Correlation between copy number variations of arm-level result and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1542KMV
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/C1542KMV
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, 63 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',  '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'.

  • 5p loss cnv correlated to 'MRNA_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' 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'.

  • 19p loss cnv correlated to 'MRNA_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, 63 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 6.9e-12
(4.74e-09) 		1.21e-09
(8.22e-07) 		0.236
(1.00) 		0.000117
(0.0756) 		1.02e-23
(7.09e-21) 		0.000521
(0.329) 		0.0175
(1.00) 		3.09e-06
(0.00205) 		0.102
(1.00) 		0.00821
(1.00)
19q gain 0 (0%) 412 1.75e-14
(1.21e-11) 		5.09e-12
(3.5e-09) 		0.0671
(1.00) 		2.31e-05
(0.0151) 		1.64e-28
(1.14e-25) 		0.0171
(1.00) 		0.0528
(1.00) 		4.31e-06
(0.00285) 		0.025
(1.00) 		0.0124
(1.00)
10q loss 0 (0%) 113 3.2e-08
(2.15e-05) 		3.38e-05
(0.022) 		0.0242
(1.00) 		7.65e-06
(0.00504) 		3.09e-31
(2.15e-28) 		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%) 129 1.03e-05
(0.00679) 		2.46e-07
(0.000165) 		0.000718
(0.449) 		1.82e-09
(1.23e-06) 		2e-16
(1.38e-13) 		0.00218
(1.00) 		0.00162
(0.992) 		0.471
(1.00) 		0.0411
(1.00) 		0.00552
(1.00)
7q gain 0 (0%) 124 3.64e-06
(0.00242) 		1.75e-05
(0.0114) 		0.00102
(0.633) 		1.56e-06
(0.00104) 		9.36e-15
(6.47e-12) 		0.00211
(1.00) 		0.0199
(1.00) 		0.361
(1.00) 		0.0916
(1.00) 		0.0115
(1.00)
20p gain 0 (0%) 383 1.24e-10
(8.47e-08) 		9.24e-11
(6.32e-08) 		0.201
(1.00) 		6.21e-05
(0.0402) 		1.54e-09
(1.04e-06) 		0.0654
(1.00) 		0.0946
(1.00) 		0.00228
(1.00) 		0.914
(1.00) 		0.000713
(0.446)
20q gain 0 (0%) 385 4.25e-11
(2.91e-08) 		1.02e-10
(6.94e-08) 		0.157
(1.00) 		6.8e-06
(0.00448) 		2.98e-09
(2.01e-06) 		0.016
(1.00) 		0.0595
(1.00) 		0.00116
(0.718) 		0.834
(1.00) 		0.000403
(0.256)
10p loss 0 (0%) 126 1.18e-07
(7.9e-05) 		2.72e-05
(0.0177) 		0.0358
(1.00) 		1.58e-08
(1.07e-05) 		1.8e-28
(1.25e-25) 		0.00564
(1.00) 		0.000567
(0.357) 		0.000656
(0.411) 		0.531
(1.00) 		0.0603
(1.00)
11p loss 0 (0%) 499 3.59e-09
(2.42e-06) 		6.68e-05
(0.0432) 		0.0946
(1.00) 		2.43e-06
(0.00162) 		7.77e-12
(5.33e-09) 		0.00192
(1.00) 		0.679
(1.00) 		0.0659
(1.00) 		0.0443
(1.00) 		0.426
(1.00)
15q loss 0 (0%) 501 0.00183
(1.00) 		0.000233
(0.149) 		0.000622
(0.391) 		4.06e-06
(0.00269) 		6.26e-06
(0.00413) 		0.000612
(0.385) 		0.108
(1.00) 		0.0224
(1.00) 		0.0153
(1.00) 		0.452
(1.00)
11q loss 0 (0%) 508 2.36e-05
(0.0154) 		0.0276
(1.00) 		0.512
(1.00) 		0.00501
(1.00) 		2.1e-10
(1.43e-07) 		0.312
(1.00) 		0.577
(1.00) 		0.0933
(1.00) 		0.648
(1.00) 		0.868
(1.00)
13q loss 0 (0%) 425 0.000132
(0.085) 		0.00138
(0.853) 		0.569
(1.00) 		0.647
(1.00) 		4.3e-13
(2.96e-10) 		0.00113
(0.7) 		0.601
(1.00) 		0.0182
(1.00) 		0.22
(1.00) 		0.309
(1.00)
14q loss 0 (0%) 442 3.55e-06
(0.00236) 		0.0185
(1.00) 		0.595
(1.00) 		0.714
(1.00) 		8.63e-34
(6.02e-31) 		0.0149
(1.00) 		0.753
(1.00) 		0.0604
(1.00) 		0.0359
(1.00) 		0.00494
(1.00)
1p gain 0 (0%) 523 0.465
(1.00) 		0.25
(1.00) 		0.934
(1.00) 		0.0651
(1.00) 		1.1e-05
(0.00723) 		0.636
(1.00) 		0.478
(1.00) 		0.925
(1.00) 		0.46
(1.00) 		0.0696
(1.00)
1q gain 0 (0%) 518 0.0132
(1.00) 		0.183
(1.00) 		0.44
(1.00) 		0.343
(1.00) 		2.64e-08
(1.77e-05) 		0.448
(1.00) 		0.713
(1.00) 		0.882
(1.00) 		1
(1.00) 		0.152
(1.00)
2q gain 0 (0%) 545 0.132
(1.00) 		0.155
(1.00) 		3.9e-05
(0.0253) 		0.0743
(1.00) 		0.372
(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%) 537 0.000176
(0.113) 		0.142
(1.00) 		0.335
(1.00) 		0.00812
(1.00) 		0.0015
(0.922) 		0.164
(1.00) 		0.0641
