Correlation between copy number variations of arm-level result and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C12N50KR
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/C12N50KR
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 10 molecular subtypes across 561 patients, 61 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'MIR_CNMF'.

  • 7p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 7q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 8p gain cnv correlated to 'MRNA_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

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

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

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 10q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CNMF'.

  • 11p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

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

  • 13q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 15q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'MRNA_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 61 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL
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
19q gain 0 (0%) 410 5.69e-15
(3.93e-12) 		6.54e-13
(4.5e-10) 		0.0879
(1.00) 		6.89e-05
(0.0446) 		6.86e-29
(4.77e-26) 		0.0171
(1.00) 		0.0528
(1.00) 		4.31e-06
(0.00286) 		0.025
(1.00) 		0.0124
(1.00)
10q loss 0 (0%) 114 3.53e-08
(2.37e-05) 		1.81e-06
(0.00121) 		0.0138
(1.00) 		2.17e-06
(0.00145) 		1.33e-31
(9.26e-29) 		0.00364
(1.00) 		6.96e-05
(0.045) 		0.00164
(1.00) 		0.729
(1.00) 		0.0908
(1.00)
7p gain 0 (0%) 130 2.63e-05
(0.0172) 		3.77e-06
(0.0025) 		0.000701
(0.438) 		1.02e-10
(6.92e-08) 		9.6e-17
(6.65e-14) 		0.00218
(1.00) 		0.00162
(0.997) 		0.471
(1.00) 		0.0411
(1.00) 		0.00552
(1.00)
7q gain 0 (0%) 125 7.66e-06
(0.00504) 		0.000149
(0.0958) 		0.000948
(0.59) 		5.94e-07
(0.000397) 		4.83e-15
(3.34e-12) 		0.00211
(1.00) 		0.0199
(1.00) 		0.361
(1.00) 		0.0916
(1.00) 		0.0115
(1.00)
19p gain 0 (0%) 385 1.62e-12
(1.11e-09) 		5.01e-09
(3.39e-06) 		0.265
(1.00) 		0.00119
(0.734) 		2.83e-23
(1.96e-20) 		0.000521
(0.329) 		0.0175
(1.00) 		3.09e-06
(0.00205) 		0.102
(1.00) 		0.00821
(1.00)
20p gain 0 (0%) 381 3.01e-10
(2.05e-07) 		9.54e-12
(6.54e-09) 		0.176
(1.00) 		4.51e-05
(0.0292) 		2.99e-09
(2.02e-06) 		0.0654
(1.00) 		0.0946
(1.00) 		0.00228
(1.00) 		0.914
(1.00) 		0.000713
(0.445)
20q gain 0 (0%) 383 9.25e-11
(6.32e-08) 		1.02e-11
(6.99e-09) 		0.14
(1.00) 		1.64e-05
(0.0108) 		5.68e-09
(3.83e-06) 		0.016
(1.00) 		0.0595
(1.00) 		0.00116
(0.714) 		0.834
(1.00) 		0.000403
(0.257)
10p loss 0 (0%) 127 1.56e-07
(0.000104) 		2.79e-05
(0.0182) 		0.0172
(1.00) 		5.6e-09
(3.78e-06) 		8.21e-29
(5.7e-26) 		0.00564
(1.00) 		0.000567
(0.357) 		0.000656
