Correlation between copy number variations of arm-level result and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1G73BM5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Glioblastoma Multiforme (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1G73BM5
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 563 patients, 60 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'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 17p loss cnv correlated to 'CN_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, 60 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL
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
19p gain 0 (0%) 387 2.15e-14
(1.48e-11) 		3.12e-10
(2.12e-07) 		0.236
(1.00) 		0.000117
(0.0755) 		1.02e-23
(7.09e-21) 		0.000451
(0.286) 		0.0175
(1.00) 		3.09e-06
(0.00205) 		0.102
(1.00) 		0.00821
(1.00)
19q gain 0 (0%) 412 7.22e-16
(4.99e-13) 		3.75e-12
(2.57e-09) 		0.0671
(1.00) 		2.31e-05
(0.015) 		1.64e-28
(1.14e-25) 		0.0112
(1.00) 		0.0528
(1.00) 		4.31e-06
(0.00285) 		0.025
(1.00) 		0.0124
(1.00)
10q loss 0 (0%) 113 2.16e-06
(0.00144) 		4.5e-06
(0.00297) 		0.0242
(1.00) 		7.65e-06
(0.00501) 		3.09e-31
(2.15e-28) 		0.00202
(1.00) 		6.96e-05
(0.045) 		0.00164
(1.00) 		0.729
(1.00) 		0.0908
(1.00)
15q loss 0 (0%) 501 5.43e-05
(0.0352) 		0.000315
(0.201) 		0.000622
(0.393) 		4.06e-06
(0.00269) 		6.26e-06
(0.00412) 		0.000258
(0.165) 		0.108
(1.00) 		0.0224
(1.00) 		0.0153
(1.00) 		0.452
(1.00)
7p gain 0 (0%) 129 4.5e-08
(3.02e-05) 		7.2e-07
(0.000482) 		0.000718
(0.451) 		1.82e-09
(1.23e-06) 		2e-16
(1.38e-13) 		0.0011
(0.687) 		0.00162
(0.995) 		0.471
(1.00) 		0.0411
(1.00) 		0.00552
(1.00)
7q gain 0 (0%) 124 3.49e-06
(0.00231) 		1.75e-05
(0.0114) 		0.00102
(0.637) 		1.56e-06
(0.00104) 		9.36e-15
(6.46e-12) 		0.00348
(1.00) 		0.0199
(1.00) 		0.361
(1.00) 		0.0916
(1.00) 		0.0115
(1.00)
20p gain 0 (0%) 383 2.17e-13
(1.49e-10) 		3.72e-12
(2.55e-09) 		0.201
(1.00) 		6.21e-05
(0.0402) 		1.54e-09
(1.04e-06) 		0.0645
(1.00) 		0.0946
(1.00) 		0.00228
(1.00) 		0.914
(1.00) 		0.000713
(0.448)
20q gain 0 (0%) 385 3.25e-13
(2.23e-10) 		4.38e-11
(2.98e-08) 		0.157
(1.00) 		6.8e-06
(0.00446) 		2.98e-09
(2.01e-06) 		0.011
(1.00) 		0.0595
(1.00) 		0.00116
(0.72) 		0.834
(1.00) 		0.000403
(0.257)
10p loss 0 (0%) 126 1.2e-06
(0.000799) 		8.37e-06
(0.00548) 		0.0358
(1.00) 		1.58e-08
(1.07e-05) 		1.8e-28
(1.25e-25) 		0.00348
(1.00) 		0.000567
(0.358) 		0.000656
(0.413) 		0.531
(1.00) 		0.0603
(1.00)
11p loss 0 (0%) 499 1.2e-07
(8.04e-05) 		6.61e-06
(0.00434) 		0.0946
(1.00) 		2.43e-06
(0.00162) 		7.77e-12
(5.31e-09) 		0.00107
(0.668) 		0.679
(1.00) 		0.0659
(1.00) 		0.0443
(1.00) 		0.426
