Correlation between copy number variations of arm-level result and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C16W98TC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16W98TC
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 571 patients, 103 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

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

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

  • 8p gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 8q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 18q gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

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

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

  • 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'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 5p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 5q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and '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', and 'CN_CNMF'.

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

  • 12q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

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

  • 20q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

  • xq 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 80 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 103 significant findings detected.

Clinical
Features 		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
7p gain 463 (81%) 108 1e-05
(0.00774) 		1e-05
(0.00774) 		0.00039
(0.262) 		1e-05
(0.00774) 		1e-05
(0.00774) 		0.00172
(1.00) 		0.00207
(1.00) 		0.0025
(1.00) 		0.0145
(1.00) 		3e-05
(0.0215)
7q gain 469 (82%) 102 1e-05
(0.00774) 		1e-05
(0.00774) 		0.00106
(0.694) 		0.00012
(0.0829) 		1e-05
(0.00774) 		0.00016
(0.109) 		0.104
(1.00) 		0.044
(1.00) 		0.055
(1.00) 		0.00166
(1.00)
10q loss 488 (85%) 83 1e-05
(0.00774) 		1e-05
(0.00774) 		0.0057
(1.00) 		0.00012
(0.0829) 		1e-05
(0.00774) 		0.00238
(1.00) 		0.00012
(0.0829) 		0.00442
(1.00) 		0.26
(1.00) 		0.0218
(1.00)
19p gain 224 (39%) 347 1e-05
(0.00774) 		3e-05
(0.0215) 		0.0809
(1.00) 		0.00043
(0.287) 		1e-05
(0.00774) 		0.00246
(1.00) 		0.00908
(1.00) 		3e-05
(0.0215) 		0.19
(1.00) 		0.655
(1.00)
20p gain 220 (39%) 351 1e-05
(0.00774) 		1e-05
(0.00774) 		0.00437
(1.00) 		1e-05
(0.00774) 		1e-05
(0.00774) 		0.101
(1.00) 		0.0531
(1.00) 		0.00192
(1.00) 		0.796
(1.00) 		0.117
(1.00)
20q gain 218 (38%) 353 1e-05
(0.00774) 		1e-05
(0.00774) 		0.00286
(1.00) 		1e-05
(0.00774) 		2e-05
(0.0144) 		0.0292
(1.00) 		0.0358
(1.00) 		0.00102
(0.67) 		0.797
(1.00) 		0.121
(1.00)
10p loss 477 (84%) 94 1e-05
(0.00774) 		1e-05
(0.00774) 		0.0114
(1.00) 		0.00014
(0.0963) 		1e-05
(0.00774) 		0.0341
(1.00) 		0.00216
(1.00) 		0.0167
(1.00) 		0.223
(1.00) 		0.0131
(1.00)
8q gain 59 (10%) 512 1e-05
(0.00774) 		2e-05
(0.0144) 		0.0405
(1.00) 		0.452
(1.00) 		1e-05
(0.00774) 		0.198
(1.00) 		0.435
(1.00) 		0.754
(1.00) 		0.125
(1.00) 		0.515
(1.00)
19q gain 197 (35%) 374 1e-05
(0.00774) 		1e-05
(0.00774) 		0.116