(0.412) 		0.531
(1.00) 		0.0603
(1.00)
11p loss 0 (0%) 498 6.25e-09
(4.21e-06) 		2.14e-05
(0.014) 		0.194
(1.00) 		4.38e-06
(0.0029) 		2.09e-11
(1.43e-08) 		0.00192
(1.00) 		0.679
(1.00) 		0.0659
(1.00) 		0.0443
(1.00) 		0.426
(1.00)
13q loss 0 (0%) 423 0.000132
(0.085) 		0.000315
(0.201) 		0.622
(1.00) 		0.751
(1.00) 		8.87e-14
(6.11e-11) 		0.00113
(0.696) 		0.601
(1.00) 		0.0182
(1.00) 		0.22
(1.00) 		0.309
(1.00)
15q loss 0 (0%) 499 0.00182
(1.00) 		2.48e-05
(0.0163) 		0.00177
(1.00) 		6.47e-06
(0.00427) 		6.61e-06
(0.00436) 		0.000612
(0.385) 		0.108
(1.00) 		0.0224
(1.00) 		0.0153
(1.00) 		0.452
(1.00)
11q loss 0 (0%) 507 3.05e-05
(0.0199) 		0.0055
(1.00) 		0.8
(1.00) 		0.00914
(1.00) 		5.26e-10
(3.58e-07) 		0.312
(1.00) 		0.577
(1.00) 		0.0933
(1.00) 		0.648
(1.00) 		0.868
(1.00)
14q loss 0 (0%) 441 2.72e-06
(0.00181) 		0.00554
(1.00) 		0.451
(1.00) 		0.665
(1.00) 		5.41e-33
(3.77e-30) 		0.0149
(1.00) 		0.753
(1.00) 		0.0604
(1.00) 		0.0359
(1.00) 		0.00494
(1.00)
1p gain 0 (0%) 522 0.614
(1.00) 		0.104
(1.00) 		0.962
(1.00) 		0.0907
(1.00) 		2.99e-05
(0.0195) 		0.636
(1.00) 		0.478
(1.00) 		0.925
(1.00) 		0.46
(1.00) 		0.0696
(1.00)
1q gain 0 (0%) 517 0.0357
(1.00) 		0.153
(1.00) 		0.443
(1.00) 		0.504
(1.00) 		6.37e-08
(4.27e-05) 		0.448
(1.00) 		0.713
(1.00) 		0.882
(1.00) 		1
(1.00) 		0.152
(1.00)
2q gain 0 (0%) 544 0.284
(1.00) 		0.322
(1.00) 		4.37e-05
(0.0284) 		0.0291
(1.00) 		0.553
(1.00) 		0.513
(1.00) 		0.535
(1.00) 		0.52
(1.00) 		0.795
(1.00) 		0.366
(1.00)
8p gain 0 (0%) 535 0.00018
(0.115) 		0.162
(1.00) 		0.343
(1.00) 		0.0111
(1.00) 		0.0015
(0.925) 		0.164
(1.00) 		0.0641
(1.00) 		0.06
(1.00) 		0.808
(1.00) 		0.551
(1.00)
10p gain 0 (0%) 550 0.000127
(0.082) 		0.00334
(1.00) 		0.0179
(1.00) 		0.000454
(0.288) 		0.00107
(0.66) 		0.307
(1.00) 		0.384
(1.00)
18p gain 0 (0%) 534 0.0502
(1.00) 		0.16
(1.00) 		0.408
(1.00) 		0.503
(1.00) 		7.58e-05
(0.0489) 		0.236
(1.00) 		0.408
(1.00) 		0.548
(1.00) 		0.0656
(1.00) 		0.259
(1.00)
18q gain 0 (0%) 532 0.0113
(1.00) 		0.124
(1.00) 		0.246
(1.00) 		0.55
(1.00) 		3.52e-05
(0.0229) 		0.236
(1.00) 		0.722
(1.00) 		0.407
(1.00) 		0.0209
(1.00) 		0.103
(1.00)
3q loss 0 (0%) 545 0.224
(1.00) 		0.467
(1.00) 		0.0291
(1.00) 		0.457
(1.00) 		0.000339
(0.216) 		0.807
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.278
(1.00)
6p loss 0 (0%) 515 0.921
(1.00) 		0.487
(1.00) 		0.339
(1.00) 		0.414
(1.00) 		9.04e-10
(6.14e-07) 		0.743
(1.00) 		0.914
(1.00) 		0.592
(1.00) 		0.662
(1.00) 		0.445
(1.00)
6q loss 0 (0%) 481 0.932
(1.00) 		0.607
(1.00) 		0.619
(1.00) 		0.0648
(1.00) 		3.56e-09
(2.41e-06) 		0.0404
(1.00) 		0.896
(1.00) 		0.678
(1.00) 		0.824
(1.00) 		0.383
(1.00)
17p loss 0 (0%) 525 0.102
(1.00) 		0.462
(1.00) 		0.858
(1.00) 		0.868
(1.00) 		6.48e-06