(1.00)
11q loss 0 (0%) 508 9.72e-05
(0.0627) 		0.00427
(1.00) 		0.512
(1.00) 		0.00501
(1.00) 		2.1e-10
(1.43e-07) 		0.254
(1.00) 		0.577
(1.00) 		0.0933
(1.00) 		0.648
(1.00) 		0.868
(1.00)
13q loss 0 (0%) 425 0.000801
(0.502) 		4.42e-05
(0.0287) 		0.569
(1.00) 		0.647
(1.00) 		4.3e-13
(2.95e-10) 		0.00114
(0.712) 		0.601
(1.00) 		0.0182
(1.00) 		0.22
(1.00) 		0.309
(1.00)
14q loss 0 (0%) 442 4.49e-07
(0.000301) 		0.025
(1.00) 		0.595
(1.00) 		0.714
(1.00) 		8.63e-34
(6.02e-31) 		0.0159
(1.00) 		0.753
(1.00) 		0.0604
(1.00) 		0.0359
(1.00) 		0.00494
(1.00)
1p gain 0 (0%) 523 0.681
(1.00) 		0.0934
(1.00) 		0.934
(1.00) 		0.0651
(1.00) 		1.1e-05
(0.00719) 		0.388
(1.00) 		0.478
(1.00) 		0.925
(1.00) 		0.46
(1.00) 		0.0696
(1.00)
1q gain 0 (0%) 518 0.621
(1.00) 		0.116
(1.00) 		0.44
(1.00) 		0.343
(1.00) 		2.64e-08
(1.78e-05) 		0.295
(1.00) 		0.713
(1.00) 		0.882
(1.00) 		1
(1.00) 		0.152
(1.00)
2q gain 0 (0%) 545 0.173
(1.00) 		0.447
(1.00) 		3.9e-05
(0.0254) 		0.0743
(1.00) 		0.372
(1.00) 		0.46
(1.00) 		0.535
(1.00) 		0.52
(1.00) 		0.795
(1.00) 		0.366
(1.00)
18p gain 0 (0%) 535 0.501
(1.00) 		0.188
(1.00) 		0.509
(1.00) 		0.364
(1.00) 		0.000326
(0.208) 		0.313
(1.00) 		0.408
(1.00) 		0.548
(1.00) 		0.0656
(1.00) 		0.259
(1.00)
18q gain 0 (0%) 533 0.11
(1.00) 		0.186
(1.00) 		0.356
(1.00) 		0.597
(1.00) 		0.000159
(0.102) 		0.313
(1.00) 		0.722
(1.00) 		0.407
(1.00) 		0.0209
(1.00) 		0.103
(1.00)
3q loss 0 (0%) 547 0.643
(1.00) 		0.473
(1.00) 		0.0271
(1.00) 		0.383
(1.00) 		0.000297
(0.19) 		0.807
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.278
(1.00)
6p loss 0 (0%) 516 0.98
(1.00) 		0.553
(1.00) 		0.375
(1.00) 		0.538
(1.00) 		2.84e-09
(1.92e-06) 		0.622
(1.00) 		0.914
(1.00) 		0.592
(1.00) 		0.896
(1.00) 		0.604
(1.00)
6q loss 0 (0%) 483 0.672
(1.00) 		0.58
(1.00) 		0.462
(1.00) 		0.112
(1.00) 		1.87e-08
(1.26e-05) 		0.0853
(1.00) 		0.896
(1.00) 		0.678
(1.00) 		0.824
(1.00) 		0.383
(1.00)
17p loss 0 (0%) 527 0.429
(1.00) 		0.62
(1.00) 		0.835
(1.00) 		0.633
(1.00) 		5.94e-06
(0.00391) 		0.18
(1.00) 		0.0555
(1.00) 		0.826
(1.00) 		0.503
(1.00) 		1
(1.00)
22q loss 0 (0%) 423 0.809
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.886
(1.00) 		0.000148
(0.0952) 		0.275
(1.00) 		0.731
(1.00) 		0.955
(1.00) 		0.156
(1.00) 		0.885
(1.00)
2p gain 0 (0%) 543 0.11
(1.00) 		0.786
(1.00) 		0.002
(1.00) 		0.128
(1.00) 		0.252
(1.00) 		0.46
(1.00) 		0.685
(1.00) 		0.385
(1.00) 		0.577
(1.00) 		0.797
(1.00)
3p gain 0 (0%) 533 0.0036
(1.00) 		0.0573
(1.00) 		0.551
(1.00) 		0.677
(1.00) 		0.0193
(1.00) 		0.15
(1.00) 		0.405
(1.00) 		0.137
(1.00) 		0.808
(1.00) 		0.779
(1.00)
