Correlation between copy number variations of arm-level result and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1NZ85VX
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/C1NZ85VX
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, 72 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 2p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MIR_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 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 'MRNASEQ_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 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',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 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',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 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',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 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, 72 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 Chi-square test Chi-square test
19q gain 151 (27%) 412 7.22e-16
(4.98e-13) 		3.75e-12
(2.56e-09) 		0.0671
(1.00) 		2.31e-05
(0.0149) 		1.64e-28
(1.14e-25) 		0.0112
(1.00) 		0.04
(1.00) 		7.6e-05
(0.0487) 		0.000315
(0.198) 		6.39e-07
(0.000425)
19p gain 176 (31%) 387 2.15e-14
(1.48e-11) 		3.12e-10
(2.11e-07) 		0.236
(1.00) 		0.000117
(0.0745) 		1.02e-23
(7.09e-21) 		0.000451
(0.282) 		0.0126
(1.00) 		9.62e-05
(0.0615) 		0.000511
(0.318) 		4.39e-06
(0.00289)
15q loss 62 (11%) 501 5.43e-05
(0.0349) 		0.000315
(0.198) 		0.000622
(0.386) 		4.06e-06
(0.00267) 		6.26e-06
(0.00409) 		0.000258
(0.163) 		0.122
(1.00) 		0.00643
(1.00) 		0.00768
(1.00) 		0.000145
(0.092)
20q gain 178 (32%) 385 3.25e-13
(2.22e-10) 		4.38e-11
(2.98e-08) 		0.157
(1.00) 		6.8e-06
(0.00443) 		2.98e-09
(2.01e-06) 		0.011
(1.00) 		0.0665
(1.00) 		0.00831
(1.00) 		0.00802
(1.00) 		0.000273
(0.172)
10p loss 437 (78%) 126 1.2e-06
(0.000793) 		8.37e-06
(0.00544) 		0.0358
(1.00) 		1.58e-08
(1.06e-05) 		1.8e-28
(1.25e-25) 		0.00348
(1.00) 		0.000677
(0.419) 		0.000111
(0.0704) 		0.208
(1.00) 		0.032
(1.00)
10q loss 450 (80%) 113 2.16e-06
(0.00143) 		4.5e-06
(0.00295) 		0.0242
(1.00) 		7.65e-06
(0.00498) 		3.09e-31
(2.15e-28) 		0.00202
(1.00) 		8.72e-05
(0.0558) 		0.00166
(1.00) 		0.51
(1.00) 		0.056
(1.00)
7p gain 434 (77%) 129 4.5e-08
(3e-05) 		7.2e-07
(0.000478) 		0.000718
(0.443) 		1.82e-09
(1.23e-06) 		2e-16
(1.38e-13) 		0.0011
(0.673) 		0.00184
(1.00) 		0.238
(1.00) 		0.0444
(1.00) 		0.00541
(1.00)
7q gain 439 (78%) 124 3.49e-06
(0.0023) 		1.75e-05
(0.0113) 		0.00102
(0.625) 		1.56e-06
(0.00103) 		9.36e-15