(1.00) 		0.00425
(1.00) 		1e-05
(0.00774) 		0.0187
(1.00) 		0.0467
(1.00) 		0.00099
(0.652) 		0.0628
(1.00) 		0.341
(1.00)
5p loss 42 (7%) 529 1e-05
(0.00774) 		3e-05
(0.0215) 		0.00182
(1.00) 		0.0957
(1.00) 		0.00016
(0.109) 		0.0354
(1.00) 		0.939
(1.00) 		0.544
(1.00) 		0.342
(1.00) 		0.0521
(1.00)
5q loss 43 (8%) 528 5e-05
(0.0351) 		4e-05
(0.0284) 		0.00104
(0.682) 		0.186
(1.00) 		0.00014
(0.0963) 		0.035
(1.00) 		0.943
(1.00) 		0.626
(1.00) 		0.222
(1.00) 		0.0428
(1.00)
11p loss 97 (17%) 474 1e-05
(0.00774) 		1e-05
(0.00774) 		0.83
(1.00) 		0.0142
(1.00) 		1e-05
(0.00774) 		0.0258
(1.00) 		0.73
(1.00) 		0.159
(1.00) 		0.0917
(1.00) 		0.0857
(1.00)
11q loss 92 (16%) 479 1e-05
(0.00774) 		9e-05
(0.0625) 		0.934
(1.00) 		0.0609
(1.00) 		1e-05
(0.00774) 		0.276
(1.00) 		0.935
(1.00) 		0.569
(1.00) 		0.345
(1.00) 		0.536
(1.00)
14q loss 146 (26%) 425 1e-05
(0.00774) 		8e-05
(0.0557) 		0.447
(1.00) 		0.483
(1.00) 		1e-05
(0.00774) 		0.0135
(1.00) 		0.813
(1.00) 		0.0931
(1.00) 		0.106
(1.00) 		0.601
(1.00)
15q loss 102 (18%) 469 5e-05
(0.0351) 		2e-05
(0.0144) 		0.00378
(1.00) 		0.0038
(1.00) 		1e-05
(0.00774) 		0.00222
(1.00) 		0.032
(1.00) 		0.0117
(1.00) 		0.00336
(1.00) 		0.022
(1.00)
20p loss 18 (3%) 553 0.00021
(0.142) 		3e-05
(0.0215) 		0.0361
(1.00) 		0.0949
(1.00) 		5e-05
(0.0351) 		0.413
(1.00) 		0.46
(1.00) 		0.0104
(1.00) 		0.00207
(1.00)
8p gain 52 (9%) 519 4e-05
(0.0284) 		0.00065
(0.432) 		0.0631
(1.00) 		0.557
(1.00) 		1e-05
(0.00774) 		0.0887
(1.00) 		0.433
(1.00) 		0.757
(1.00) 		0.139
(1.00) 		0.674
(1.00)
17p gain 48 (8%) 523 0.00037
(0.249) 		0.02
(1.00) 		0.0797
(1.00) 		0.04
(1.00) 		8e-05
(0.0557) 		0.0573
(1.00) 		0.15
(1.00) 		0.237
(1.00) 		0.338
(1.00) 		0.391
(1.00)
18p gain 58 (10%) 513 1e-05
(0.00774) 		0.00039
(0.262) 		0.157
(1.00) 		0.367
(1.00) 		1e-05
(0.00774) 		0.377
(1.00) 		0.423
(1.00) 		0.15
(1.00) 		0.019
(1.00) 		0.0974
(1.00)
18q gain 58 (10%) 513 1e-05
(0.00774) 		0.00073
(0.485) 		0.159
(1.00) 		0.432
(1.00) 		1e-05
(0.00774) 		0.515
(1.00) 		0.692
(1.00) 		0.479
(1.00) 		0.0186
(1.00) 		0.112
(1.00)
22q gain 34 (6%) 537 1e-05
(0.00774) 		0.00308
(1.00) 		0.469
(1.00) 		0.216
(1.00) 		0.0002
(0.136) 		0.186
(1.00) 		0.211
(1.00) 		0.0353
(1.00) 		0.244
(1.00) 		0.193
(1.00)
13q loss 183 (32%) 388 4e-05
(0.0284) 		0.00165
(1.00) 		0.75
(1.00) 		0.589
(1.00) 		1e-05
(0.00774) 		0.00119
(0.776) 		0.595
(1.00) 		0.017
(1.00) 		0.0495
(1.00) 		0.401
(1.00)
20q loss 16 (3%) 555 0.00154
(1.00) 		0.00015
(0.103) 		0.364
(1.00) 		0.266
(1.00) 		0.00015
(0.103) 		0.415
(1.00) 		0.459
(1.00) 		0.0387
(1.00) 		0.0127
(1.00)
1p gain 82 (14%) 489 0.607
(1.00) 		0.131
(1.00) 		0.484
(1.00) 		0.247
(1.00) 		1e-05
(0.00774) 		0.675
(1.00) 		0.501
(1.00) 		0.0843
(1.00) 		0.342
(1.00) 		0.273
(1.00)
1q gain 89 (16%) 482 0.0767
(1.00) 		0.0886
(1.00) 		0.129
(1.00) 		0.627
(1.00) 		1e-05
(0.00774) 		0.26
(1.00) 		0.579
(1.00) 		0.257
(1.00) 		0.826
(1.00) 		0.505
(1.00)
2p gain 36 (6%) 535 0.457
(1.00) 		0.682
(1.00) 		0.376
(1.00) 		0.158
(1.00) 		0.00016