(1.00) 		0.06
(1.00) 		0.808
(1.00) 		0.551
(1.00)
10p gain 0 (0%) 551 3.57e-05
(0.0232) 		0.0038
(1.00) 		0.0911
(1.00) 		0.00145
(0.891) 		0.00123
(0.76) 		0.307
(1.00) 		0.384
(1.00)
18p gain 0 (0%) 535 0.0193
(1.00) 		0.507
(1.00) 		0.509
(1.00) 		0.364
(1.00) 		0.000326
(0.208) 		0.236
(1.00) 		0.408
(1.00) 		0.548
(1.00) 		0.0656
(1.00) 		0.259
(1.00)
18q gain 0 (0%) 533 0.0052
(1.00) 		0.643
(1.00) 		0.356
(1.00) 		0.597
(1.00) 		0.000159
(0.102) 		0.236
(1.00) 		0.722
(1.00) 		0.407
(1.00) 		0.0209
(1.00) 		0.103
(1.00)
3q loss 0 (0%) 547 0.255
(1.00) 		0.713
(1.00) 		0.0271
(1.00) 		0.383
(1.00) 		0.000297
(0.189) 		0.807
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.278
(1.00)
5p loss 0 (0%) 542 0.00029
(0.185) 		0.106
(1.00) 		0.186
(1.00) 		0.0966
(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)
6p loss 0 (0%) 516 0.923
(1.00) 		0.545
(1.00) 		0.375
(1.00) 		0.538
(1.00) 		2.84e-09
(1.92e-06) 		0.743
(1.00) 		0.914
(1.00) 		0.592
(1.00) 		0.896
(1.00) 		0.604
(1.00)
6q loss 0 (0%) 483 0.923
(1.00) 		0.544
(1.00) 		0.462
(1.00) 		0.112
(1.00) 		1.87e-08
(1.26e-05) 		0.0404
(1.00) 		0.896
(1.00) 		0.678
(1.00) 		0.824
(1.00) 		0.383
(1.00)
17p loss 0 (0%) 527 0.0987
(1.00) 		0.408
(1.00) 		0.835
(1.00) 		0.633
(1.00) 		5.94e-06
(0.00392) 		0.38
(1.00) 		0.0555
(1.00) 		0.826
(1.00) 		0.503
(1.00) 		1
(1.00)
19p loss 0 (0%) 550 0.000388
(0.246) 		0.0038
(1.00) 		0.000418
(0.265) 		0.00738
(1.00) 		0.158
(1.00) 		0.821
(1.00) 		0.371
(1.00) 		0.574
(1.00) 		0.577
(1.00) 		0.157
(1.00)
21q loss 0 (0%) 538 0.000263
(0.168) 		0.0154
(1.00) 		0.0903
(1.00) 		0.0121
(1.00) 		0.0284
(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%) 423 0.862
(1.00) 		0.908
(1.00) 		0.511
(1.00) 		0.886
(1.00) 		0.000148
(0.0952) 		0.322
(1.00) 		0.731
(1.00) 		0.955
(1.00) 		0.156
(1.00) 		0.885
(1.00)
2p gain 0 (0%) 543 0.1
(1.00) 		0.347
(1.00) 		0.002
(1.00) 		0.128
(1.00) 		0.252
(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%) 533 0.0106
(1.00) 		0.145
(1.00) 		0.551
(1.00) 		0.677
(1.00) 		0.0193
(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%) 533 0.0106
(1.00) 		0.145
(1.00) 		0.551
(1.00) 		0.907
(1.00) 		0.0473
(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%) 548 0.0312
(1.00) 		0.739
(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 0.4
(1.00) 		0.682
(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 0.301
(1.00) 		0.129
(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 0.258
(1.00) 		0.0524
(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 0.742
(1.00) 		0.675
(1.00) 		0.657
(1.00) 		0.395
(1.00) 		0.161
(1.00)
6q gain 0 (0%) 554 0.47
(1.00) 		0.665
(1.00) 		0.595
(1.00) 		0.746
(1.00) 		0.0295
(1.00)
8q gain 0 (0%) 532 0.000483
(0.305) 		0.0623
(1.00) 		0.286
(1.00) 		0.00535
(1.00) 		0.00362
(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%) 546 0.0293
(1.00) 		0.211
(1.00) 		0.738
(1.00) 		0.56
(1.00) 		0.0422
(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%) 529 0.115
(1.00) 		0.0676
(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)
11p gain 0 (0%) 559 0.881
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.497
(1.00) 		0.259
(1.00)
11q gain 0 (0%) 556 0.0768
(1.00) 		0.18
(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 0.419
(1.00) 		0.285
(1.00) 		1
(1.00) 		0.265
(1.00) 		0.00126
(0.778) 		0.49
(1.00) 		0.36
(1.00) 		0.8
(1.00) 		0.0427
(1.00) 		0.259
(1.00)
12q gain 0 (0%) 530 0.183
(1.00) 		0.0616
(1.00) 		0.993
(1.00) 		0.209
(1.00) 		0.00567
(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%) 560 0.149
(1.00) 		0.79
(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 0.535
(1.00) 		0.21
(1.00) 		0.0567
(1.00) 		0.564
(1.00) 		0.638
(1.00)
15q gain 0 (0%) 557 0.256
(1.00) 		0.533
(1.00) 		0.512