3q gain 0 (0%) 533 0.0036
(1.00) 		0.0573
(1.00) 		0.551
(1.00) 		0.907
(1.00) 		0.0473
(1.00) 		0.15
(1.00) 		0.405
(1.00) 		0.137
(1.00) 		0.748
(1.00) 		0.58
(1.00)
4p gain 0 (0%) 548 0.747
(1.00) 		0.656
(1.00) 		0.382
(1.00) 		0.0456
(1.00) 		0.29
(1.00) 		0.444
(1.00) 		0.149
(1.00)
4q gain 0 (0%) 549 0.733
(1.00) 		0.633
(1.00) 		0.206
(1.00) 		0.0828
(1.00) 		0.193
(1.00) 		0.444
(1.00) 		0.149
(1.00)
5p gain 0 (0%) 533 0.112
(1.00) 		0.31
(1.00) 		0.241
(1.00) 		0.353
(1.00) 		0.0037
(1.00) 		0.169
(1.00) 		0.652
(1.00) 		0.201
(1.00) 		0.202
(1.00)
5q gain 0 (0%) 540 0.0427
(1.00) 		0.183
(1.00) 		0.0508
(1.00) 		0.0905
(1.00) 		0.0152
(1.00) 		0.442
(1.00) 		0.365
(1.00)
6p gain 0 (0%) 556 0.79
(1.00) 		0.769
(1.00) 		0.657
(1.00) 		0.395
(1.00) 		0.161
(1.00)
6q gain 0 (0%) 554 0.237
(1.00) 		0.601
(1.00) 		0.595
(1.00) 		0.746
(1.00) 		0.0295
(1.00)
8p gain 0 (0%) 537 0.00124
(0.767) 		0.0814
(1.00) 		0.335
(1.00) 		0.00812
(1.00) 		0.0015
(0.924) 		0.15
(1.00) 		0.0641
(1.00) 		0.06
(1.00) 		0.808
(1.00) 		0.551
(1.00)
8q gain 0 (0%) 532 0.000511
(0.324) 		0.0416
(1.00) 		0.286
(1.00) 		0.00535
(1.00) 		0.00362
(1.00) 		0.0434
(1.00) 		0.0641
(1.00) 		0.06
(1.00) 		0.338
(1.00) 		0.547
(1.00)
9p gain 0 (0%) 546 0.234
(1.00) 		0.0394
(1.00) 		0.738
(1.00) 		0.56
(1.00) 		0.0422
(1.00) 		0.544
(1.00) 		0.215
(1.00) 		0.305
(1.00) 		0.319
(1.00) 		0.766
(1.00)
9q gain 0 (0%) 529 0.431
(1.00) 		0.0317
(1.00) 		0.619
(1.00) 		0.739
(1.00) 		0.169
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.116
(1.00) 		0.588
(1.00) 		0.67
(1.00)
10p gain 0 (0%) 551 0.00052
(0.329) 		0.00472
(1.00) 		0.0911
(1.00) 		0.00145
(0.893) 		0.00123
(0.762) 		0.307
(1.00) 		0.384
(1.00)
11p gain 0 (0%) 559 1
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.497
(1.00) 		0.259
(1.00)
11q gain 0 (0%) 556 0.152
(1.00) 		0.209
(1.00) 		0.265
(1.00) 		0.0781
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.421
(1.00)
12p gain 0 (0%) 520 0.413
(1.00) 		0.201
(1.00) 		1
(1.00) 		0.265
(1.00) 		0.00126
(0.78) 		0.446
(1.00) 		0.36
(1.00) 		0.8
(1.00) 		0.0427
(1.00) 		0.259
(1.00)
12q gain 0 (0%) 530 0.32
(1.00) 		0.0664
(1.00) 		0.993
(1.00) 		0.209
(1.00) 		0.00567
(1.00) 		0.634
(1.00) 		0.55
(1.00) 		0.695
(1.00) 		0.109
(1.00) 		0.7
(1.00)
13q gain 0 (0%) 560 0.777
(1.00) 		0.792
(1.00) 		0.156
(1.00) 		0.497
(1.00) 		0.289
(1.00) 		1
(1.00) 		0.527
(1.00)
14q gain 0 (0%) 556 0.706
(1.00) 		0.674
(1.00) 		0.0567
(1.00) 		0.564
(1.00) 		0.638
(1.00)
15q gain 0 (0%) 557 0.379
(1.00) 		0.536
(1.00) 		0.512
(1.00) 		0.588
(1.00) 		0.0126
(1.00)
16p gain 0 (0%) 545 0.0318
(1.00) 		0.297
(1.00) 		0.6
(1.00) 		0.263