(6.44e-12) 		0.00348
(1.00) 		0.0239
(1.00) 		0.117
(1.00) 		0.0327
(1.00) 		0.00714
(1.00)
20p gain 180 (32%) 383 2.17e-13
(1.49e-10) 		3.72e-12
(2.54e-09) 		0.201
(1.00) 		6.21e-05
(0.0398) 		1.54e-09
(1.04e-06) 		0.0645
(1.00) 		0.111
(1.00) 		0.0136
(1.00) 		0.0158
(1.00) 		0.000628
(0.389)
11p loss 64 (11%) 499 1.2e-07
(7.99e-05) 		6.61e-06
(0.00432) 		0.0946
(1.00) 		2.43e-06
(0.00161) 		7.77e-12
(5.29e-09) 		0.00107
(0.655) 		0.721
(1.00) 		0.0947
(1.00) 		0.0342
(1.00) 		0.0741
(1.00)
1q gain 45 (8%) 518 0.621
(1.00) 		0.116
(1.00) 		0.44
(1.00) 		0.343
(1.00) 		2.64e-08
(1.77e-05) 		0.295
(1.00) 		0.539
(1.00) 		0.887
(1.00) 		0.0876
(1.00) 		9.74e-06
(0.00632)
2q gain 18 (3%) 545 0.173
(1.00) 		0.447
(1.00) 		3.9e-05
(0.0252) 		0.0743
(1.00) 		0.372
(1.00) 		0.46
(1.00) 		0.5
(1.00) 		0.886
(1.00) 		0.147
(1.00) 		2.7e-22
(1.87e-19)
11q loss 55 (10%) 508 9.72e-05
(0.062) 		0.00427
(1.00) 		0.512
(1.00) 		0.00501
(1.00) 		2.1e-10
(1.42e-07) 		0.254
(1.00) 		0.622
(1.00) 		0.198
(1.00) 		0.348
(1.00) 		0.328
(1.00)
13q loss 138 (25%) 425 0.000801
(0.492) 		4.42e-05
(0.0285) 		0.569
(1.00) 		0.647
(1.00) 		4.3e-13
(2.94e-10) 		0.00114
(0.698) 		0.658
(1.00) 		0.01
(1.00) 		0.341
(1.00) 		0.0161
(1.00)
14q loss 121 (21%) 442 4.49e-07
(0.000299) 		0.025
(1.00) 		0.595
(1.00) 		0.714
(1.00) 		8.63e-34
(6.02e-31) 		0.0159
(1.00) 		0.561
(1.00) 		0.133
(1.00) 		0.0272
(1.00) 		0.0272
(1.00)
1p gain 40 (7%) 523 0.681
(1.00) 		0.0934
(1.00) 		0.934
(1.00) 		0.0651
(1.00) 		1.1e-05
(0.00714) 		0.388
(1.00) 		0.27
(1.00) 		1
(1.00) 		0.0956
(1.00) 		0.421
(1.00)
2p gain 20 (4%) 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) 		0.684
(1.00) 		0.641
(1.00) 		0.348
(1.00) 		1.41e-17
(9.76e-15)
8p gain 26 (5%) 537 0.00124
(0.754) 		0.0814
(1.00) 		0.335
(1.00) 		0.00812
(1.00) 		0.0015
(0.907) 		0.15
(1.00) 		0.0671
(1.00) 		0.0194
(1.00) 		0.442
(1.00) 		1.71e-09
(1.16e-06)
8q gain 31 (6%) 532 0.000511
(0.318) 		0.0416
(1.00) 		0.286
(1.00) 		0.00535
(1.00) 		0.00362
(1.00) 		0.0434
(1.00) 		0.0671
(1.00) 		0.0194
(1.00) 		0.412
(1.00) 		3.66e-08
(2.45e-05)
18p gain 28 (5%) 535 0.501
(1.00) 		0.188
(1.00) 		0.509
(1.00) 		0.364
(1.00) 		0.000326
(0.204) 		0.313
(1.00) 		0.398
(1.00) 		0.259
(1.00) 		0.0195
(1.00) 		0.0135
(1.00)
18q gain 30 (5%) 533 0.11
(1.00) 		0.186
(1.00) 		0.356
(1.00) 		0.597
(1.00) 		0.000159
(0.101) 		0.313
(1.00) 		0.768
(1.00) 		0.179
(1.00) 		0.00815
(1.00) 		0.00591
(1.00)
3q loss 16 (3%) 547 0.643
(1.00) 		0.473
(1.00) 		0.0271
(1.00) 		0.383
(1.00) 		0.000297
(0.187) 		0.806
(1.00) 		1
