Correlation between copy number variations of arm-level result and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1GB22GQ
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/C1GB22GQ
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 560 patients, 94 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', and 'CN_CNMF'.

  • 7q gain cnv correlated to 'MRNA_CNMF' and 'CN_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'.

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

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

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

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

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', 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'.

  • 5q loss cnv correlated to 'MRNA_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 12q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

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

  • 20q loss cnv correlated to '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, 94 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
19p gain 220 (39%) 340 9.83e-11
(7.48e-08) 		1.47e-06
(0.00108) 		0.0812
(1.00) 		0.000154
(0.107) 		1.55e-14
(1.19e-11) 		0.00891
(1.00) 		0.00922
(1.00) 		1.6e-05
(0.0114) 		0.188
(1.00) 		0.0129
(1.00)
10q loss 478 (85%) 82 4.48e-08
(3.35e-05) 		1.28e-06
(0.000937) 		0.00673
(1.00) 		8.68e-05
(0.0603) 		3.79e-23
(2.92e-20) 		0.0361
(1.00) 		0.000207
(0.142) 		0.0287
(1.00) 		0.25
(1.00) 		0.207
(1.00)
7p gain 455 (81%) 105 1.89e-06
(0.00138) 		6.81e-07
(0.000503) 		0.000437
(0.296) 		1.34e-08
(1e-05) 		5.66e-10
(4.28e-07) 		0.00731
(1.00) 		0.00223
(1.00) 		0.294
(1.00) 		0.0162
(1.00) 		0.00177
(1.00)
19q gain 193 (34%) 367 2.93e-12
(2.23e-09) 		6.36e-09
(4.79e-06) 		0.144
(1.00) 		0.00159
(1.00) 		3.49e-16
(2.68e-13) 		0.00601
(1.00) 		0.0476
(1.00) 		6.47e-05
(0.045) 		0.0637
(1.00) 		0.0186
(1.00)
20p gain 217 (39%) 343 1.45e-07
(0.000107) 		2.97e-09
(2.24e-06) 		0.00443
(1.00) 		1.05e-06
(0.000775) 		8.78e-05
(0.0609) 		0.0226
(1.00) 		0.0537
(1.00) 		0.0064
(1.00) 		0.776
(1.00) 		0.00123
(0.814)
20q gain 215 (38%) 345 9.04e-08
(6.72e-05) 		7.31e-09
(5.5e-06) 		0.00303
(1.00) 		5.44e-06
(0.00394) 		0.000192
(0.133) 		0.0046
(1.00) 		0.036
(1.00) 		0.00512
(1.00) 		0.776
(1.00) 		0.00123
(0.814)