(1.00) 		0.0155
(1.00) 		0.332
(1.00) 		0.442
(1.00)
16q gain 0 (0%) 545 0.048
(1.00) 		0.253
(1.00) 		0.439
(1.00) 		0.0325
(1.00) 		0.0155
(1.00) 		0.433
(1.00) 		0.442
(1.00)
17p gain 0 (0%) 552 0.0188
(1.00) 		0.389
(1.00) 		0.721
(1.00) 		0.349
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.284
(1.00)
17q gain 0 (0%) 544 0.22
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.609
(1.00) 		0.0584
(1.00) 		0.786
(1.00) 		0.384
(1.00) 		0.208
(1.00) 		0.562
(1.00)
21q gain 0 (0%) 527 0.00268
(1.00) 		0.0318
(1.00) 		0.00816
(1.00) 		0.00191
(1.00) 		0.0469
(1.00) 		0.411
(1.00) 		0.912
(1.00) 		0.0171
(1.00) 		0.0329
(1.00)
22q gain 0 (0%) 552 0.0378
(1.00) 		0.143
(1.00) 		0.127
(1.00) 		0.48
(1.00) 		0.0767
(1.00) 		1
(1.00) 		0.284
(1.00)
Xq gain 0 (0%) 559 0.331
(1.00) 		0.468
(1.00) 		0.757
(1.00) 		0.259
(1.00) 		0.0702
(1.00)
1p loss 0 (0%) 558 0.849
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.0996
(1.00) 		0.532
(1.00)
1q loss 0 (0%) 559 0.218
(1.00) 		1
(1.00) 		0.682
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 0 (0%) 553 0.0274
(1.00) 		0.0705
(1.00) 		0.656
(1.00) 		0.112
(1.00) 		0.163
(1.00) 		0.135
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.0393
(1.00) 		0.12
(1.00)
2q loss 0 (0%) 554 0.035
(1.00) 		0.071
(1.00) 		0.236
(1.00) 		0.0562
(1.00) 		0.183
(1.00) 		0.135
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.0393
(1.00) 		0.12
(1.00)
3p loss 0 (0%) 541 0.854
(1.00) 		0.513
(1.00) 		0.582
(1.00) 		0.502
(1.00) 		0.00763
(1.00) 		0.15
(1.00) 		0.0835
(1.00) 		0.653
(1.00) 		0.37
(1.00) 		0.436
(1.00)
4p loss 0 (0%) 537 0.0199
(1.00) 		0.669
(1.00) 		0.175
(1.00) 		0.0211
(1.00) 		0.876
(1.00) 		0.761
(1.00) 		0.0903
(1.00) 		0.43
(1.00) 		0.14
(1.00) 		0.436
(1.00)
4q loss 0 (0%) 538 0.0426
(1.00) 		0.644
(1.00) 		0.162
(1.00) 		0.145
(1.00) 		0.101
(1.00) 		0.701
(1.00) 		0.0985
(1.00) 		0.551
(1.00) 		0.517
(1.00) 		0.562
(1.00)
5p loss 0 (0%) 542 0.00423
(1.00) 		0.0947
(1.00) 		0.186
(1.00) 		0.0966
(1.00) 		0.11
(1.00) 		0.0858
(1.00) 		0.469
(1.00) 		1
(1.00) 		0.785
(1.00) 		0.495
(1.00)
5q loss 0 (0%) 543 0.0743
(1.00) 		0.872
(1.00) 		0.304
(1.00) 		0.122
(1.00) 		0.0512
(1.00) 		0.0858
(1.00) 		0.873
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.483
(1.00)
7p loss 0 (0%) 558 0.542
(1.00) 		0.453
(1.00) 		0.81
(1.00) 		0.0341
(1.00) 		0.532
(1.00)
7q loss 0 (0%) 559 0.849
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.0996
(1.00) 		0.833
(1.00)
8p loss 0 (0%) 529 0.894
(1.00) 		0.593
(1.00) 		0.783
(1.00) 		0.239
(1.00) 		0.272
(1.00) 		0.134
(1.00) 		0.651
(1.00) 		0.912
(1.00) 		0.726
(1.00) 		0.7
(1.00)