(1.00) 		0.438
(1.00) 		0.00512
(1.00)
5q loss 20 (4%) 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) 		0.583
(1.00) 		0.00014
(0.0892)
6p loss 47 (8%) 516 0.98
(1.00) 		0.553
(1.00) 		0.375
(1.00) 		0.538
(1.00) 		2.84e-09
(1.91e-06) 		0.622
(1.00) 		0.949
(1.00) 		0.85
(1.00) 		0.857
(1.00) 		0.863
(1.00)
6q loss 80 (14%) 483 0.672
(1.00) 		0.58
(1.00) 		0.462
(1.00) 		0.112
(1.00) 		1.87e-08
(1.25e-05) 		0.0853
(1.00) 		0.902
(1.00) 		0.295
(1.00) 		0.963
(1.00) 		0.89
(1.00)
17p loss 36 (6%) 527 0.429
(1.00) 		0.62
(1.00) 		0.835
(1.00) 		0.633
(1.00) 		5.94e-06
(0.00389) 		0.18
(1.00) 		0.061
(1.00) 		0.436
(1.00) 		0.735
(1.00) 		0.304
(1.00)
22q loss 140 (25%) 423 0.809
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.886
(1.00) 		0.000148
(0.0937) 		0.275
(1.00) 		0.659
(1.00) 		0.525
(1.00) 		0.376
(1.00) 		0.0141
(1.00)
3p gain 30 (5%) 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) 		0.418
(1.00) 		0.0686
(1.00) 		0.7
(1.00) 		0.233
(1.00)
3q gain 30 (5%) 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) 		0.418
(1.00) 		0.0686
(1.00) 		0.637
(1.00) 		0.377
(1.00)
4p gain 15 (3%) 548 0.747
(1.00) 		0.656
(1.00) 		0.382
(1.00) 		0.0456
(1.00) 		0.29
(1.00) 		0.47
(1.00) 		0.174
(1.00)
4q gain 14 (2%) 549 0.733
(1.00) 		0.633
(1.00) 		0.206
(1.00) 		0.0828
(1.00) 		0.193
(1.00) 		0.47
(1.00) 		0.174
(1.00)
5p gain 30 (5%) 533 0.112
(1.00) 		0.31
(1.00) 		0.241
(1.00) 		0.353
(1.00) 		0.0037
(1.00) 		0.147
(1.00) 		0.41
(1.00) 		0.0294
(1.00) 		0.156
(1.00)
5q gain 23 (4%) 540 0.0427
(1.00) 		0.183
(1.00) 		0.0508
(1.00) 		0.0905
(1.00) 		0.0152
(1.00) 		0.148
(1.00) 		0.476
(1.00)
6p gain 7 (1%) 556 0.79
(1.00) 		0.769
(1.00) 		0.657
(1.00) 		0.395
(1.00) 		0.161
(1.00)
6q gain 9 (2%) 554 0.237
(1.00) 		0.601
(1.00) 		0.595
(1.00) 		0.746
(1.00) 		0.0295
(1.00)
9p gain 17 (3%) 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) 		0.229
(1.00) 		0.847
(1.00) 		0.355
(1.00) 		0.347
(1.00)
9q gain 34 (6%) 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) 		0.478
(1.00) 		0.217
(1.00) 		0.291
(1.00)
10p gain 12 (2%) 551 0.00052
(0.323) 		0.00472
(1.00) 		0.0911
(1.00) 		0.00145
(0.877) 		0.00123
(0.749) 		0.307
(1.00) 		0.258
(1.00)
11p gain 4 (1%) 559 1
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.497
(1.00) 		0.259
(1.00)
11q gain 7 (1%) 556 0.152
(1.00) 		0.209
(1.00) 		0.265
(1.00) 		0.0781
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.14
(1.00)
12p gain 43 (8%) 520 0.413
(1.00) 		0.201
(1.00) 		1
(1.00) 		0.265
(1.00) 		0.00126
(0.766) 		0.446