10p loss 467 (83%) 93 6.19e-08
(4.61e-05) 		2.86e-05
(0.0203) 		0.0104
(1.00) 		1.76e-06
(0.00129) 		4.86e-21
(3.74e-18) 		0.0745
(1.00) 		0.00269
(1.00) 		0.0287
(1.00) 		0.212
(1.00) 		0.168
(1.00)
15q loss 99 (18%) 461 3.38e-05
(0.0238) 		4.29e-06
(0.00312) 		0.00396
(1.00) 		0.00437
(1.00) 		2.47e-08
(1.85e-05) 		1.64e-05
(0.0117) 		0.0345
(1.00) 		0.00865
(1.00) 		0.00368
(1.00) 		0.161
(1.00)
8q gain 58 (10%) 502 5.51e-06
(0.00398) 		0.000265
(0.181) 		0.0417
(1.00) 		0.00972
(1.00) 		8.96e-08
(6.67e-05) 		0.165
(1.00) 		0.427
(1.00) 		0.0777
(1.00) 		0.119
(1.00) 		0.148
(1.00)
22q gain 34 (6%) 526 2.32e-06
(0.00169) 		0.000225
(0.154) 		0.474
(1.00) 		0.327
(1.00) 		6.39e-05
(0.0445) 		0.253
(1.00) 		0.212
(1.00) 		0.0286
(1.00) 		0.245
(1.00) 		0.416
(1.00)
11p loss 96 (17%) 464 5.43e-07
(0.000401) 		5.97e-05
(0.0418) 		0.846
(1.00) 		0.00589
(1.00) 		4.38e-15
(3.36e-12) 		0.0472
(1.00) 		0.719
(1.00) 		0.121
(1.00) 		0.0935
(1.00) 		0.466
(1.00)
13q loss 182 (32%) 378 2.34e-05
(0.0166) 		0.000196
(0.135) 		0.745
(1.00) 		0.207
(1.00) 		1.42e-21
(1.09e-18) 		0.000484
(0.326) 		0.594
(1.00) 		0.0743
(1.00) 		0.052
(1.00) 		0.405
(1.00)
7q gain 460 (82%) 100 8.72e-07
(0.000642) 		0.000474
(0.32) 		0.00186
(1.00) 		0.000456
(0.308) 		5.31e-08
(3.97e-05) 		0.0024
(1.00) 		0.11
(1.00) 		0.178
(1.00) 		0.0513
(1.00) 		0.00799
(1.00)
8p gain 51 (9%) 509 5.21e-05
(0.0365) 		0.00311
(1.00) 		0.0654
(1.00) 		0.00562
(1.00) 		1.3e-09
(9.83e-07) 		0.0742
(1.00) 		0.427
(1.00) 		0.0777
(1.00) 		0.137
(1.00) 		0.272
(1.00)
18p gain 58 (10%) 502 4.13e-07
(0.000306) 		0.000418
(0.284) 		0.16
(1.00) 		0.142
(1.00) 		3.56e-10
(2.7e-07) 		0.534
(1.00) 		0.425
(1.00) 		0.465
(1.00) 		0.0181
(1.00) 		0.547
(1.00)
18q gain 57 (10%) 503 5.07e-07
(0.000375) 		0.000728
(0.487) 		0.174
(1.00) 		0.162
(1.00) 		9.9e-11
(7.53e-08) 		0.682
(1.00) 		0.477
(1.00) 		0.622
(1.00) 		0.0181
(1.00) 		0.277
(1.00)
11q loss 90 (16%) 470 1.31e-05
(0.00944) 		0.0034
(1.00) 		0.909
(1.00) 		0.119
(1.00) 		3.1e-14
(2.37e-11) 		0.381
(1.00) 		0.914
(1.00) 		0.306
(1.00) 		0.346
(1.00) 		0.584
(1.00)
14q loss 141 (25%) 419 1.61e-06
(0.00118) 		0.00312
(1.00) 		0.508
(1.00) 		0.777
(1.00) 		1.26e-29
(9.75e-27) 		0.0128
(1.00) 		0.803
(1.00) 		0.143
(1.00) 		0.163
(1.00) 		0.014
(1.00)
20p loss 18 (3%) 542 0.000214
(0.147) 		0.00626
(1.00) 		0.0394