8q loss 0 (0%) 542 0.717
(1.00) 		0.144
(1.00) 		0.384
(1.00) 		0.185
(1.00) 		0.0154
(1.00) 		0.212
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.365
(1.00)
9p loss 0 (0%) 399 0.0137
(1.00) 		0.00133
(0.822) 		0.832
(1.00) 		0.147
(1.00) 		0.227
(1.00) 		0.921
(1.00) 		0.282
(1.00) 		0.0585
(1.00) 		0.0348
(1.00) 		0.026
(1.00)
9q loss 0 (0%) 500 0.0461
(1.00) 		0.0252
(1.00) 		0.564
(1.00) 		0.262
(1.00) 		0.0587
(1.00) 		0.552
(1.00) 		0.0367
(1.00) 		0.0528
(1.00) 		0.636
(1.00) 		0.184
(1.00)
12p loss 0 (0%) 525 0.0116
(1.00) 		0.0172
(1.00) 		0.151
(1.00) 		0.0306
(1.00) 		0.756
(1.00) 		0.425
(1.00) 		0.1
(1.00) 		0.474
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 0 (0%) 528 0.00882
(1.00) 		0.0185
(1.00) 		0.61
(1.00) 		0.0536
(1.00) 		0.127
(1.00) 		0.14
(1.00) 		0.102
(1.00) 		0.695
(1.00) 		0.839
(1.00) 		0.547
(1.00)
16p loss 0 (0%) 540 0.2
(1.00) 		0.684
(1.00) 		0.46
(1.00) 		0.793
(1.00) 		0.127
(1.00) 		0.397
(1.00) 		0.644
(1.00) 		0.89
(1.00) 		0.501
(1.00) 		0.185
(1.00)
16q loss 0 (0%) 522 0.112
(1.00) 		0.0209
(1.00) 		0.122
(1.00) 		0.52
(1.00) 		0.287
(1.00) 		0.228
(1.00) 		0.0754
(1.00) 		0.945
(1.00) 		0.706
(1.00) 		0.569
(1.00)
17q loss 0 (0%) 544 0.39
(1.00) 		0.136
(1.00) 		0.402
(1.00) 		0.347
(1.00) 		0.0017
(1.00) 		0.214
(1.00) 		0.277
(1.00) 		0.168
(1.00) 		0.0933
(1.00)
18p loss 0 (0%) 519 0.0244
(1.00) 		0.0871
(1.00) 		0.504
(1.00) 		0.712
(1.00) 		0.00156
(0.96) 		0.0747
(1.00) 		0.246
(1.00) 		0.0387
(1.00) 		0.0596
(1.00) 		0.521
(1.00)
18q loss 0 (0%) 524 0.28
(1.00) 		0.381
(1.00) 		0.337
(1.00) 		0.923
(1.00) 		0.0795
(1.00) 		0.0599
(1.00) 		0.154
(1.00) 		0.00651
(1.00) 		0.567
(1.00) 		0.687
(1.00)
19p loss 0 (0%) 550 0.00284
(1.00) 		0.024
(1.00) 		0.000418
(0.266) 		0.00738
(1.00) 		0.158
(1.00) 		0.592
(1.00) 		0.371
(1.00) 		0.574
(1.00) 		0.577
(1.00) 		0.157
(1.00)
19q loss 0 (0%) 545 0.00902
(1.00) 		0.047
(1.00) 		0.00964
(1.00) 		0.00144
(0.888) 		0.0738
(1.00) 		0.592
(1.00) 		0.371
(1.00) 		0.574
(1.00) 		0.858
(1.00) 		0.365
(1.00)
20p loss 0 (0%) 552 0.054
(1.00) 		0.129
(1.00) 		0.116
(1.00) 		0.0621
(1.00) 		0.00377
(1.00) 		0.414
(1.00) 		0.384
(1.00)
20q loss 0 (0%) 553 0.0789
(1.00) 		0.171
(1.00) 		0.656
(1.00) 		0.399
(1.00) 		0.019
(1.00) 		0.414
(1.00) 		0.384
(1.00)
21q loss 0 (0%) 538 0.0133
(1.00) 		0.0152
(1.00) 		0.0903
(1.00) 		0.0121
(1.00) 		0.0284
(1.00) 		0.219
(1.00) 		0.0279
(1.00) 		0.326
(1.00) 		0.602
(1.00) 		0.848
(1.00)
Xq loss 0 (0%) 552 0.443
(1.00) 		0.468
(1.00) 		0.116
(1.00) 		0.37
(1.00) 		0.153
(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 = 1.1e-05 (Fisher's exact test), Q value = 0.0072