(1.00) 		0.588
(1.00) 		0.0126
(1.00)
16p gain 0 (0%) 545 0.0401
(1.00) 		0.0978
(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 0.0239
(1.00) 		0.0978
(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 0.0262
(1.00) 		0.392
(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 0.354
(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 0.028
(1.00) 		0.0353
(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 0.0151
(1.00) 		0.117
(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 0.256
(1.00) 		1
(1.00) 		0.757
(1.00) 		0.259
(1.00) 		0.0702
(1.00)
1p loss 0 (0%) 558 0.474
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.0996
(1.00) 		0.532
(1.00)
1q loss 0 (0%) 559 0.366
(1.00) 		1
(1.00) 		0.682
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 0 (0%) 553 0.0894
(1.00) 		0.0807
(1.00) 		0.656
(1.00) 		0.112
(1.00) 		0.163
(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%) 554 0.0647
(1.00) 		0.0735
(1.00) 		0.236
(1.00) 		0.0562
(1.00) 		0.183
(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%) 541 0.923
(1.00) 		0.323
(1.00) 		0.582
(1.00) 		0.502
(1.00) 		0.00763
(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%) 537 0.0755
(1.00) 		0.196
(1.00) 		0.175
(1.00) 		0.0211
(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%) 538 0.000818
(0.51) 		0.452
(1.00) 		0.162
(1.00) 		0.145
(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)
5q loss 0 (0%) 543 0.00339
(1.00) 		0.875
(1.00) 		0.304
(1.00) 		0.122
(1.00) 		0.0512
(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%) 558 0.236
(1.00) 		0.455
(1.00) 		0.81
(1.00) 		0.0341
(1.00) 		0.532
(1.00)
7q loss 0 (0%) 559 0.311
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.0996
(1.00) 		0.833
(1.00)
8p loss 0 (0%) 529 0.455
(1.00) 		0.561
(1.00) 		0.783
(1.00) 		0.239
(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%) 542 0.651
(1.00) 		0.127
(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 0.00515
(1.00) 		0.0102
(1.00) 		0.832
(1.00) 		0.147
(1.00) 		0.227
(1.00) 		0.843
(1.00) 		0.282
(1.00) 		0.0585
(1.00) 		0.0348
(1.00) 		0.026
(1.00)
9q loss 0 (0%) 500 0.376
(1.00) 		0.00152
(0.929) 		0.564
(1.00) 		0.262
(1.00) 		0.0587
(1.00) 		0.561
(1.00) 		0.0367
(1.00) 		0.0528
(1.00) 		0.636
(1.00) 		0.184
(1.00)
12p loss 0 (0%) 525 0.0419
(1.00) 		0.00836
(1.00) 		0.151
(1.00) 		0.0306
(1.00) 		0.756
(1.00) 		0.606
(1.00) 		0.1
(1.00) 		0.474
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 0 (0%) 528 0.0752
(1.00) 		0.00646
(1.00) 		0.61
(1.00) 		0.0536
(1.00) 		0.127
(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%) 540 0.128
(1.00) 		0.684
(1.00) 		0.46
(1.00) 		0.793
(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%) 522 0.0572
(1.00) 		0.192
(1.00) 		0.122
(1.00) 		0.52
(1.00) 		0.287
(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%) 544 0.176
(1.00) 		0.362
(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 0.00514
(1.00) 		0.0741
(1.00) 		0.504
(1.00) 		0.712
(1.00) 		0.00156
(0.957) 		0.181
(1.00) 		0.246
(1.00) 		0.0387
(1.00) 		0.0596
(1.00) 		0.521
(1.00)
18q loss 0 (0%) 524 0.443
(1.00) 		0.529
(1.00) 		0.337
(1.00) 		0.923
(1.00) 		0.0795
(1.00) 		0.187
(1.00) 		0.154
(1.00) 		0.00651
(1.00) 		0.567
(1.00) 		0.687
(1.00)
19q loss 0 (0%) 545 0.000875
(0.545) 		0.0145
(1.00) 		0.00964
(1.00) 		0.00144
(0.887) 		0.0738
(1.00) 		0.821
(1.00) 		0.371
(1.00) 		0.574
(1.00) 		0.858
(1.00) 		0.365
(1.00)
20p loss 0 (0%) 552 0.00328
(1.00) 		0.117
(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 0.0132
(1.00) 		0.16
(1.00) 		0.656
(1.00) 		0.399
(1.00) 		0.019
(1.00) 		0.414
(1.00) 		0.384
(1.00)
Xq loss 0 (0%) 552 0.448
(1.00) 		0.547
(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 = 1.03e-05 (Fisher's exact test), Q value = 0.0068