(0.00428) 		0.38
(1.00) 		0.0555
(1.00) 		0.826
(1.00) 		0.503
(1.00) 		1
(1.00)
21q loss 0 (0%) 536 0.000317
(0.202) 		0.0217
(1.00) 		0.0887
(1.00) 		0.00494
(1.00) 		0.0296
(1.00) 		0.0765
(1.00) 		0.0279
(1.00) 		0.326
(1.00) 		0.602
(1.00) 		0.848
(1.00)
22q loss 0 (0%) 421 0.869
(1.00) 		0.718
(1.00) 		0.537
(1.00) 		0.886
(1.00) 		0.000167
(0.107) 		0.322
(1.00) 		0.731
(1.00) 		0.955
(1.00) 		0.156
(1.00) 		0.885
(1.00)
2p gain 0 (0%) 542 0.2
(1.00) 		0.568
(1.00) 		0.00188
(1.00) 		0.0741
(1.00) 		0.374
(1.00) 		0.513
(1.00) 		0.685
(1.00) 		0.385
(1.00) 		0.577
(1.00) 		0.797
(1.00)
3p gain 0 (0%) 531 0.0116
(1.00) 		0.0508
(1.00) 		0.342
(1.00) 		0.617
(1.00) 		0.0206
(1.00) 		0.164
(1.00) 		0.405
(1.00) 		0.137
(1.00) 		0.808
(1.00) 		0.779
(1.00)
3q gain 0 (0%) 531 0.0116
(1.00) 		0.0508
(1.00) 		0.342
(1.00) 		0.799
(1.00) 		0.053
(1.00) 		0.164
(1.00) 		0.405
(1.00) 		0.137
(1.00) 		0.748
(1.00) 		0.58
(1.00)
4p gain 0 (0%) 546 0.0366
(1.00) 		0.537
(1.00) 		0.383
(1.00) 		0.0525
(1.00) 		0.29
(1.00) 		0.444
(1.00) 		0.149
(1.00)
4q gain 0 (0%) 547 0.406
(1.00) 		0.587
(1.00) 		0.196
(1.00) 		0.0869
(1.00) 		0.193
(1.00) 		0.444
(1.00) 		0.149
(1.00)
5p gain 0 (0%) 531 0.328
(1.00) 		0.0864
(1.00) 		0.25
(1.00) 		0.502
(1.00) 		0.00383
(1.00) 		0.169
(1.00) 		0.652
(1.00) 		0.201
(1.00) 		0.202
(1.00)
5q gain 0 (0%) 538 0.257
(1.00) 		0.0463
(1.00) 		0.055
(1.00) 		0.214
(1.00) 		0.0158
(1.00) 		0.442
(1.00) 		0.365
(1.00)
6p gain 0 (0%) 554 0.741
(1.00) 		0.769
(1.00) 		0.627
(1.00) 		0.391
(1.00) 		0.161
(1.00)
6q gain 0 (0%) 552 0.514
(1.00) 		0.729
(1.00) 		0.616
(1.00) 		0.227
(1.00) 		0.0299
(1.00)
8q gain 0 (0%) 530 0.000495
(0.313) 		0.124
(1.00) 		0.276
(1.00) 		0.0074
(1.00) 		0.00363
(1.00) 		0.0589
(1.00) 		0.0641
(1.00) 		0.06
(1.00) 		0.338
(1.00) 		0.547
(1.00)
9p gain 0 (0%) 544 0.0323
(1.00) 		0.0621
(1.00) 		0.721
(1.00) 		0.0931
(1.00) 		0.0424
(1.00) 		0.573
(1.00) 		0.215
(1.00) 		0.305
(1.00) 		0.319
(1.00) 		0.766
(1.00)
9q gain 0 (0%) 528 0.228
(1.00) 		0.209
(1.00) 		0.44
(1.00) 		0.346
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.116
(1.00) 		0.588
(1.00) 		0.67
(1.00)
11p gain 0 (0%) 557 0.884
(1.00) 		0.797
(1.00) 		0.684
(1.00) 		0.635
(1.00) 		0.261
(1.00)
11q gain 0 (0%) 554 0.0826
(1.00) 		0.205
(1.00) 		0.232
(1.00) 		0.101
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.421
(1.00)
12p gain 0 (0%) 519 0.645
(1.00) 		0.448
(1.00) 		0.936
(1.00) 		0.222
(1.00) 		0.00275
(1.00) 		0.49
(1.00) 		0.36
(1.00) 		0.8
(1.00) 		0.0427
(1.00) 		0.259
(1.00)
12q gain 0 (0%) 529 0.323
(1.00) 		0.164
(1.00) 		0.893
(1.00) 		0.097
(1.00) 		0.00916
(1.00) 		0.749
(1.00) 		0.55
(1.00) 		0.695
(1.00) 		0.109
(1.00) 		0.7
(1.00)
13q gain 0 (0%) 558 0.15
(1.00) 		0.797
(1.00) 		0.158