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
1P GAIN CNV 25 6 9
1P GAIN WILD-TYPE 136 208 179

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

'1q gain' versus 'CN_CNMF'

P value = 2.64e-08 (Fisher's exact test), Q value = 1.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
1Q GAIN CNV 30 4 11
1Q GAIN WILD-TYPE 131 210 177

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

'2q gain' versus 'MIR_CNMF'

P value = 3.9e-05 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 157 72 104
2Q GAIN CNV 6 0 0 10
2Q GAIN WILD-TYPE 133 157 72 94

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

'7p gain' versus 'MRNA_CNMF'

P value = 4.5e-08 (Fisher's exact test), Q value = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
7P GAIN CNV 141 104 145
7P GAIN WILD-TYPE 31 66 22

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

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 7.2e-07 (Fisher's exact test), Q value = 0.00048

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
7P GAIN CNV 179 108 103
7P GAIN WILD-TYPE 38 18 63

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

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1.82e-09 (Fisher's exact test), Q value = 1.2e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
7P GAIN CNV 135 157 75
7P GAIN WILD-TYPE 28 22 55

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

'7p gain' versus 'CN_CNMF'

P value = 2e-16 (Fisher's exact test), Q value = 1.4e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
7P GAIN CNV 140 190 104
7P GAIN WILD-TYPE 21 24 84

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

'7q gain' versus 'MRNA_CNMF'

P value = 3.49e-06 (Fisher's exact test), Q value = 0.0023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
7Q GAIN CNV 140 109 144
7Q GAIN WILD-TYPE 32 61 23

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

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
7Q GAIN CNV 179 107 107
7Q GAIN WILD-TYPE 38 19 59

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

'7q gain' versus 'MIR_CHIERARCHICAL'

P value = 1.56e-06 (Fisher's exact test), Q value = 0.001

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
7Q GAIN CNV 135 153 80
7Q GAIN WILD-TYPE 28 26 50

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

'7q gain' versus 'CN_CNMF'

P value = 9.36e-15 (Fisher's exact test), Q value = 6.5e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
7Q GAIN CNV 137 193 109
7Q GAIN WILD-TYPE 24 21 79

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

'18p gain' versus 'CN_CNMF'

P value = 0.000326 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #31: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
18P GAIN CNV 17 3 8
18P GAIN WILD-TYPE 144 211 180

Figure S12.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.1

Table S13.  Gene #32: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
18Q GAIN CNV 18 3 9
18Q GAIN WILD-TYPE 143 211 179

Figure S13.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'MRNA_CNMF'

P value = 2.15e-14 (Fisher's exact test), Q value = 1.5e-11

Table S14.  Gene #33: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
19P GAIN CNV 46 23 88
19P GAIN WILD-TYPE 126 147 79

Figure S14.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.12e-10 (Fisher's exact test), Q value = 2.1e-07

Table S15.  Gene #33: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
19P GAIN CNV 64 66 27
19P GAIN WILD-TYPE 153 60 139

Figure S15.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.075

Table S16.  Gene #33: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
19P GAIN CNV 52 75 25
19P GAIN WILD-TYPE 111 104 105

Figure S16.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.02e-23 (Fisher's exact test), Q value = 7.1e-21

Table S17.  Gene #33: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
19P GAIN CNV 24 122 30
19P GAIN WILD-TYPE 137 92 158