(0.109) 		0.188
(1.00) 		0.578
(1.00) 		0.415
(1.00) 		1
(1.00) 		0.536
(1.00)
2q gain 35 (6%) 536 0.64
(1.00) 		0.864
(1.00) 		0.162
(1.00) 		0.202
(1.00) 		0.0002
(0.136) 		0.189
(1.00) 		0.921
(1.00) 		0.413
(1.00) 		0.771
(1.00) 		0.177
(1.00)
3p gain 57 (10%) 514 0.00046
(0.307) 		0.0282
(1.00) 		0.668
(1.00) 		0.0263
(1.00) 		1e-05
(0.00774) 		0.041
(1.00) 		0.635
(1.00) 		0.341
(1.00) 		0.812
(1.00) 		0.255
(1.00)
3q gain 62 (11%) 509 0.0009
(0.595) 		0.0964
(1.00) 		0.923
(1.00) 		0.0765
(1.00) 		1e-05
(0.00774) 		0.0164
(1.00) 		0.625
(1.00) 		0.304
(1.00) 		0.516
(1.00) 		0.151
(1.00)
5p gain 49 (9%) 522 0.115
(1.00) 		0.156
(1.00) 		0.176
(1.00) 		0.344
(1.00) 		1e-05
(0.00774) 		0.621
(1.00) 		0.281
(1.00) 		0.526
(1.00) 		0.128
(1.00) 		0.231
(1.00)
5q gain 41 (7%) 530 0.141
(1.00) 		0.232
(1.00) 		0.118
(1.00) 		0.055
(1.00) 		5e-05
(0.0351) 		0.381
(1.00) 		0.39
(1.00) 		0.296
(1.00) 		0.169
(1.00) 		0.399
(1.00)
9p gain 47 (8%) 524 0.00334
(1.00) 		0.0305
(1.00) 		0.702
(1.00) 		0.434
(1.00) 		5e-05
(0.0351) 		0.158
(1.00) 		0.798
(1.00) 		0.366
(1.00) 		0.429
(1.00) 		0.113
(1.00)
9q gain 72 (13%) 499 0.0883
(1.00) 		0.0506
(1.00) 		0.561
(1.00) 		0.127
(1.00) 		7e-05
(0.0489) 		0.0357
(1.00) 		0.32
(1.00) 		0.385
(1.00) 		0.669
(1.00) 		0.0784
(1.00)
10p gain 12 (2%) 559 0.00106
(0.694) 		9e-05
(0.0625) 		0.118
(1.00) 		0.0589
(1.00) 		0.0029
(1.00) 		0.308
(1.00) 		0.562
(1.00)
12p gain 59 (10%) 512 0.671
(1.00) 		0.794
(1.00) 		0.644
(1.00) 		0.165
(1.00) 		4e-05
(0.0284) 		0.592
(1.00) 		0.234
(1.00) 		0.664
(1.00) 		0.00413
(1.00) 		0.0759
(1.00)
15q gain 24 (4%) 547 0.0609
(1.00) 		0.11
(1.00) 		0.568
(1.00) 		0.134
(1.00) 		9e-05
(0.0625) 		0.536
(1.00) 		0.341
(1.00) 		0.035
(1.00) 		0.385
(1.00)
16p gain 38 (7%) 533 0.00777
(1.00) 		0.0648
(1.00) 		0.413
(1.00) 		0.27
(1.00) 		2e-05
(0.0144) 		0.617
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00)
16q gain 37 (6%) 534 0.0188
(1.00) 		0.00551
(1.00) 		0.358
(1.00) 		0.0667
(1.00) 		0.00016
(0.109) 		0.754
(1.00) 		0.418
(1.00) 		0.423
(1.00) 		0.736
(1.00)
17q gain 59 (10%) 512 0.00101
(0.665) 		0.0441
(1.00) 		0.15
(1.00) 		0.0437
(1.00) 		1e-05
(0.00774) 		0.179
(1.00) 		0.0787
(1.00) 		0.161
(1.00) 		0.945
(1.00) 		0.617
(1.00)
21q gain 63 (11%) 508 0.00127
(0.827) 		0.00728
(1.00) 		0.0118
(1.00) 		0.00389
(1.00) 		0.00034
(0.229) 		0.166
(1.00) 		0.318
(1.00) 		0.0267
(1.00) 		0.0187
(1.00) 		0.333
(1.00)
2p loss 32 (6%) 539 0.0341
(1.00) 		0.0341
(1.00) 		0.312
(1.00) 		0.663
(1.00) 		0.00036
(0.242) 		0.00505
(1.00) 		0.935
(1.00) 		0.218
(1.00) 		0.241
(1.00) 		0.226
(1.00)
2q loss 32 (6%) 539 0.0337
(1.00) 		0.0346
(1.00) 		0.312
(1.00) 		0.663
(1.00) 		0.00034
(0.229) 		0.00537
(1.00) 		0.827
(1.00) 		0.133
(1.00) 		0.083
(1.00) 		0.0748
(1.00)
3p loss 40 (7%) 531 0.91
(1.00) 		0.789
(1.00) 		0.717
(1.00) 		0.149
(1.00) 		0.00018
(0.122) 		0.0574
(1.00) 		0.236
(1.00) 		0.901
(1.00) 		0.639
(1.00) 		0.231
(1.00)
3q loss 34 (6%) 537 0.23
(1.00) 		0.129
(1.00) 		0.509
(1.00) 		0.678