(1.00) 		0.635
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.527
(1.00)
14q gain 0 (0%) 554 0.559
(1.00) 		0.111
(1.00) 		0.0578
(1.00) 		0.443
(1.00) 		0.637
(1.00)
15q gain 0 (0%) 555 0.275
(1.00) 		0.624
(1.00) 		0.514
(1.00) 		0.521
(1.00) 		0.0127
(1.00)
16p gain 0 (0%) 544 0.0828
(1.00) 		0.282
(1.00) 		0.346
(1.00) 		0.283
(1.00) 		0.0289
(1.00) 		0.332
(1.00) 		0.442
(1.00)
16q gain 0 (0%) 544 0.0567
(1.00) 		0.156
(1.00) 		0.251
(1.00) 		0.0371
(1.00) 		0.0289
(1.00) 		0.433
(1.00) 		0.442
(1.00)
17p gain 0 (0%) 550 0.0259
(1.00) 		0.462
(1.00) 		0.707
(1.00) 		0.55
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.284
(1.00)
17q gain 0 (0%) 542 0.373
(1.00) 		1
(1.00) 		0.987
(1.00) 		0.337
(1.00) 		0.0614
(1.00) 		0.786
(1.00) 		0.384
(1.00) 		0.208
(1.00) 		0.562
(1.00)
21q gain 0 (0%) 526 0.0342
(1.00) 		0.00755
(1.00) 		0.0109
(1.00) 		0.000684
(0.429) 		0.0623
(1.00) 		0.411
(1.00) 		0.912
(1.00) 		0.0171
(1.00) 		0.0329
(1.00)
22q gain 0 (0%) 550 0.0156
(1.00) 		0.174
(1.00) 		0.135
(1.00) 		0.407
(1.00) 		0.0768
(1.00) 		1
(1.00) 		0.284
(1.00)
Xq gain 0 (0%) 558 0.556
(1.00) 		0.797
(1.00) 		0.339
(1.00) 		0.635
(1.00) 		0.197
(1.00)
1p loss 0 (0%) 556 0.474
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.532
(1.00)
1q loss 0 (0%) 557 0.367
(1.00) 		1
(1.00) 		0.684
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 0 (0%) 551 0.101
(1.00) 		0.0337
(1.00) 		0.678
(1.00) 		0.0195
(1.00) 		0.164
(1.00) 		0.271
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.0393
(1.00) 		0.12
(1.00)
2q loss 0 (0%) 552 0.0756
(1.00) 		0.0239
(1.00) 		0.239
(1.00) 		0.00287
(1.00) 		0.184
(1.00) 		0.271
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.0393
(1.00) 		0.12
(1.00)
3p loss 0 (0%) 539 0.906
(1.00) 		0.744
(1.00) 		0.593
(1.00) 		0.527
(1.00) 		0.00769
(1.00) 		0.164
(1.00) 		0.0835
(1.00) 		0.653
(1.00) 		0.37
(1.00) 		0.436
(1.00)
4p loss 0 (0%) 535 0.085
(1.00) 		0.0432
(1.00) 		0.168
(1.00) 		0.0821
(1.00) 		0.876
(1.00) 		0.573
(1.00) 		0.0903
(1.00) 		0.43
(1.00) 		0.14
(1.00) 		0.436
(1.00)
4q loss 0 (0%) 536 0.00105
(0.651) 		0.135
(1.00) 		0.155
(1.00) 		0.181
(1.00) 		0.101
(1.00) 		0.821
(1.00) 		0.0985
(1.00) 		0.551
(1.00) 		0.517
(1.00) 		0.562
(1.00)
5p loss 0 (0%) 540 0.000407
(0.259) 		0.0757
(1.00) 		0.172
(1.00) 		0.123
(1.00) 		0.11
(1.00) 		0.048
(1.00) 		0.469
(1.00) 		1
(1.00) 		0.785
(1.00) 		0.495
(1.00)
5q loss 0 (0%) 541 0.00432
(1.00) 		0.87
(1.00) 		0.297
(1.00) 		0.158
(1.00) 		0.0584
(1.00) 		0.048
(1.00) 		0.873
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.483
(1.00)
7p loss 0 (0%) 556 0.236
(1.00) 		0.453
(1.00) 		0.764
(1.00) 		0.0371
(1.00) 		0.532
(1.00)
7q loss 0 (0%) 557 0.311
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.834
(1.00)