(1.00) 		0.0114
(1.00) 		9.12e-06
(0.00657) 		0.414
(1.00) 		0.384
(1.00) 		0.0104
(1.00) 		0.0794
(1.00)
1p gain 82 (15%) 478 0.597
(1.00) 		0.301
(1.00) 		0.484
(1.00) 		0.443
(1.00) 		6.39e-13
(4.88e-10) 		0.925
(1.00) 		0.502
(1.00) 		0.589
(1.00) 		0.33
(1.00) 		0.26
(1.00)
1q gain 88 (16%) 472 0.0781
(1.00) 		0.234
(1.00) 		0.131
(1.00) 		0.342
(1.00) 		1.83e-16
(1.4e-13) 		0.762
(1.00) 		0.577
(1.00) 		0.38
(1.00) 		0.818
(1.00) 		0.368
(1.00)
2p gain 36 (6%) 524 0.452
(1.00) 		0.905
(1.00) 		0.379
(1.00) 		0.729
(1.00) 		4.87e-05
(0.0342) 		0.196
(1.00) 		0.572
(1.00) 		0.172
(1.00) 		1
(1.00) 		0.182
(1.00)
2q gain 35 (6%) 525 0.645
(1.00) 		0.719
(1.00) 		0.166
(1.00) 		0.711
(1.00) 		0.000111
(0.077) 		0.196
(1.00) 		0.92
(1.00) 		0.172
(1.00) 		0.77
(1.00) 		0.0623
(1.00)
3p gain 57 (10%) 503 0.000522
(0.35) 		0.00681
(1.00) 		0.663
(1.00) 		0.0314
(1.00) 		5.36e-08
(4e-05) 		0.133
(1.00) 		0.635
(1.00) 		0.539
(1.00) 		0.788
(1.00) 		0.395
(1.00)
3q gain 63 (11%) 497 0.000581
(0.389) 		0.0153
(1.00) 		0.884
(1.00) 		0.0559
(1.00) 		6.89e-07
(0.000508) 		0.0621
(1.00) 		0.707
(1.00) 		0.529
(1.00) 		0.525
(1.00) 		0.27
(1.00)
5p gain 48 (9%) 512 0.118
(1.00) 		0.279
(1.00) 		0.18
(1.00) 		0.428
(1.00) 		2.12e-06
(0.00154) 		0.685
(1.00) 		0.282
(1.00) 		0.344
(1.00) 		0.128
(1.00) 		0.259
(1.00)
5q gain 40 (7%) 520 0.143
(1.00) 		0.428
(1.00) 		0.118
(1.00) 		0.0784
(1.00) 		2.98e-06
(0.00217) 		0.441
(1.00) 		0.39
(1.00) 		0.0953
(1.00) 		0.169
(1.00) 		0.739
(1.00)
9p gain 47 (8%) 513 0.00379
(1.00) 		0.132
(1.00) 		0.7
(1.00) 		0.711
(1.00) 		3.5e-05
(0.0246) 		0.195
(1.00) 		0.799
(1.00) 		0.705
(1.00) 		0.452
(1.00) 		0.24
(1.00)
9q gain 72 (13%) 488 0.0553
(1.00) 		0.107
(1.00) 		0.521
(1.00) 		0.137
(1.00) 		3.12e-05
(0.0221) 		0.0624
(1.00) 		0.321
(1.00) 		0.441
(1.00) 		0.673
(1.00) 		0.152
(1.00)
12p gain 58 (10%) 502 0.673
(1.00) 		0.7
(1.00) 		0.54
(1.00) 		0.721
(1.00) 		5.24e-05
(0.0367) 		0.195
(1.00) 		0.236
(1.00) 		0.711
(1.00) 		0.00716
(1.00) 		0.256
(1.00)
15q gain 24 (4%) 536 0.068
(1.00) 		0.541
(1.00) 		0.563
(1.00) 		1
(1.00) 		6.28e-05
(0.0439) 		0.535
(1.00) 		1
(1.00) 		0.0347
(1.00) 		0.226
(1.00)
16p gain 37 (7%) 523 0.00831
(1.00) 		0.147
(1.00) 		0.411
(1.00) 		0.594
(1.00) 		2.43e-05
(0.0173) 		0.615
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.766
(1.00)
