 (Fisher's exact test), Q value = 0.00045

Table S58.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
12P LOSS CNV 20 2 7 4
12P LOSS WILD-TYPE 166 239 140 11

Figure S58.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 6.35e-06 (Fisher's exact test), Q value = 0.0054

Table S59.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
12Q LOSS CNV 16 2 7 4
12Q LOSS WILD-TYPE 170 239 140 11

Figure S59.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.12

Table S60.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
14Q LOSS CNV 7 27 26 4
14Q LOSS WILD-TYPE 36 35 43 37

Figure S60.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0015

Table S61.  Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
14Q LOSS CNV 20 17 4 23
14Q LOSS WILD-TYPE 22 33 59 37

Figure S61.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.07e-37 (Fisher's exact test), Q value = 9.7e-35

Table S62.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
14Q LOSS CNV 111 20 12 3
14Q LOSS WILD-TYPE 75 221 135 12

Figure S62.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.34e-07 (Fisher's exact test), Q value = 0.00012

Table S63.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
14Q LOSS CNV 57 13 11
14Q LOSS WILD-TYPE 99 103 80

Figure S63.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.024

Table S64.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
14Q LOSS CNV 16 39 15
14Q LOSS WILD-TYPE 79 64 101

Figure S64.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.35e-06 (Fisher's exact test), Q value = 0.0045

Table S65.  Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
14Q LOSS CNV 26 31 13
14Q LOSS WILD-TYPE 58 63 123

Figure S65.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.9e-07 (Fisher's exact test), Q value = 0.00042

Table S66.  Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
14Q LOSS CNV 39 9 19
14Q LOSS WILD-TYPE 61 100 66

Figure S66.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1.86e-18 (Fisher's exact test), Q value = 1.7e-15

Table S67.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
15Q LOSS CNV 82 21 46 9
15Q LOSS WILD-TYPE 104 220 101 6

Figure S67.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.12

Table S68.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
15Q LOSS CNV 29 28 17
15Q LOSS WILD-TYPE 55 66 119

Figure S68.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S69.  Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
15Q LOSS CNV 32 12 25
15Q LOSS WILD-TYPE 68 97 60

Figure S69.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1.5e-23 (Fisher's exact test), Q value = 1.4e-20

Table S70.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
17P LOSS CNV 113 45 89 9
17P LOSS WILD-TYPE 73 196 58 6

Figure S70.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 6.11e-08 (Fisher's exact test), Q value = 5.3e-05

Table S71.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
17P LOSS CNV 93 35 26
17P LOSS WILD-TYPE 63 81 65

Figure S71.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 4.73e-05 (Fisher's exact test), Q value = 0.04

Table S72.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
17P LOSS CNV 41 59 32
17P LOSS WILD-TYPE 54 44 84

Figure S72.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.78e-08 (Fisher's exact test), Q value = 2.4e-05

Table S73.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
17P LOSS CNV 48 52 32
17P LOSS WILD-TYPE 36 42 104

Figure S73.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.83e-06 (Fisher's exact test), Q value = 0.0024

Table S74.  Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
17P LOSS CNV 60 28 35
17P LOSS WILD-TYPE 40 81 50

Figure S74.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 5.24e-13 (Fisher's exact test), Q value = 4.6e-10

Table S75.  Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18P LOSS CNV 11 52 52 12
18P LOSS WILD-TYPE 32 10 17 29

Figure S75.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.58e-11 (Fisher's exact test), Q value = 1.4e-08

Table S76.  Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18P LOSS CNV 35 30 15 47
18P LOSS WILD-TYPE 7 20 48 13

Figure S76.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 9.96e-49 (Fisher's exact test), Q value = 9e-46

Table S77.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
18P LOSS CNV 165 55 101 14
18P LOSS WILD-TYPE 21 186 46 1

Figure S77.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 7.74e-22 (Fisher's exact test), Q value = 7e-19

Table S78.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
18P LOSS CNV 133 39 34
18P LOSS WILD-TYPE 23 77 57

Figure S78.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 5.84e-14 (Fisher's exact test), Q value = 5.2e-11

Table S79.  Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
18P LOSS CNV 54 84 35
18P LOSS WILD-TYPE 41 19 81

Figure S79.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.02e-16 (Fisher's exact test), Q value = 7.1e-13

Table S80.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
18P LOSS CNV 63 71 39
18P LOSS WILD-TYPE 21 23 97

Figure S80.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.21e-14 (Fisher's exact test), Q value = 2e-11

Table S81.  Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
18P LOSS CNV 79 29 53
18P LOSS WILD-TYPE 21 80 32

Figure S81.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 1.36e-12 (Fisher's exact test), Q value = 1.2e-09

Table S82.  Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q LOSS CNV 13 54 54 14
18Q LOSS WILD-TYPE 30 8 15 27

Figure S82.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.31e-12 (Fisher's exact test), Q value = 3.8e-09

Table S83.  Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18Q LOSS CNV 36 32 17 50
18Q LOSS WILD-TYPE 6 18 46 10

Figure S83.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 6.64e-51 (Fisher's exact test), Q value = 6e-48

Table S84.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
18Q LOSS CNV 165 62 119 15
18Q LOSS WILD-TYPE 21 179 28 0

Figure S84.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 8.81e-23 (Fisher's exact test), Q value = 7.9e-20

Table S85.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
18Q LOSS CNV 140 46 37
18Q LOSS WILD-TYPE 16 70 54

Figure S85.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 2.55e-14 (Fisher's exact test), Q value = 2.3e-11

Table S86.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 103 116
18Q LOSS CNV 57 89 41
18Q LOSS WILD-TYPE 38 14 75

Figure S86.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.73e-14 (Fisher's exact test), Q value = 1.5e-11

Table S87.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 94 136
18Q LOSS CNV 66 74 47
18Q LOSS WILD-TYPE 18 20 89

Figure S87.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.89e-13 (Fisher's exact test), Q value = 2.5e-10

Table S88.  Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
18Q LOSS CNV 83 36 56
18Q LOSS WILD-TYPE 17 73 29

Figure S88.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 3.51e-11 (Fisher's exact test), Q value = 3.1e-08

Table S89.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 186 241 147 15
22Q LOSS CNV 70 24 28 6
22Q LOSS WILD-TYPE 116 217 119 9

Figure S89.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 589

  • Number of significantly arm-level cnvs = 79

  • 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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