8p loss 0 (0%) 527 0.348
(1.00) 		0.89
(1.00) 		0.772
(1.00) 		0.235
(1.00) 		0.272
(1.00) 		0.331
(1.00) 		0.651
(1.00) 		0.912
(1.00) 		0.726
(1.00) 		0.7
(1.00)
8q loss 0 (0%) 540 0.546
(1.00) 		0.361
(1.00) 		0.389
(1.00) 		0.16
(1.00) 		0.0155
(1.00) 		0.212
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.365
(1.00)
9p loss 0 (0%) 396 0.00239
(1.00) 		0.00993
(1.00) 		0.859
(1.00) 		0.0987
(1.00) 		0.216
(1.00) 		0.843
(1.00) 		0.236
(1.00) 		0.036
(1.00) 		0.0344
(1.00) 		0.0372
(1.00)
9q loss 0 (0%) 497 0.289
(1.00) 		0.00246
(1.00) 		0.733
(1.00) 		0.091
(1.00) 		0.0395
(1.00) 		0.561
(1.00) 		0.0236
(1.00) 		0.0282
(1.00) 		0.469
(1.00) 		0.19
(1.00)
12p loss 0 (0%) 523 0.0482
(1.00) 		0.0177
(1.00) 		0.169
(1.00) 		0.0365
(1.00) 		0.757
(1.00) 		0.606
(1.00) 		0.1
(1.00) 		0.474
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 0 (0%) 526 0.0752
(1.00) 		0.0067
(1.00) 		0.741
(1.00) 		0.0457
(1.00) 		0.137
(1.00) 		0.405
(1.00) 		0.102
(1.00) 		0.695
(1.00) 		0.839
(1.00) 		0.547
(1.00)
16p loss 0 (0%) 538 0.148
(1.00) 		0.536
(1.00) 		0.462
(1.00) 		0.705
(1.00) 		0.127
(1.00) 		0.327
(1.00) 		0.644
(1.00) 		0.89
(1.00) 		0.501
(1.00) 		0.185
(1.00)
16q loss 0 (0%) 520 0.0618
(1.00) 		0.0851
(1.00) 		0.124
(1.00) 		0.407
(1.00) 		0.288
(1.00) 		0.406
(1.00) 		0.0754
(1.00) 		0.945
(1.00) 		0.706
(1.00) 		0.569
(1.00)
17q loss 0 (0%) 542 0.196
(1.00) 		0.332
(1.00) 		0.4
(1.00) 		0.297
(1.00) 		0.0018
(1.00) 		0.214
(1.00) 		0.277
(1.00) 		0.168
(1.00) 		0.0933
(1.00)
18p loss 0 (0%) 517 0.00262
(1.00) 		0.0566
(1.00) 		0.489
(1.00) 		0.641
(1.00) 		0.00098
(0.609) 		0.181
(1.00) 		0.246
(1.00) 		0.0387
(1.00) 		0.0596
(1.00) 		0.521
(1.00)
18q loss 0 (0%) 523 0.249
(1.00) 		0.124
(1.00) 		0.346
(1.00) 		0.973
(1.00) 		0.0517
(1.00) 		0.187
(1.00) 		0.0353
(1.00) 		0.000695
(0.435) 		0.567
(1.00) 		0.687
(1.00)
19p loss 0 (0%) 549 0.00046
(0.291) 		0.0586
(1.00) 		0.000922
(0.574) 		0.0198
(1.00) 		0.0889
(1.00) 		0.513
(1.00) 		0.371
(1.00) 		0.574
(1.00) 		0.454
(1.00) 		0.366
(1.00)
19q loss 0 (0%) 545 0.00341
(1.00) 		0.175
(1.00) 		0.0335
(1.00) 		0.0311
(1.00) 		0.0472
(1.00) 		0.513
(1.00) 		0.371
(1.00) 		0.574
(1.00) 		0.812
(1.00) 		0.797
(1.00)
20p loss 0 (0%) 550 0.00426
(1.00) 		0.156
(1.00) 		0.117
(1.00) 		0.0932
(1.00) 		0.00386
(1.00) 		0.414
(1.00) 		0.384
(1.00)
20q loss 0 (0%) 551 0.0161
(1.00) 		0.169
(1.00) 		0.678
(1.00) 		0.446
(1.00) 		0.0216
(1.00) 		0.414
(1.00) 		0.384
(1.00)
Xq loss 0 (0%) 550 0.425
(1.00) 		0.461
(1.00) 		0.117
(1.00) 		0.259
(1.00) 		0.154
(1.00) 		0.636
(1.00) 		0.316
(1.00) 		0.517
(1.00) 		0.454
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 2.99e-05 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
1P GAIN CNV 24 9 6
1P GAIN WILD-TYPE 137 179 206