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.00635
(1.00) 		0.246
(1.00)
12q gain 33 (6%) 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) 		0.517
(1.00) 		0.362
(1.00) 		0.0317
(1.00) 		0.184
(1.00)
13q gain 3 (1%) 560 0.777
(1.00) 		0.792
(1.00) 		0.156
(1.00) 		0.497
(1.00) 		0.289
(1.00) 		0.8
(1.00) 		0.577
(1.00)
14q gain 7 (1%) 556 0.706
(1.00) 		0.674
(1.00) 		0.0567
(1.00) 		0.564
(1.00) 		0.638
(1.00)
15q gain 6 (1%) 557 0.379
(1.00) 		0.536
(1.00) 		0.512
(1.00) 		0.588
(1.00) 		0.0126
(1.00)
16p gain 18 (3%) 545 0.0318
(1.00) 		0.297
(1.00) 		0.6
(1.00) 		0.263
(1.00) 		0.0155
(1.00) 		0.34
(1.00) 		0.0473
(1.00)
16q gain 18 (3%) 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) 		0.0473
(1.00)
17p gain 11 (2%) 552 0.0188
(1.00) 		0.389
(1.00) 		0.721
(1.00) 		0.349
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.423
(1.00)
17q gain 19 (3%) 544 0.22
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.609
(1.00) 		0.0584
(1.00) 		0.785
(1.00) 		0.258
(1.00) 		0.321
(1.00) 		0.0799
(1.00)
21q gain 36 (6%) 527 0.00268
(1.00) 		0.0318
(1.00) 		0.00816
(1.00) 		0.00191
(1.00) 		0.0469
(1.00) 		0.449
(1.00) 		0.698
(1.00) 		0.0345
(1.00) 		0.00074
(0.456)
22q gain 11 (2%) 552 0.0378
(1.00) 		0.143
(1.00) 		0.127
(1.00) 		0.48
(1.00) 		0.0767
(1.00) 		1
(1.00) 		0.14
(1.00)
Xq gain 4 (1%) 559 0.331
(1.00) 		0.468
(1.00) 		0.757
(1.00) 		0.259
(1.00) 		0.0702
(1.00)
1p loss 5 (1%) 558 0.849
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.0996
(1.00) 		0.532
(1.00)
1q loss 4 (1%) 559 0.218
(1.00) 		1
(1.00) 		0.682
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 10 (2%) 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) 		0.847
(1.00) 		0.0785
(1.00) 		0.0342
(1.00)
2q loss 9 (2%) 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) 		0.847
(1.00) 		0.0785
(1.00) 		0.0342
(1.00)
3p loss 22 (4%) 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) 		0.0763
(1.00) 		0.824
(1.00) 		0.711
(1.00) 		0.431
(1.00)
4p loss 26 (5%) 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) 		0.0842
(1.00) 		0.495
(1.00) 		0.0543
(1.00) 		0.768
(1.00)
4q loss 25 (4%) 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) 		0.084
(1.00) 		0.639
(1.00) 		0.781
(1.00) 		0.0772
(1.00)
5p loss 21 (4%) 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) 		0.698
(1.00) 		0.464
(1.00) 		0.0601
(1.00)
7p loss 5 (1%) 558 0.542
(1.00) 		0.453
(1.00) 		0.81
(1.00) 		0.0341
(1.00) 		0.532
(1.00)
7q loss 4 (1%) 559 0.849
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.0996
(1.00) 		0.833
(1.00)