Figure S17.  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 = 0.002

Table S18.  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 S18.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 7.22e-16 (Fisher's exact test), Q value = 5e-13

Table S19.  Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
19Q GAIN CNV 41 14 79
19Q GAIN WILD-TYPE 131 156 88

Figure S19.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.75e-12 (Fisher's exact test), Q value = 2.6e-09

Table S20.  Gene #34: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
19Q GAIN CNV 57 60 17
19Q GAIN WILD-TYPE 160 66 149

Figure S20.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'MIR_CHIERARCHICAL'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.015

Table S21.  Gene #34: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
19Q GAIN CNV 48 66 18
19Q GAIN WILD-TYPE 115 113 112

Figure S21.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1.64e-28 (Fisher's exact test), Q value = 1.1e-25

Table S22.  Gene #34: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
19Q GAIN CNV 14 115 22
19Q GAIN WILD-TYPE 147 99 166

Figure S22.  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 S23.  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 S23.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 2.17e-13 (Fisher's exact test), Q value = 1.5e-10

Table S24.  Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
20P GAIN CNV 41 27 88
20P GAIN WILD-TYPE 131 143 79

Figure S24.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.72e-12 (Fisher's exact test), Q value = 2.5e-09

Table S25.  Gene #35: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
20P GAIN CNV 59 70 27
20P GAIN WILD-TYPE 158 56 139

Figure S25.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 6.21e-05 (Fisher's exact test), Q value = 0.04

Table S26.  Gene #35: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
20P GAIN CNV 58 69 22
20P GAIN WILD-TYPE 105 110 108

Figure S26.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1.54e-09 (Fisher's exact test), Q value = 1e-06

Table S27.  Gene #35: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
20P GAIN CNV 42 102 36
20P GAIN WILD-TYPE 119 112 152

Figure S27.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 3.25e-13 (Fisher's exact test), Q value = 2.2e-10

Table S28.  Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
20Q GAIN CNV 42 26 87
20Q GAIN WILD-TYPE 130 144 80

Figure S28.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.38e-11 (Fisher's exact test), Q value = 3e-08

Table S29.  Gene #36: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
20Q GAIN CNV 62 67 26
20Q GAIN WILD-TYPE 155 59 140

Figure S29.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 6.8e-06 (Fisher's exact test), Q value = 0.0045

Table S30.  Gene #36: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
20Q GAIN CNV 57 71 20
20Q GAIN WILD-TYPE 106 108 110

Figure S30.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 2.98e-09 (Fisher's exact test), Q value = 2e-06

Table S31.  Gene #36: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
20Q GAIN CNV 40 101 37
20Q GAIN WILD-TYPE 121 113 151

Figure S31.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.000297 (Fisher's exact test), Q value = 0.19

Table S32.  Gene #45: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
3Q LOSS CNV 10 0 6
3Q LOSS WILD-TYPE 151 214 182

Figure S32.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 2.84e-09 (Fisher's exact test), Q value = 1.9e-06

Table S33.  Gene #50: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
6P LOSS CNV 33 6 8
6P LOSS WILD-TYPE 128 208 180

Figure S33.  Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1.87e-08 (Fisher's exact test), Q value = 1.3e-05

Table S34.  Gene #51: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
6Q LOSS CNV 46 21 13
6Q LOSS WILD-TYPE 115 193 175

Figure S34.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'MRNA_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 8e-04

Table S35.  Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
10P LOSS CNV 131 112 149
10P LOSS WILD-TYPE 41 58 18

Figure S35.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.37e-06 (Fisher's exact test), Q value = 0.0055

Table S36.  Gene #58: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
10P LOSS CNV 169 113 110
10P LOSS WILD-TYPE 48 13 56

Figure S36.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 1.58e-08 (Fisher's exact test), Q value = 1.1e-05

Table S37.  Gene #58: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
10P LOSS CNV 136 156 77
10P LOSS WILD-TYPE 27 23 53

Figure S37.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1.8e-28 (Fisher's exact test), Q value = 1.2e-25

Table S38.  Gene #58: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
10P LOSS CNV 137 205 95
10P LOSS WILD-TYPE 24 9 93

Figure S38.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.0014

Table S39.  Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
10Q LOSS CNV 133 120 153
10Q LOSS WILD-TYPE 39 50 14