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

'1q gain' versus 'CN_CNMF'

P value = 6.37e-08 (Fisher's exact test), Q value = 4.3e-05

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
1Q GAIN CNV 29 11 4
1Q GAIN WILD-TYPE 132 177 208

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'MIR_CNMF'

P value = 4.37e-05 (Fisher's exact test), Q value = 0.028

Table S3.  Gene #4: '2q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 155 73 104
2Q GAIN CNV 5 0 0 10
2Q GAIN WILD-TYPE 134 155 73 94

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.017

Table S4.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7P GAIN CNV 123 63 129 74
7P GAIN WILD-TYPE 24 33 23 39

Figure S4.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.77e-06 (Fisher's exact test), Q value = 0.0025

Table S5.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
7P GAIN CNV 99 108 182
7P GAIN WILD-TYPE 18 63 38

Figure S5.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1.02e-10 (Fisher's exact test), Q value = 6.9e-08

Table S6.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
7P GAIN CNV 161 128 77
7P GAIN WILD-TYPE 20 27 58

Figure S6.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 9.6e-17 (Fisher's exact test), Q value = 6.6e-14

Table S7.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
7P GAIN CNV 140 103 188
7P GAIN WILD-TYPE 21 85 24

Figure S7.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'MRNA_CNMF'

P value = 7.66e-06 (Fisher's exact test), Q value = 0.005

Table S8.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7Q GAIN CNV 124 59 130 79
7Q GAIN WILD-TYPE 23 37 22 34

Figure S8.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000149 (Fisher's exact test), Q value = 0.096

Table S9.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
7Q GAIN CNV 99 113 180
7Q GAIN WILD-TYPE 18 58 40

Figure S9.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'MIR_CHIERARCHICAL'

P value = 5.94e-07 (Fisher's exact test), Q value = 4e-04

Table S10.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
7Q GAIN CNV 156 128 83
7Q GAIN WILD-TYPE 25 27 52

Figure S10.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 4.83e-15 (Fisher's exact test), Q value = 3.3e-12

Table S11.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
7Q GAIN CNV 137 108 191
7Q GAIN WILD-TYPE 24 80 21

Figure S11.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'8p gain' versus 'MRNA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S12.  Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
8P GAIN CNV 2 10 2 10
8P GAIN WILD-TYPE 145 86 150 103

Figure S12.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.082

Table S13.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10P GAIN CNV 0 6 0 5
10P GAIN WILD-TYPE 147 90 152 108

Figure S13.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 7.58e-05 (Fisher's exact test), Q value = 0.049

Table S14.  Gene #31: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
18P GAIN CNV 17 8 2
18P GAIN WILD-TYPE 144 180 210

Figure S14.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 3.52e-05 (Fisher's exact test), Q value = 0.023

Table S15.  Gene #32: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
18Q GAIN CNV 18 9 2
18Q GAIN WILD-TYPE 143 179 210

Figure S15.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'MRNA_CNMF'

P value = 1.62e-12 (Fisher's exact test), Q value = 1.1e-09

Table S16.  Gene #33: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19P GAIN CNV 36 24 82 15
19P GAIN WILD-TYPE 111 72 70 98

Figure S16.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.01e-09 (Fisher's exact test), Q value = 3.4e-06

Table S17.  Gene #33: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
19P GAIN CNV 60 29 68
19P GAIN WILD-TYPE 57 142 152

Figure S17.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 2.83e-23 (Fisher's exact test), Q value = 2e-20

Table S18.  Gene #33: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
19P GAIN CNV 26 29 121
19P GAIN WILD-TYPE 135 159 91

Figure S18.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3.09e-06 (Fisher's exact test), Q value = 0.0021

Table S19.  Gene #33: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
19P GAIN CNV 35 6 20
19P GAIN WILD-TYPE 29 27 84

Figure S19.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 5.69e-15 (Fisher's exact test), Q value = 3.9e-12