16q gain 36 (6%) 524 0.0192
(1.00) 		0.114
(1.00) 		0.36
(1.00) 		0.104
(1.00) 		0.000352
(0.239) 		0.757
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.669
(1.00)
17p gain 45 (8%) 515 0.000491
(0.331) 		0.0489
(1.00) 		0.08
(1.00) 		0.263
(1.00) 		1.61e-05
(0.0116) 		0.685
(1.00) 		0.15
(1.00) 		0.121
(1.00) 		0.338
(1.00) 		0.307
(1.00)
17q gain 56 (10%) 504 0.00116
(0.769) 		0.1
(1.00) 		0.151
(1.00) 		0.323
(1.00) 		6.42e-06
(0.00463) 		0.585
(1.00) 		0.0801
(1.00) 		0.0296
(1.00) 		0.898
(1.00) 		0.572
(1.00)
21q gain 62 (11%) 498 0.00134
(0.882) 		0.00253
(1.00) 		0.012
(1.00) 		0.00414
(1.00) 		0.000228
(0.156) 		0.728
(1.00) 		0.328
(1.00) 		0.602
(1.00) 		0.0179
(1.00) 		0.0346
(1.00)
2p loss 30 (5%) 530 0.0724
(1.00) 		0.0343
(1.00) 		0.387
(1.00) 		0.502
(1.00) 		3.06e-05
(0.0217) 		0.00395
(1.00) 		0.926
(1.00) 		0.445
(1.00) 		0.244
(1.00) 		0.669
(1.00)
2q loss 30 (5%) 530 0.0724
(1.00) 		0.0343
(1.00) 		0.387
(1.00) 		0.502
(1.00) 		3.06e-05
(0.0217) 		0.00395
(1.00) 		0.85
(1.00) 		0.458
(1.00) 		0.0836
(1.00) 		0.423
(1.00)
3p loss 39 (7%) 521 0.898
(1.00) 		0.73
(1.00) 		0.704
(1.00) 		0.621
(1.00) 		0.00033
(0.225) 		0.109
(1.00) 		0.239
(1.00) 		0.436
(1.00) 		0.638
(1.00) 		0.0547
(1.00)
3q loss 33 (6%) 527 0.231
(1.00) 		0.897
(1.00) 		0.513
(1.00) 		0.766
(1.00) 		5.79e-06
(0.00418) 		0.253
(1.00) 		0.786
(1.00) 		0.806
(1.00) 		0.888
(1.00) 		0.0427
(1.00)
5p loss 42 (8%) 518 1.76e-05
(0.0126) 		0.00318
(1.00) 		0.00202
(1.00) 		0.0188
(1.00) 		0.00129
(0.85) 		0.0773
(1.00) 		0.94
(1.00) 		0.388
(1.00) 		0.325
(1.00) 		0.747
(1.00)
5q loss 43 (8%) 517 3.87e-05
(0.0272) 		0.00985
(1.00) 		0.00109
(0.727) 		0.0187
(1.00) 		0.000862
(0.575) 		0.0773
(1.00) 		0.944
(1.00) 		0.264
(1.00) 		0.212
(1.00) 		0.85
(1.00)
6p loss 84 (15%) 476 0.565
(1.00) 		0.397
(1.00) 		0.774
(1.00) 		0.892
(1.00) 		3.48e-13
(2.66e-10) 		0.283
(1.00) 		0.775
(1.00) 		0.118
(1.00) 		0.857
(1.00) 		0.355
(1.00)
6q loss 121 (22%) 439 0.937
(1.00) 		0.698
(1.00) 		0.567
(1.00) 		0.612
(1.00) 		1.78e-10
(1.35e-07) 		0.749
(1.00) 		0.959
(1.00) 		0.267
(1.00) 		0.494
(1.00) 		0.786
(1.00)
12q loss 57 (10%) 503 0.0604
(1.00) 		0.0196
(1.00) 		0.547
(1.00) 		0.28
(1.00) 		2.82e-05
(0.02) 		0.682
(1.00) 		0.178
(1.00) 		0.657
(1.00) 		0.941
(1.00) 		0.698
(1.00)
17p loss 63 (11%) 497 0.0205
(1.00) 		0.912