(1.00) 		4e-05
(0.0284) 		0.118
(1.00) 		0.788
(1.00) 		0.321
(1.00) 		0.889
(1.00) 		0.183
(1.00)
6p loss 86 (15%) 485 0.567
(1.00) 		0.334
(1.00) 		0.772
(1.00) 		0.706
(1.00) 		1e-05
(0.00774) 		0.306
(1.00) 		0.794
(1.00) 		0.301
(1.00) 		0.871
(1.00) 		0.596
(1.00)
6q loss 124 (22%) 447 0.94
(1.00) 		0.578
(1.00) 		0.568
(1.00) 		0.941
(1.00) 		1e-05
(0.00774) 		0.19
(1.00) 		0.969
(1.00) 		0.646
(1.00) 		0.498
(1.00) 		0.293
(1.00)
12q loss 58 (10%) 513 0.107
(1.00) 		0.0624
(1.00) 		0.352
(1.00) 		0.59
(1.00) 		4e-05
(0.0284) 		0.517
(1.00) 		0.181
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.662
(1.00)
17p loss 64 (11%) 507 0.0201
(1.00) 		0.0212
(1.00) 		0.653
(1.00) 		0.583
(1.00) 		1e-05
(0.00774) 		0.0902
(1.00) 		0.212
(1.00) 		0.35
(1.00) 		0.302
(1.00) 		0.705
(1.00)
17q loss 42 (7%) 529 0.005
(1.00) 		0.0597
(1.00) 		0.253
(1.00) 		0.0425
(1.00) 		3e-05
(0.0215) 		0.254
(1.00) 		0.481
(1.00) 		0.34
(1.00) 		0.145
(1.00) 		0.109
(1.00)
18p loss 69 (12%) 502 0.0479
(1.00) 		0.0318
(1.00) 		0.359
(1.00) 		0.22
(1.00) 		3e-05
(0.0215) 		0.27
(1.00) 		0.0632
(1.00) 		0.0066
(1.00) 		0.135
(1.00) 		0.599
(1.00)
18q loss 61 (11%) 510 0.145
(1.00) 		0.00695
(1.00) 		0.621
(1.00) 		0.238
(1.00) 		7e-05
(0.0489) 		0.26
(1.00) 		0.00958
(1.00) 		0.00334
(1.00) 		0.416
(1.00) 		0.12
(1.00)
21q loss 40 (7%) 531 0.0213
(1.00) 		0.00112
(0.731) 		0.0345
(1.00) 		0.319
(1.00) 		0.00025
(0.169) 		0.0672
(1.00) 		0.0119
(1.00) 		0.0838
(1.00) 		0.824
(1.00) 		1
(1.00)
22q loss 179 (31%) 392 0.721
(1.00) 		0.606
(1.00) 		0.209
(1.00) 		0.933
(1.00) 		1e-05
(0.00774) 		0.159
(1.00) 		0.908
(1.00) 		0.137
(1.00) 		0.201
(1.00) 		0.0927
(1.00)
xq loss 105 (18%) 466 0.0206
(1.00) 		0.0243
(1.00) 		0.147
(1.00) 		0.16
(1.00) 		1e-05
(0.00774) 		0.124
(1.00) 		0.96
(1.00) 		0.554
(1.00) 		0.415
(1.00) 		0.96
(1.00)
4p gain 36 (6%) 535 0.241
(1.00) 		0.614
(1.00) 		0.486
(1.00) 		0.519
(1.00) 		0.00298
(1.00) 		0.826
(1.00) 		0.758
(1.00) 		0.551
(1.00) 		0.616
(1.00) 		0.791
(1.00)
4q gain 33 (6%) 538 0.312
(1.00) 		0.319
(1.00) 		0.495
(1.00) 		0.541
(1.00) 		0.0109
(1.00) 		0.622
(1.00) 		0.927
(1.00) 		0.687
(1.00) 		0.366
(1.00) 		0.663
(1.00)
6p gain 24 (4%) 547 0.0121
(1.00) 		0.118
(1.00) 		0.878
(1.00) 		0.16
(1.00) 		0.0773
(1.00) 		0.319
(1.00) 		0.812
(1.00) 		0.583
(1.00) 		1
(1.00) 		1
(1.00)
6q gain 23 (4%) 548 0.00174
(1.00) 		0.037
(1.00) 		0.784
(1.00) 		0.103
(1.00) 		0.00674
(1.00) 		0.0648
(1.00) 		0.932
(1.00) 		0.529
(1.00) 		0.81
(1.00) 		1
(1.00)
10q gain 3 (1%) 568 0.557
(1.00) 		1
(1.00) 		0.0515
(1.00) 		0.796
(1.00) 		0.196
(1.00)
11p gain 17 (3%) 554 0.904
(1.00) 		0.88
(1.00) 		0.243
(1.00) 		0.943
(1.00) 		0.22
(1.00) 		0.869
(1.00) 		0.532
(1.00) 		0.695
(1.00) 		1
(1.00)
11q gain 14 (2%) 557 0.185
(1.00) 		0.0651
(1.00) 		0.216
(1.00) 		0.362
(1.00) 		0.123
(1.00) 		0.87
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12q gain 48 (8%) 523 0.523
(1.00) 		0.954
(1.00) 		0.538
(1.00) 		0.00993
(1.00) 		0.00074
(0.49) 		0.751
(1.00) 		0.312
(1.00) 		0.299