8p loss 34 (6%) 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) 		0.664
(1.00) 		0.698
(1.00) 		0.408
(1.00) 		0.838
(1.00)
8q loss 21 (4%) 542 0.717
(1.00) 		0.144
(1.00) 		0.384
(1.00) 		0.185
(1.00) 		0.0154
(1.00) 		0.211
(1.00) 		0.331
(1.00) 		0.353
(1.00) 		0.21
(1.00)
9p loss 164 (29%) 399 0.0137
(1.00) 		0.00133
(0.808) 		0.832
(1.00) 		0.147
(1.00) 		0.227
(1.00) 		0.921
(1.00) 		0.284
(1.00) 		0.212
(1.00) 		0.0773
(1.00) 		0.0594
(1.00)
9q loss 63 (11%) 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) 		0.037
(1.00) 		0.0244
(1.00) 		0.404
(1.00) 		0.603
(1.00)
12p loss 38 (7%) 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) 		0.0898
(1.00) 		0.166
(1.00) 		0.774
(1.00) 		0.597
(1.00)
12q loss 35 (6%) 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) 		0.0852
(1.00) 		0.362
(1.00) 		0.404
(1.00) 		0.261
(1.00)
16p loss 23 (4%) 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) 		0.641
(1.00) 		0.736
(1.00) 		0.33
(1.00)
16q loss 41 (7%) 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) 		0.0793
(1.00) 		0.807
(1.00) 		0.882
(1.00) 		0.699
(1.00)
17q loss 19 (3%) 544 0.39
(1.00) 		0.136
(1.00) 		0.402
(1.00) 		0.347
(1.00) 		0.0017
(1.00) 		0.212
(1.00) 		0.608
(1.00) 		0.0771
(1.00) 		0.0155
(1.00)
18p loss 44 (8%) 519 0.0244
(1.00) 		0.0871
(1.00) 		0.504
(1.00) 		0.712
(1.00) 		0.00156
(0.943) 		0.0747
(1.00) 		0.252
(1.00) 		0.101
(1.00) 		0.355
(1.00) 		0.482
(1.00)
18q loss 39 (7%) 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) 		0.159
(1.00) 		0.253
(1.00) 		0.833
(1.00) 		0.825
(1.00)
19p loss 13 (2%) 550 0.00284
(1.00) 		0.024
(1.00) 		0.000418
(0.261) 		0.00738
(1.00) 		0.158
(1.00) 		0.592
(1.00) 		0.345
(1.00) 		0.351
(1.00) 		0.0414
(1.00) 		0.0227
(1.00)
19q loss 18 (3%) 545 0.00902
(1.00) 		0.047
(1.00) 		0.00964
(1.00) 		0.00144
(0.872) 		0.0738
(1.00) 		0.592
(1.00) 		0.345
(1.00) 		0.351
(1.00) 		0.123
(1.00) 		0.0876
(1.00)
20p loss 11 (2%) 552 0.054
(1.00) 		0.129
(1.00) 		0.116
(1.00) 		0.0621
(1.00) 		0.00377
(1.00) 		0.449
(1.00) 		0.187
(1.00)
20q loss 10 (2%) 553 0.0789
(1.00) 		0.171
(1.00) 		0.656
(1.00) 		0.399
(1.00) 		0.019
(1.00) 		0.449
(1.00) 		0.187
(1.00)
21q loss 25 (4%) 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) 		0.0223
(1.00) 		0.364
(1.00) 		0.129
(1.00) 		0.378
(1.00)
Xq loss 11 (2%) 552 0.443
(1.00) 		0.468
(1.00) 		0.116
(1.00) 		0.37
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.296
(1.00) 		0.788
(1.00) 		0.0626
(1.00)
'1p gain mutation analysis' versus 'CN_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0071