Figure S39.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.5e-06 (Fisher's exact test), Q value = 0.003

Table S40.  Gene #59: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
10Q LOSS CNV 172 117 117
10Q LOSS WILD-TYPE 45 9 49

Figure S40.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 7.65e-06 (Fisher's exact test), Q value = 0.005

Table S41.  Gene #59: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
10Q LOSS CNV 137 159 87
10Q LOSS WILD-TYPE 26 20 43

Figure S41.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 3.09e-31 (Fisher's exact test), Q value = 2.2e-28

Table S42.  Gene #59: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
10Q LOSS CNV 140 210 100
10Q LOSS WILD-TYPE 21 4 88

Figure S42.  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 S43.  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 S43.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'11p loss' versus 'MRNA_CNMF'

P value = 1.2e-07 (Fisher's exact test), Q value = 8e-05

Table S44.  Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
11P LOSS CNV 18 38 5
11P LOSS WILD-TYPE 154 132 162

Figure S44.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.61e-06 (Fisher's exact test), Q value = 0.0043

Table S45.  Gene #60: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
11P LOSS CNV 22 4 35
11P LOSS WILD-TYPE 195 122 131

Figure S45.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'MIR_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0016

Table S46.  Gene #60: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
11P LOSS CNV 18 9 32
11P LOSS WILD-TYPE 145 170 98

Figure S46.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 7.77e-12 (Fisher's exact test), Q value = 5.3e-09

Table S47.  Gene #60: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
11P LOSS CNV 38 3 23
11P LOSS WILD-TYPE 123 211 165

Figure S47.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 9.72e-05 (Fisher's exact test), Q value = 0.063

Table S48.  Gene #61: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
11Q LOSS CNV 18 30 6
11Q LOSS WILD-TYPE 154 140 161

Figure S48.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 2.1e-10 (Fisher's exact test), Q value = 1.4e-07

Table S49.  Gene #61: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
11Q LOSS CNV 36 4 15
11Q LOSS WILD-TYPE 125 210 173

Figure S49.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.029

Table S50.  Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
13Q LOSS CNV 63 13 48
13Q LOSS WILD-TYPE 154 113 118

Figure S50.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 4.3e-13 (Fisher's exact test), Q value = 2.9e-10

Table S51.  Gene #64: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
13Q LOSS CNV 68 20 50
13Q LOSS WILD-TYPE 93 194 138

Figure S51.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 4.49e-07 (Fisher's exact test), Q value = 3e-04

Table S52.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
14Q LOSS CNV 47 52 15
14Q LOSS WILD-TYPE 125 118 152

Figure S52.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 8.63e-34 (Fisher's exact test), Q value = 6e-31

Table S53.  Gene #65: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
14Q LOSS CNV 85 4 32
14Q LOSS WILD-TYPE 76 210 156

Figure S53.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MRNA_CNMF'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.035

Table S54.  Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 170 167
15Q LOSS CNV 17 34 8
15Q LOSS WILD-TYPE 155 136 159

Figure S54.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S55.  Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 217 126 166
15Q LOSS CNV 23 5 31
15Q LOSS WILD-TYPE 194 121 135

Figure S55.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 4.06e-06 (Fisher's exact test), Q value = 0.0027

Table S56.  Gene #66: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 179 130
15Q LOSS CNV 6 20 29
15Q LOSS WILD-TYPE 157 159 101

Figure S56.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0041

Table S57.  Gene #66: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
15Q LOSS CNV 35 13 14
15Q LOSS WILD-TYPE 126 201 174

Figure S57.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.000258 (Fisher's exact test), Q value = 0.17

Table S58.  Gene #66: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 20 24 27
15Q LOSS CNV 1 2 0 9
15Q LOSS WILD-TYPE 37 18 24 18

Figure S58.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 5.94e-06 (Fisher's exact test), Q value = 0.0039

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
17P LOSS CNV 20 2 14
17P LOSS WILD-TYPE 141 212 174

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

'22q loss' versus 'CN_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.095

Table S60.  Gene #78: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 214 188
22Q LOSS CNV 60 43 37
22Q LOSS WILD-TYPE 101 171 151

Figure S60.  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 = 563

  • 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] 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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