(1.00) 		0.0222
(1.00) 		0.124
(1.00)
13q gain 10 (2%) 561 0.0532
(1.00) 		0.497
(1.00) 		0.181
(1.00) 		0.822
(1.00) 		0.017
(1.00) 		0.367
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.423
(1.00) 		1
(1.00)
14q gain 22 (4%) 549 0.431
(1.00) 		0.778
(1.00) 		0.0102
(1.00) 		0.806
(1.00) 		0.828
(1.00) 		0.47
(1.00) 		0.858
(1.00) 		0.426
(1.00) 		0.328
(1.00)
xq gain 16 (3%) 555 0.252
(1.00) 		0.948
(1.00) 		0.985
(1.00) 		0.361
(1.00) 		0.66
(1.00) 		0.624
(1.00) 		0.79
(1.00) 		1
(1.00) 		0.0388
(1.00) 		0.259
(1.00)
1p loss 16 (3%) 555 0.639
(1.00) 		0.828
(1.00) 		0.94
(1.00) 		0.195
(1.00) 		0.0877
(1.00) 		0.677
(1.00) 		0.341
(1.00) 		0.18
(1.00) 		0.11
(1.00) 		0.0184
(1.00)
1q loss 15 (3%) 556 0.831
(1.00) 		0.978
(1.00) 		0.854
(1.00) 		0.363
(1.00) 		0.368
(1.00) 		0.678
(1.00) 		0.34
(1.00) 		0.209
(1.00) 		0.518
(1.00) 		0.0835
(1.00)
4p loss 54 (9%) 517 0.0794
(1.00) 		0.00331
(1.00) 		0.0337
(1.00) 		0.225
(1.00) 		0.00949
(1.00) 		1
(1.00) 		0.294
(1.00) 		0.121
(1.00) 		0.746
(1.00) 		1
(1.00)
4q loss 55 (10%) 516 0.00098
(0.647) 		0.00064
(0.426) 		0.0191
(1.00) 		0.152
(1.00) 		0.0004
(0.268) 		0.0106
(1.00) 		0.733
(1.00) 		0.482
(1.00) 		0.56
(1.00) 		1
(1.00)
7p loss 8 (1%) 563 0.0221
(1.00) 		0.0341
(1.00) 		0.457
(1.00) 		0.041
(1.00) 		0.205
(1.00)
7q loss 6 (1%) 565 0.0995
(1.00) 		0.304
(1.00) 		0.941
(1.00) 		0.125
(1.00) 		0.591
(1.00)
8p loss 58 (10%) 513 0.546
(1.00) 		0.441
(1.00) 		0.18
(1.00) 		0.777
(1.00) 		0.0678
(1.00) 		0.591
(1.00) 		0.906
(1.00) 		0.95
(1.00) 		0.575
(1.00) 		0.391
(1.00)
8q loss 42 (7%) 529 0.618
(1.00) 		0.15
(1.00) 		0.0219
(1.00) 		0.808
(1.00) 		0.0142
(1.00) 		0.258
(1.00) 		0.859
(1.00) 		0.655
(1.00) 		0.457
(1.00) 		0.147
(1.00)
9p loss 200 (35%) 371 0.00917
(1.00) 		0.134
(1.00) 		0.527
(1.00) 		0.446
(1.00) 		0.688
(1.00) 		0.569
(1.00) 		0.618
(1.00) 		0.0467
(1.00) 		0.022
(1.00) 		0.00885
(1.00)
9q loss 91 (16%) 480 0.373
(1.00) 		0.0692
(1.00) 		0.115
(1.00) 		0.206
(1.00) 		0.333
(1.00) 		0.324
(1.00) 		0.366
(1.00) 		0.118
(1.00) 		0.753
(1.00) 		0.179
(1.00)
12p loss 59 (10%) 512 0.0884
(1.00) 		0.0653
(1.00) 		0.473
(1.00) 		0.809
(1.00) 		0.00274
(1.00) 		0.9
(1.00) 		0.155
(1.00) 		0.0579
(1.00) 		1
(1.00) 		0.662
(1.00)
16p loss 63 (11%) 508 0.287
(1.00) 		0.853
(1.00) 		0.66
(1.00) 		0.735
(1.00) 		0.0201
(1.00) 		0.43
(1.00) 		0.454
(1.00) 		0.189
(1.00) 		0.565
(1.00) 		0.647
(1.00)
16q loss 83 (15%) 488 0.0618
(1.00) 		0.43
(1.00) 		0.463
(1.00) 		0.898
(1.00) 		0.0102
(1.00) 		0.822
(1.00) 		0.0478
(1.00) 		0.0182
(1.00) 		0.663
(1.00) 		0.598
(1.00)
19p loss 25 (4%) 546 0.00207
(1.00) 		0.00719
(1.00) 		0.149
(1.00) 		0.41
(1.00) 		0.014
(1.00) 		0.00203
(1.00) 		0.0199
(1.00) 		0.0107
(1.00) 		0.839
(1.00) 		0.802
(1.00)
19q loss 33 (6%) 538 0.00211
(1.00) 		0.0104
(1.00) 		0.392
(1.00) 		0.104
(1.00) 		0.00073
(0.485) 		0.0904
(1.00) 		0.0804
(1.00) 		0.337
(1.00) 		0.782
(1.00) 		0.485
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
1P GAIN MUTATED 50 12 20
1P GAIN WILD-TYPE 109 200 180