Table S20.  Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19Q GAIN CNV 31 16 77 10
19Q GAIN WILD-TYPE 116 80 75 103

Figure S20.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.54e-13 (Fisher's exact test), Q value = 4.5e-10

Table S21.  Gene #34: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
19Q GAIN CNV 56 16 62
19Q GAIN WILD-TYPE 61 155 158

Figure S21.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'MIR_CHIERARCHICAL'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.045

Table S22.  Gene #34: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
19Q GAIN CNV 68 43 21
19Q GAIN WILD-TYPE 113 112 114

Figure S22.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 6.86e-29 (Fisher's exact test), Q value = 4.8e-26

Table S23.  Gene #34: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
19Q GAIN CNV 14 22 115
19Q GAIN WILD-TYPE 147 166 97

Figure S23.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 4.31e-06 (Fisher's exact test), Q value = 0.0029

Table S24.  Gene #34: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
19Q GAIN CNV 30 4 15
19Q GAIN WILD-TYPE 34 29 89

Figure S24.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 3.01e-10 (Fisher's exact test), Q value = 2e-07

Table S25.  Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20P GAIN CNV 36 21 79 19
20P GAIN WILD-TYPE 111 75 73 94

Figure S25.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.54e-12 (Fisher's exact test), Q value = 6.5e-09

Table S26.  Gene #35: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
20P GAIN CNV 64 26 65
20P GAIN WILD-TYPE 53 145 155

Figure S26.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.029

Table S27.  Gene #35: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
20P GAIN CNV 71 54 23
20P GAIN WILD-TYPE 110 101 112

Figure S27.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 2.99e-09 (Fisher's exact test), Q value = 2e-06

Table S28.  Gene #35: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
20P GAIN CNV 42 37 101
20P GAIN WILD-TYPE 119 151 111

Figure S28.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 9.25e-11 (Fisher's exact test), Q value = 6.3e-08

Table S29.  Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20Q GAIN CNV 35 23 79 17
20Q GAIN WILD-TYPE 112 73 73 96

Figure S29.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.02e-11 (Fisher's exact test), Q value = 7e-09

Table S30.  Gene #36: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
20Q GAIN CNV 63 25 66
20Q GAIN WILD-TYPE 54 146 154

Figure S30.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.011

Table S31.  Gene #36: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
20Q GAIN CNV 72 53 22
20Q GAIN WILD-TYPE 109 102 113

Figure S31.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 5.68e-09 (Fisher's exact test), Q value = 3.8e-06

Table S32.  Gene #36: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
20Q GAIN CNV 40 38 100
20Q GAIN WILD-TYPE 121 150 112

Figure S32.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.000339 (Fisher's exact test), Q value = 0.22

Table S33.  Gene #45: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
3Q LOSS CNV 10 6 0
3Q LOSS WILD-TYPE 151 182 212

Figure S33.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 9.04e-10 (Fisher's exact test), Q value = 6.1e-07

Table S34.  Gene #50: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
6P LOSS CNV 33 8 5
6P LOSS WILD-TYPE 128 180 207

Figure S34.  Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 3.56e-09 (Fisher's exact test), Q value = 2.4e-06

Table S35.  Gene #51: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
6Q LOSS CNV 47 12 21
6Q LOSS WILD-TYPE 114 176 191

Figure S35.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'MRNA_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 1e-04

Table S36.  Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10P LOSS CNV 116 61 138 76
10P LOSS WILD-TYPE 31 35 14 37

Figure S36.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.018

Table S37.  Gene #58: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
10P LOSS CNV 105 115 171
10P LOSS WILD-TYPE 12 56 49

Figure S37.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 5.6e-09 (Fisher's exact test), Q value = 3.8e-06

Table S38.  Gene #58: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
10P LOSS CNV 159 129 80
10P LOSS WILD-TYPE 22 26 55

Figure S38.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 8.21e-29 (Fisher's exact test), Q value = 5.7e-26

Table S39.  Gene #58: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
10P LOSS CNV 137 94 203
10P LOSS WILD-TYPE 24 94 9

Figure S39.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 3.53e-08 (Fisher's exact test), Q value = 2.4e-05

Table S40.  Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10Q LOSS CNV 117 66 143 79
10Q LOSS WILD-TYPE 30 30 9 34

Figure S40.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.81e-06 (Fisher's exact test), Q value = 0.0012