Table S1.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S1.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'1q gain mutation analysis' versus 'CN_CNMF'

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

Table S2.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S2.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'1q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.74e-06 (Chi-square test), Q value = 0.0063

Table S3.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
1Q GAIN MUTATED 2 3 2 0 3 5
1Q GAIN WILD-TYPE 28 0 31 21 15 38

Figure S3.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'2p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.41e-17 (Chi-square test), Q value = 9.8e-15

Table S4.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
2P GAIN MUTATED 1 3 0 0 0 1
2P GAIN WILD-TYPE 29 0 33 21 18 42

Figure S4.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'2q gain mutation analysis' versus 'MIR_CNMF'

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

Table S5.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'MIR_CNMF'

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

Figure S5.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'MIR_CNMF'

'2q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.7e-22 (Chi-square test), Q value = 1.9e-19

Table S6.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
2Q GAIN MUTATED 0 3 0 0 0 1
2Q GAIN WILD-TYPE 30 0 33 21 18 42

Figure S6.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'MRNA_CNMF'

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

Table S7.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S7.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'7p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S8.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S8.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'7p gain mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S9.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S9.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'7p gain mutation analysis' versus 'CN_CNMF'

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

Table S10.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S10.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'7q gain mutation analysis' versus 'MRNA_CNMF'

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

Table S11.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S11.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'7q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S12.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S12.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'7q gain mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S13.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S13.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 9.36e-15 (Fisher's exact test), Q value = 6.4e-12

Table S14.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S14.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'8p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.71e-09 (Chi-square test), Q value = 1.2e-06

Table S15.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
8P GAIN MUTATED 2 3 1 2 0 1
8P GAIN WILD-TYPE 28 0 32 19 18 42

Figure S15.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'8q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.66e-08 (Chi-square test), Q value = 2.4e-05

Table S16.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
8Q GAIN MUTATED 4 3 1 2 0 1
8Q GAIN WILD-TYPE 26 0 32 19 18 42

Figure S16.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'18p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000326 (Fisher's exact test), Q value = 0.2

Table S17.  Gene #31: '18p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S17.  Get High-res Image Gene #31: '18p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'18q gain mutation analysis' versus 'CN_CNMF'

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

Table S18.  Gene #32: '18q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S18.  Get High-res Image Gene #32: '18q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'19p gain mutation analysis' versus 'MRNA_CNMF'

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

Table S19.  Gene #33: '19p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S19.  Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'19p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S20.  Gene #33: '19p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S20.  Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'19p gain mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S21.  Gene #33: '19p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S21.  Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'19p gain mutation analysis' versus 'CN_CNMF'

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

Table S22.  Gene #33: '19p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S22.  Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'19p gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 9.62e-05 (Fisher's exact test), Q value = 0.061

Table S23.  Gene #33: '19p gain mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 71 39
19P GAIN MUTATED 17 35 9
19P GAIN WILD-TYPE 74 36 30

Figure S23.  Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

'19p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.39e-06 (Chi-square test), Q value = 0.0029

Table S24.  Gene #33: '19p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
19P GAIN MUTATED 5 1 10 0 14 11
19P GAIN WILD-TYPE 25 2 23 21 4 32

Figure S24.  Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'19q gain mutation analysis' versus 'MRNA_CNMF'

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

Table S25.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S25.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'19q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S26.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S26.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'19q gain mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S27.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S27.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'19q gain mutation analysis' versus 'CN_CNMF'

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

Table S28.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S28.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'19q gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.049

Table S29.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 71 39
19Q GAIN MUTATED 12 30 7
19Q GAIN WILD-TYPE 79 41 32

Figure S29.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

'19q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000315 (Chi-square test), Q value = 0.2

Table S30.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 35 32 27 25 5 24
19Q GAIN MUTATED 3 7 16 6 2 4
19Q GAIN WILD-TYPE 32 25 11 19 3 20

Figure S30.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

'19q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.39e-07 (Chi-square test), Q value = 0.00043

Table S31.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
19Q GAIN MUTATED 3 1 9 0 14 11
19Q GAIN WILD-TYPE 27 2 24 21 4 32

Figure S31.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'20p gain mutation analysis' versus 'MRNA_CNMF'

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

Table S32.  Gene #35: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S32.  Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S33.  Gene #35: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S33.  Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20p gain mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S34.  Gene #35: '20p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S34.  Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'20p gain mutation analysis' versus 'CN_CNMF'

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

Table S35.  Gene #35: '20p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S35.  Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'20q gain mutation analysis' versus 'MRNA_CNMF'

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

Table S36.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S36.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S37.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S37.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MIR_CHIERARCHICAL'

P value = 6.8e-06 (Fisher's exact test), Q value = 0.0044

Table S38.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S38.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'20q gain mutation analysis' versus 'CN_CNMF'

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

Table S39.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S39.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000273 (Chi-square test), Q value = 0.17

Table S40.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
20Q GAIN MUTATED 3 3 11 3 10 9
20Q GAIN WILD-TYPE 27 0 22 18 8 34

Figure S40.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'3q loss mutation analysis' versus 'CN_CNMF'

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

Table S41.  Gene #45: '3q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S41.  Get High-res Image Gene #45: '3q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'5q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Chi-square test), Q value = 0.089