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
1Q GAIN MUTATED 57 10 22
1Q GAIN WILD-TYPE 102 202 178

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

'2p gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
2P GAIN MUTATED 22 7 7
2P GAIN WILD-TYPE 137 205 193

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S4.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
2Q GAIN MUTATED 21 7 7
2Q GAIN WILD-TYPE 138 205 193

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S5.  Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
3P GAIN MUTATED 34 4 19
3P GAIN WILD-TYPE 125 208 181

Figure S5.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S6.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
3Q GAIN MUTATED 35 6 21
3Q GAIN WILD-TYPE 124 206 179

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S7.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
5P GAIN MUTATED 28 6 15
5P GAIN WILD-TYPE 131 206 185

Figure S7.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S8.  Gene #10: '5q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
5Q GAIN MUTATED 24 6 11
5Q GAIN WILD-TYPE 135 206 189

Figure S8.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S9.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7P GAIN MUTATED 135 65 128 82
7P GAIN WILD-TYPE 12 31 24 31

Figure S9.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7P GAIN MUTATED 132 55 85 138
7P GAIN WILD-TYPE 16 47 15 20

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7P GAIN MUTATED 214 113 117
7P GAIN WILD-TYPE 79 11 12

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
7P GAIN MUTATED 143 188 132
7P GAIN WILD-TYPE 16 24 68

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
7P GAIN MUTATED 16 84 20
7P GAIN WILD-TYPE 14 8 5

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S14.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
7Q GAIN MUTATED 135 62 129 87
7Q GAIN WILD-TYPE 12 34 23 26

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7Q GAIN MUTATED 130 61 84 138
7Q GAIN WILD-TYPE 18 41 16 20

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7Q GAIN MUTATED 221 112 114
7Q GAIN WILD-TYPE 72 12 15

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
7Q GAIN MUTATED 139 191 139
7Q GAIN WILD-TYPE 20 21 61

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 47 33
7Q GAIN MUTATED 39 44 22
7Q GAIN WILD-TYPE 1 3 11

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p gain' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S19.  Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
8P GAIN MUTATED 7 18 6 17
8P GAIN WILD-TYPE 140 78 146 96

Figure S19.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S20.  Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
8P GAIN MUTATED 31 4 17
8P GAIN WILD-TYPE 128 208 183

Figure S20.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S21.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
8Q GAIN MUTATED 7 20 7 20
8Q GAIN WILD-TYPE 140 76 145 93

Figure S21.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S22.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
8Q GAIN MUTATED 9 26 4 15
8Q GAIN WILD-TYPE 139 76 96 143

Figure S22.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S23.  Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
8Q GAIN MUTATED 30 6 23
8Q GAIN WILD-TYPE 129 206 177

Figure S23.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S24.  Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
9P GAIN MUTATED 25 6 16
9P GAIN WILD-TYPE 134 206 184

Figure S24.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S25.  Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
9Q GAIN MUTATED 34 13 25
9Q GAIN WILD-TYPE 125 199 175

Figure S25.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.062

Table S26.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P GAIN MUTATED 2 9 0 1
10P GAIN WILD-TYPE 146 93 100 157

Figure S26.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S27.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
12P GAIN MUTATED 31 10 18
12P GAIN WILD-TYPE 128 202 182

Figure S27.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.062

Table S28.  Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
15Q GAIN MUTATED 14 1 9
15Q GAIN WILD-TYPE 145 211 191

Figure S28.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S29.  Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
16P GAIN MUTATED 21 3 14
16P GAIN WILD-TYPE 138 209 186

Figure S29.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S30.  Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
16Q GAIN MUTATED 20 4 13
16Q GAIN WILD-TYPE 139 208 187

Figure S30.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

'17p gain' versus 'MRNA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.25

Table S31.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
17P GAIN MUTATED 9 14 4 16
17P GAIN WILD-TYPE 138 82 148 97

Figure S31.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S32.  Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
17P GAIN MUTATED 27 9 12
17P GAIN WILD-TYPE 132 203 188

Figure S32.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S33.  Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
17Q GAIN MUTATED 33 11 15
17Q GAIN WILD-TYPE 126 201 185

Figure S33.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S34.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
18P GAIN MUTATED 10 25 5 15
18P GAIN WILD-TYPE 137 71 147 98

Figure S34.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S35.  Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
18P GAIN MUTATED 29 3 26
18P GAIN WILD-TYPE 130 209 174