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
7P GAIN CNV 123 62 130 75
7P GAIN WILD-TYPE 24 32 22 41

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

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.46e-07 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
7P GAIN CNV 111 102 177
7P GAIN WILD-TYPE 19 64 36

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 = 3.64e-06 (Fisher's exact test), Q value = 0.0024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
7Q GAIN CNV 124 58 131 80
7Q GAIN WILD-TYPE 23 36 21 36

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 130 166 213
7Q GAIN CNV 110 107 176
7Q GAIN WILD-TYPE 20 59 37

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'

'8p gain' versus 'MRNA_CNMF'

P value = 0.000176 (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 94 152 116
8P GAIN CNV 2 10 2 10
8P GAIN WILD-TYPE 145 84 150 106

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

'10p gain' versus 'MRNA_CNMF'

P value = 3.57e-05 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
10P GAIN CNV 0 7 0 5
10P GAIN WILD-TYPE 147 87 152 111

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

'18p gain' versus 'CN_CNMF'

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

Table S14.  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 S14.  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 S15.  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 S15.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'MRNA_CNMF'

P value = 6.9e-12 (Fisher's exact test), Q value = 4.7e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
19P GAIN CNV 36 24 81 16
19P GAIN WILD-TYPE 111 70 71 100

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

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-09 (Fisher's exact test), Q value = 8.2e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
19P GAIN CNV 64 25 68
19P GAIN WILD-TYPE 66 141 145

Figure S17.  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 = 0.076

Table S18.  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 S18.  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 S19.  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 S19.  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 S20.  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 S20.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 1.75e-14 (Fisher's exact test), Q value = 1.2e-11

Table S21.  Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
19Q GAIN CNV 31 17 76 10
19Q GAIN WILD-TYPE 116 77 76 106

Figure S21.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.09e-12 (Fisher's exact test), Q value = 3.5e-09

Table S22.  Gene #34: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
19Q GAIN CNV 58 15 61
19Q GAIN WILD-TYPE 72 151 152