Table S41.  Gene #59: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
10Q LOSS CNV 110 121 174
10Q LOSS WILD-TYPE 7 50 46

Figure S41.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 2.17e-06 (Fisher's exact test), Q value = 0.0014

Table S42.  Gene #59: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
10Q LOSS CNV 162 130 90
10Q LOSS WILD-TYPE 19 25 45

Figure S42.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1.33e-31 (Fisher's exact test), Q value = 9.3e-29

Table S43.  Gene #59: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
10Q LOSS CNV 140 99 208
10Q LOSS WILD-TYPE 21 89 4

Figure S43.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 6.96e-05 (Fisher's exact test), Q value = 0.045

Table S44.  Gene #59: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 58 44 45
10Q LOSS CNV 42 40 44 39
10Q LOSS WILD-TYPE 12 18 0 6

Figure S44.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'11p loss' versus 'MRNA_CNMF'

P value = 6.25e-09 (Fisher's exact test), Q value = 4.2e-06

Table S45.  Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11P LOSS CNV 12 28 4 16
11P LOSS WILD-TYPE 135 68 148 97

Figure S45.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.014

Table S46.  Gene #60: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
11P LOSS CNV 4 35 21
11P LOSS WILD-TYPE 113 136 199

Figure S46.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'MIR_CHIERARCHICAL'

P value = 4.38e-06 (Fisher's exact test), Q value = 0.0029

Table S47.  Gene #60: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
11P LOSS CNV 9 17 32
11P LOSS WILD-TYPE 172 138 103

Figure S47.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 2.09e-11 (Fisher's exact test), Q value = 1.4e-08

Table S48.  Gene #60: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
11P LOSS CNV 37 23 3
11P LOSS WILD-TYPE 124 165 209

Figure S48.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.02

Table S49.  Gene #61: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11Q LOSS CNV 15 22 5 11
11Q LOSS WILD-TYPE 132 74 147 102

Figure S49.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 5.26e-10 (Fisher's exact test), Q value = 3.6e-07

Table S50.  Gene #61: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
11Q LOSS CNV 35 15 4
11Q LOSS WILD-TYPE 126 173 208

Figure S50.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.085

Table S51.  Gene #64: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
13Q LOSS CNV 45 28 18 33
13Q LOSS WILD-TYPE 102 68 134 80

Figure S51.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000315 (Fisher's exact test), Q value = 0.2

Table S52.  Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
13Q LOSS CNV 13 49 62
13Q LOSS WILD-TYPE 104 122 158

Figure S52.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 8.87e-14 (Fisher's exact test), Q value = 6.1e-11

Table S53.  Gene #64: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
13Q LOSS CNV 69 50 19
13Q LOSS WILD-TYPE 92 138 193

Figure S53.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 2.72e-06 (Fisher's exact test), Q value = 0.0018

Table S54.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
14Q LOSS CNV 38 31 13 32
14Q LOSS WILD-TYPE 109 65 139 81

Figure S54.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 5.41e-33 (Fisher's exact test), Q value = 3.8e-30

Table S55.  Gene #65: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
14Q LOSS CNV 84 32 4
14Q LOSS WILD-TYPE 77 156 208

Figure S55.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.016

Table S56.  Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
15Q LOSS CNV 3 33 23
15Q LOSS WILD-TYPE 114 138 197

Figure S56.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 6.47e-06 (Fisher's exact test), Q value = 0.0043

Table S57.  Gene #66: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 155 135
15Q LOSS CNV 19 6 30
15Q LOSS WILD-TYPE 162 149 105

Figure S57.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 6.61e-06 (Fisher's exact test), Q value = 0.0044

Table S58.  Gene #66: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
15Q LOSS CNV 35 14 13
15Q LOSS WILD-TYPE 126 174 199

Figure S58.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 6.48e-06 (Fisher's exact test), Q value = 0.0043

Table S59.  Gene #69: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
17P LOSS CNV 20 14 2
17P LOSS WILD-TYPE 141 174 210

Figure S59.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'21q loss' versus 'MRNA_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.2

Table S60.  Gene #77: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
21Q LOSS CNV 1 12 5 5
21Q LOSS WILD-TYPE 146 84 147 108

Figure S60.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #78: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 188 212
22Q LOSS CNV 60 37 43
22Q LOSS WILD-TYPE 101 151 169

Figure S61.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 561

  • Number of significantly arm-level cnvs = 79

  • Number of molecular subtypes = 10

  • 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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