Figure S35.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S36.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
18Q GAIN MUTATED 9 24 6 16
18Q GAIN WILD-TYPE 138 72 146 97

Figure S36.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S37.  Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
18Q GAIN MUTATED 31 4 23
18Q GAIN WILD-TYPE 128 208 177

Figure S37.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S38.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19P GAIN MUTATED 52 35 91 21
19P GAIN WILD-TYPE 95 61 61 92

Figure S38.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S39.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19P GAIN MUTATED 62 26 58 53
19P GAIN WILD-TYPE 86 76 42 105

Figure S39.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S40.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
19P GAIN MUTATED 41 138 45
19P GAIN WILD-TYPE 118 74 155

Figure S40.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S41.  Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 76 56
19P GAIN MUTATED 22 18 35
19P GAIN WILD-TYPE 47 58 21

Figure S41.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S42.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
19Q GAIN MUTATED 46 28 85 16
19Q GAIN WILD-TYPE 101 68 67 97

Figure S42.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S43.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19Q GAIN MUTATED 55 18 55 47
19Q GAIN WILD-TYPE 93 84 45 111

Figure S43.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S44.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
19Q GAIN MUTATED 35 127 35
19Q GAIN WILD-TYPE 124 85 165

Figure S44.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S45.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20P GAIN MUTATED 51 26 86 29
20P GAIN WILD-TYPE 96 70 66 84

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S46.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P GAIN MUTATED 55 21 64 52
20P GAIN WILD-TYPE 93 81 36 106

Figure S46.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S47.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20P GAIN MUTATED 85 58 69
20P GAIN WILD-TYPE 208 66 60

Figure S47.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S48.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
20P GAIN MUTATED 60 109 51
20P GAIN WILD-TYPE 99 103 149

Figure S48.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S49.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20Q GAIN MUTATED 50 28 86 27
20Q GAIN WILD-TYPE 97 68 66 86

Figure S49.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S50.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q GAIN MUTATED 58 22 62 49
20Q GAIN WILD-TYPE 90 80 38 109

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20Q GAIN MUTATED 85 57 68
20Q GAIN WILD-TYPE 208 67 61

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
20Q GAIN MUTATED 58 108 52
20Q GAIN WILD-TYPE 101 104 148

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S53.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
21Q GAIN MUTATED 26 10 27
21Q GAIN WILD-TYPE 133 202 173

Figure S53.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'22q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S54.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
22Q GAIN MUTATED 6 14 0 11
22Q GAIN WILD-TYPE 141 82 152 102

Figure S54.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S55.  Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
22Q GAIN MUTATED 18 3 13
22Q GAIN WILD-TYPE 141 209 187

Figure S55.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.24

Table S56.  Gene #43: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
2P LOSS MUTATED 17 3 12
2P LOSS WILD-TYPE 142 209 188

Figure S56.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S57.  Gene #44: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
2Q LOSS MUTATED 17 3 12
2Q LOSS WILD-TYPE 142 209 188

Figure S57.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #45: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
3P LOSS MUTATED 19 4 17
3P LOSS WILD-TYPE 140 208 183

Figure S58.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S59.  Gene #46: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
3Q LOSS MUTATED 18 2 14
3Q LOSS WILD-TYPE 141 210 186

Figure S59.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S60.  Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
5P LOSS MUTATED 5 20 6 9
5P LOSS WILD-TYPE 142 76 146 104

Figure S60.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S61.  Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5P LOSS MUTATED 6 22 5 7
5P LOSS WILD-TYPE 142 80 95 151

Figure S61.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S62.  Gene #49: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
5P LOSS MUTATED 16 4 22
5P LOSS WILD-TYPE 143 208 178

Figure S62.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S63.  Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
5Q LOSS MUTATED 6 19 5 11
5Q LOSS WILD-TYPE 141 77 147 102

Figure S63.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S64.  Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5Q LOSS MUTATED 9 21 4 7
5Q LOSS WILD-TYPE 139 81 96 151

Figure S64.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.096

Table S65.  Gene #50: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
5Q LOSS MUTATED 17 4 22
5Q LOSS WILD-TYPE 142 208 178

Figure S65.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S66.  Gene #51: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
6P LOSS MUTATED 51 12 23
6P LOSS WILD-TYPE 108 200 177

Figure S66.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S67.  Gene #52: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
6Q LOSS MUTATED 62 28 34
6Q LOSS WILD-TYPE 97 184 166

Figure S67.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S68.  Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10P LOSS MUTATED 132 64 140 84
10P LOSS WILD-TYPE 15 32 12 29

Figure S68.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S69.  Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P LOSS MUTATED 127 63 93 137
10P LOSS WILD-TYPE 21 39 7 21

Figure S69.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.096

Table S70.  Gene #59: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10P LOSS MUTATED 227 108 120
10P LOSS WILD-TYPE 66 16 9