(1.00) 		0.65
(1.00) 		0.517
(1.00) 		1.19e-09
(8.99e-07) 		0.0279
(1.00) 		0.215
(1.00) 		0.296
(1.00) 		0.292
(1.00) 		0.256
(1.00)
17q loss 42 (8%) 518 0.00571
(1.00) 		0.123
(1.00) 		0.252
(1.00) 		0.573
(1.00) 		4.89e-06
(0.00355) 		0.0742
(1.00) 		0.481
(1.00) 		0.288
(1.00) 		0.146
(1.00) 		0.0156
(1.00)
18p loss 68 (12%) 492 0.0477
(1.00) 		0.0338
(1.00) 		0.359
(1.00) 		0.3
(1.00) 		0.000182
(0.125) 		0.387
(1.00) 		0.0656
(1.00) 		0.0179
(1.00) 		0.125
(1.00) 		0.556
(1.00)
19q loss 34 (6%) 526 0.00191
(1.00) 		0.023
(1.00) 		0.511
(1.00) 		0.0603
(1.00) 		0.000222
(0.152) 		0.0742
(1.00) 		0.0701
(1.00) 		0.539
(1.00) 		0.783
(1.00) 		0.31
(1.00)
20q loss 16 (3%) 544 0.00162
(1.00) 		0.01
(1.00) 		0.361
(1.00) 		0.294
(1.00) 		1.37e-05
(0.00984) 		0.414
(1.00) 		0.384
(1.00) 		0.0393
(1.00) 		0.12
(1.00)
21q loss 40 (7%) 520 0.0234
(1.00) 		0.0431
(1.00) 		0.0355
(1.00) 		0.261
(1.00) 		9.66e-05
(0.067) 		0.102
(1.00) 		0.0122
(1.00) 		0.138
(1.00) 		0.823
(1.00) 		0.215
(1.00)
22q loss 173 (31%) 387 0.654
(1.00) 		0.278
(1.00) 		0.237
(1.00) 		0.309
(1.00) 		1.66e-05
(0.0118) 		0.117
(1.00) 		0.899
(1.00) 		0.609
(1.00) 		0.175
(1.00) 		0.676
(1.00)
xq loss 102 (18%) 458 0.0118
(1.00) 		0.123
(1.00) 		0.186
(1.00) 		0.366
(1.00) 		4.42e-08
(3.31e-05) 		0.0365
(1.00) 		0.99
(1.00) 		0.776
(1.00) 		0.406
(1.00) 		0.666
(1.00)
4p gain 35 (6%) 525 0.242
(1.00) 		0.531
(1.00) 		0.491
(1.00) 		0.185
(1.00) 		0.00358
(1.00) 		1
(1.00) 		0.757
(1.00) 		0.42
(1.00) 		0.615
(1.00) 		0.281
(1.00)
4q gain 33 (6%) 527 0.429
(1.00) 		0.211
(1.00) 		0.447
(1.00) 		0.443
(1.00) 		0.0128
(1.00) 		0.685
(1.00) 		0.926
(1.00) 		0.638
(1.00) 		0.366
(1.00) 		0.151
(1.00)
6p gain 23 (4%) 537 0.0138
(1.00) 		0.119
(1.00) 		0.872
(1.00) 		0.61
(1.00) 		0.159
(1.00) 		0.685
(1.00) 		0.812
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.797
(1.00)
6q gain 22 (4%) 538 0.00216
(1.00) 		0.119
(1.00) 		0.77
(1.00) 		0.506
(1.00) 		0.0269
(1.00) 		0.196
(1.00) 		0.932
(1.00) 		0.375
(1.00) 		0.812
(1.00) 		0.797
(1.00)
10p gain 12 (2%) 548 0.000973
(0.648) 		0.0074
(1.00) 		0.117
(1.00) 		0.0166
(1.00) 		0.00157
(1.00) 		0.307
(1.00) 		0.384
(1.00)
10q gain 3 (1%) 557 0.556
(1.00) 		0.797
(1.00) 		0.0526
(1.00) 		0.661
(1.00) 		0.191
(1.00)
11p gain 18 (3%) 542 0.913
(1.00) 		0.799
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.116