Table S42.  Gene #49: '5q loss mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
5Q LOSS MUTATED 2 2 0 3 1 1
5Q LOSS WILD-TYPE 28 1 33 18 17 42

Figure S42.  Get High-res Image Gene #49: '5q loss mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'6p loss mutation analysis' versus 'CN_CNMF'

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

Table S43.  Gene #50: '6p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S43.  Get High-res Image Gene #50: '6p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'6q loss mutation analysis' versus 'CN_CNMF'

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

Table S44.  Gene #51: '6q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S44.  Get High-res Image Gene #51: '6q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'10p loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00079

Table S45.  Gene #58: '10p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S45.  Get High-res Image Gene #58: '10p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'10p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.37e-06 (Fisher's exact test), Q value = 0.0054

Table S46.  Gene #58: '10p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S46.  Get High-res Image Gene #58: '10p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'10p loss mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S47.  Gene #58: '10p loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S47.  Get High-res Image Gene #58: '10p loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'10p loss mutation analysis' versus 'CN_CNMF'

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

Table S48.  Gene #58: '10p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S48.  Get High-res Image Gene #58: '10p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'10p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.07

Table S49.  Gene #58: '10p loss mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 71 39
10P LOSS MUTATED 66 68 29
10P LOSS WILD-TYPE 25 3 10

Figure S49.  Get High-res Image Gene #58: '10p loss mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

'10q loss mutation analysis' versus 'MRNA_CNMF'

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

Table S50.  Gene #59: '10q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S50.  Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'10q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S51.  Gene #59: '10q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S51.  Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'10q loss mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S52.  Gene #59: '10q loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S52.  Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'10q loss mutation analysis' versus 'CN_CNMF'

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

Table S53.  Gene #59: '10q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S53.  Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'10q loss mutation analysis' versus 'RPPA_CNMF'

P value = 8.72e-05 (Fisher's exact test), Q value = 0.056

Table S54.  Gene #59: '10q loss mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 58 43 45
10Q LOSS MUTATED 43 40 43 39
10Q LOSS WILD-TYPE 12 18 0 6

Figure S54.  Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'

'11p loss mutation analysis' versus 'MRNA_CNMF'

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

Table S55.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S55.  Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'11p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S56.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S56.  Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'11p loss mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S57.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S57.  Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'11p loss mutation analysis' versus 'CN_CNMF'

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

Table S58.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S58.  Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'11q loss mutation analysis' versus 'MRNA_CNMF'

P value = 9.72e-05 (Fisher's exact test), Q value = 0.062

Table S59.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S59.  Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

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

Table S60.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S60.  Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'13q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.028

Table S61.  Gene #64: '13q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S61.  Get High-res Image Gene #64: '13q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'13q loss mutation analysis' versus 'CN_CNMF'

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

Table S62.  Gene #64: '13q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S62.  Get High-res Image Gene #64: '13q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'14q loss mutation analysis' versus 'MRNA_CNMF'

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

Table S63.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S63.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'14q loss mutation analysis' versus 'CN_CNMF'

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

Table S64.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S64.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'15q loss mutation analysis' versus 'MRNA_CNMF'

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

Table S65.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S65.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'15q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S66.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S66.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'15q loss mutation analysis' versus 'MIR_CHIERARCHICAL'

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

Table S67.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

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

Figure S67.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'15q loss mutation analysis' versus 'CN_CNMF'

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

Table S68.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S68.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'15q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000258 (Fisher's exact test), Q value = 0.16

Table S69.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

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

Figure S69.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'15q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000145 (Chi-square test), Q value = 0.092

Table S70.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 30 3 33 21 18 43
15Q LOSS MUTATED 9 0 0 8 1 3
15Q LOSS WILD-TYPE 21 3 33 13 17 40

Figure S70.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'17p loss mutation analysis' versus 'CN_CNMF'

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

Table S71.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S71.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.094

Table S72.  Gene #78: '22q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

Figure S72.  Get High-res Image Gene #78: '22q loss mutation analysis' versus Clinical Feature #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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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