Figure S70.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S71.  Gene #59: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
10P LOSS MUTATED 149 204 124
10P LOSS WILD-TYPE 10 8 76

Figure S71.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S72.  Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
10Q LOSS MUTATED 132 68 146 87
10Q LOSS WILD-TYPE 15 28 6 26

Figure S72.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S73.  Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10Q LOSS MUTATED 128 69 97 139
10Q LOSS WILD-TYPE 20 33 3 19

Figure S73.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S74.  Gene #60: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10Q LOSS MUTATED 236 109 123
10Q LOSS WILD-TYPE 57 15 6

Figure S74.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S75.  Gene #60: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
10Q LOSS MUTATED 148 206 134
10Q LOSS WILD-TYPE 11 6 66

Figure S75.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S76.  Gene #60: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 58 44 45
10Q LOSS MUTATED 50 42 44 41
10Q LOSS WILD-TYPE 4 16 0 4

Figure S76.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'11p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S77.  Gene #61: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11P LOSS MUTATED 27 32 9 22
11P LOSS WILD-TYPE 120 64 143 91

Figure S77.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S78.  Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11P LOSS MUTATED 26 36 4 24
11P LOSS WILD-TYPE 122 66 96 134

Figure S78.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S79.  Gene #61: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
11P LOSS MUTATED 54 8 35
11P LOSS WILD-TYPE 105 204 165

Figure S79.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S80.  Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
11Q LOSS MUTATED 31 28 10 18
11Q LOSS WILD-TYPE 116 68 142 95

Figure S80.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.062

Table S81.  Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11Q LOSS MUTATED 28 28 5 26
11Q LOSS WILD-TYPE 120 74 95 132

Figure S81.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S82.  Gene #62: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
11Q LOSS MUTATED 54 10 28
11Q LOSS WILD-TYPE 105 202 172

Figure S82.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S83.  Gene #64: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
12Q LOSS MUTATED 27 8 23
12Q LOSS WILD-TYPE 132 204 177

Figure S83.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S84.  Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
13Q LOSS MUTATED 57 35 26 45
13Q LOSS WILD-TYPE 90 61 126 68

Figure S84.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S85.  Gene #65: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
13Q LOSS MUTATED 100 20 63
13Q LOSS WILD-TYPE 59 192 137

Figure S85.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S86.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
14Q LOSS MUTATED 46 34 17 39
14Q LOSS WILD-TYPE 101 62 135 74

Figure S86.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S87.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
14Q LOSS MUTATED 43 36 10 47
14Q LOSS WILD-TYPE 105 66 90 111

Figure S87.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S88.  Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
14Q LOSS MUTATED 86 9 51
14Q LOSS WILD-TYPE 73 203 149

Figure S88.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S89.  Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
15Q LOSS MUTATED 26 26 12 31
15Q LOSS WILD-TYPE 121 70 140 82

Figure S89.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S90.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
15Q LOSS MUTATED 22 37 7 29
15Q LOSS WILD-TYPE 126 65 93 129

Figure S90.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S91.  Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
15Q LOSS MUTATED 52 18 32
15Q LOSS WILD-TYPE 107 194 168

Figure S91.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S92.  Gene #70: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
17P LOSS MUTATED 34 6 24
17P LOSS WILD-TYPE 125 206 176

Figure S92.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S93.  Gene #71: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
17Q LOSS MUTATED 23 4 15
17Q LOSS WILD-TYPE 136 208 185

Figure S93.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S94.  Gene #72: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
18P LOSS MUTATED 32 10 27
18P LOSS WILD-TYPE 127 202 173

Figure S94.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S95.  Gene #73: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
18Q LOSS MUTATED 28 9 24
18Q LOSS WILD-TYPE 131 203 176

Figure S95.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

'20p loss' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S96.  Gene #76: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
20P LOSS MUTATED 4 10 0 3
20P LOSS WILD-TYPE 143 86 152 110

Figure S96.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S97.  Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P LOSS MUTATED 5 11 0 1
20P LOSS WILD-TYPE 143 91 100 157

Figure S97.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S98.  Gene #76: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
20P LOSS MUTATED 12 0 6
20P LOSS WILD-TYPE 147 212 194

Figure S98.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S99.  Gene #77: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q LOSS MUTATED 4 10 0 1
20Q LOSS WILD-TYPE 144 92 100 157

Figure S99.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S100.  Gene #77: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
20Q LOSS MUTATED 12 1 3
20Q LOSS WILD-TYPE 147 211 197

Figure S100.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S101.  Gene #78: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
21Q LOSS MUTATED 22 6 12
21Q LOSS WILD-TYPE 137 206 188

Figure S101.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S102.  Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
22Q LOSS MUTATED 75 46 58
22Q LOSS WILD-TYPE 84 166 142

Figure S102.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S103.  Gene #80: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
XQ LOSS MUTATED 57 25 23
XQ LOSS WILD-TYPE 102 187 177

Figure S103.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 571

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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