Figure S22.  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 S23.  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 S23.  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 S24.  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 S24.  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 S25.  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 S25.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 1.24e-10 (Fisher's exact test), Q value = 8.5e-08

Table S26.  Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
20P GAIN CNV 36 20 80 20
20P GAIN WILD-TYPE 111 74 72 96

Figure S26.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.24e-11 (Fisher's exact test), Q value = 6.3e-08

Table S27.  Gene #35: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
20P GAIN CNV 68 26 62
20P GAIN WILD-TYPE 62 140 151

Figure S27.  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 S28.  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 S28.  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 S29.  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 S29.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 4.25e-11 (Fisher's exact test), Q value = 2.9e-08

Table S30.  Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
20Q GAIN CNV 35 22 80 18
20Q GAIN WILD-TYPE 112 72 72 98

Figure S30.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S31.  Gene #36: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
20Q GAIN CNV 66 24 65
20Q GAIN WILD-TYPE 64 142 148

Figure S31.  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 S32.  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 S32.  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 S33.  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 S33.  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 S34.  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 S34.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.19

Table S35.  Gene #48: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
5P LOSS CNV 1 11 6 2
5P LOSS WILD-TYPE 146 83 146 114

Figure S35.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'CN_CNMF'

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

Table S36.  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 S36.  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 S37.  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 S37.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'MRNA_CNMF'

P value = 1.18e-07 (Fisher's exact test), Q value = 7.9e-05

Table S38.  Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
10P LOSS CNV 116 58 138 80
10P LOSS WILD-TYPE 31 36 14 36

Figure S38.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.018

Table S39.  Gene #58: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
10P LOSS CNV 115 110 167
10P LOSS WILD-TYPE 15 56 46

Figure S39.  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 S40.  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 S40.  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 S41.  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 S41.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 3.2e-08 (Fisher's exact test), Q value = 2.2e-05

Table S42.  Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
10Q LOSS CNV 117 63 143 83
10Q LOSS WILD-TYPE 30 31 9 33

Figure S42.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.38e-05 (Fisher's exact test), Q value = 0.022

Table S43.  Gene #59: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
10Q LOSS CNV 118 116 172
10Q LOSS WILD-TYPE 12 50 41

Figure S43.  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 S44.  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 S44.  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 S45.  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 S45.  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 S46.  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 S46.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'11p loss' versus 'MRNA_CNMF'

P value = 3.59e-09 (Fisher's exact test), Q value = 2.4e-06

Table S47.  Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
11P LOSS CNV 12 28 4 17
11P LOSS WILD-TYPE 135 66 148 99

Figure S47.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.68e-05 (Fisher's exact test), Q value = 0.043

Table S48.  Gene #60: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
11P LOSS CNV 7 35 19
11P LOSS WILD-TYPE 123 131 194

Figure S48.  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 S49.  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 S49.  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 S50.  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 S50.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.015

Table S51.  Gene #61: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
11Q LOSS CNV 15 22 5 12
11Q LOSS WILD-TYPE 132 72 147 104

Figure S51.  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 S52.  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 S52.  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 S53.  Gene #64: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
13Q LOSS CNV 45 26 18 35
13Q LOSS WILD-TYPE 102 68 134 81

Figure S53.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 4.3e-13 (Fisher's exact test), Q value = 3e-10

Table S54.  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 S54.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 3.55e-06 (Fisher's exact test), Q value = 0.0024

Table S55.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
14Q LOSS CNV 38 29 13 34
14Q LOSS WILD-TYPE 109 65 139 82

Figure S55.  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 S56.  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 S56.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000233 (Fisher's exact test), Q value = 0.15

Table S57.  Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 130 166 213
15Q LOSS CNV 5 31 23
15Q LOSS WILD-TYPE 125 135 190

Figure S57.  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 S58.  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 S58.  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 S59.  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 S59.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

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

Table S60.  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 S60.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'19p loss' versus 'MRNA_CNMF'

P value = 0.000388 (Fisher's exact test), Q value = 0.25

Table S61.  Gene #73: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
19P LOSS CNV 1 7 0 4
19P LOSS WILD-TYPE 146 87 152 112

Figure S61.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.17

Table S62.  Gene #77: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 94 152 116
21Q LOSS CNV 1 12 5 5
21Q LOSS WILD-TYPE 146 82 147 111

Figure S62.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

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

Table S63.  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 S63.  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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