(1.00) 		0.869
(1.00) 		0.574
(1.00) 		0.696
(1.00) 		0.428
(1.00)
11q gain 15 (3%) 545 0.125
(1.00) 		0.189
(1.00) 		0.455
(1.00) 		0.649
(1.00) 		0.0803
(1.00) 		0.869
(1.00) 		0.574
(1.00) 		1
(1.00) 		1
(1.00)
12q gain 48 (9%) 512 0.523
(1.00) 		0.3
(1.00) 		0.535
(1.00) 		0.355
(1.00) 		0.000501
(0.336) 		0.381
(1.00) 		0.314
(1.00) 		0.519
(1.00) 		0.0225
(1.00) 		0.517
(1.00)
13q gain 9 (2%) 551 0.053
(1.00) 		0.507
(1.00) 		0.18
(1.00) 		0.846
(1.00) 		0.00314
(1.00) 		0.894
(1.00) 		1
(1.00) 		0.425
(1.00) 		1
(1.00)
14q gain 22 (4%) 538 0.437
(1.00) 		0.552
(1.00) 		0.0122
(1.00) 		0.463
(1.00) 		0.724
(1.00) 		0.471
(1.00) 		0.461
(1.00) 		0.425
(1.00) 		0.62
(1.00)
xq gain 16 (3%) 544 0.253
(1.00) 		0.321
(1.00) 		0.986
(1.00) 		0.772
(1.00) 		0.321
(1.00) 		0.509
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.0394
(1.00) 		0.0933
(1.00)
1p loss 16 (3%) 544 0.637
(1.00) 		0.226
(1.00) 		0.935
(1.00) 		0.111
(1.00) 		0.0682
(1.00) 		0.0693
(1.00) 		0.342
(1.00) 		0.116
(1.00) 		0.11
(1.00) 		0.0794
(1.00)
1q loss 15 (3%) 545 0.83
(1.00) 		0.338
(1.00) 		0.853
(1.00) 		0.366
(1.00) 		0.293
(1.00) 		0.0693
(1.00) 		0.339
(1.00) 		0.173
(1.00) 		0.517
(1.00) 		0.284
(1.00)
4p loss 53 (9%) 507 0.0828
(1.00) 		0.00723
(1.00) 		0.0342
(1.00) 		0.353
(1.00) 		0.00929
(1.00) 		0.829
(1.00) 		0.301
(1.00) 		0.22
(1.00) 		0.748
(1.00) 		0.838
(1.00)
4q loss 54 (10%) 506 0.000451
(0.305) 		0.0035
(1.00) 		0.0138
(1.00) 		0.0921
(1.00) 		0.000538
(0.361) 		0.0559
(1.00) 		0.767
(1.00) 		0.35
(1.00) 		0.423
(1.00) 		0.893
(1.00)
7p loss 8 (1%) 552 0.022
(1.00) 		0.0639
(1.00) 		0.456
(1.00) 		0.0796
(1.00) 		0.0356
(1.00)
7q loss 6 (1%) 554 0.1
(1.00) 		0.279
(1.00) 		0.941
(1.00) 		0.336
(1.00) 		0.0927
(1.00)
8p loss 58 (10%) 502 0.541
(1.00) 		0.437
(1.00) 		0.182
(1.00) 		0.906
(1.00) 		0.0309
(1.00) 		0.65
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.245
(1.00)
8q loss 42 (8%) 518 0.611
(1.00) 		0.228
(1.00) 		0.0226
(1.00) 		0.943
(1.00) 		0.00778
(1.00) 		0.331
(1.00) 		0.858
(1.00) 		0.922
(1.00) 		0.46
(1.00) 		0.052
(1.00)
9p loss 194 (35%) 366 0.0034
(1.00) 		0.143
(1.00) 		0.526
(1.00) 		0.15
(1.00) 		0.685
(1.00) 		0.715
(1.00) 		0.587
(1.00) 		0.0617
(1.00) 		0.0181
(1.00) 		0.107
(1.00)
9q loss 86 (15%) 474 0.137
(1.00) 		0.0215
(1.00) 		0.178
(1.00) 		0.115
(1.00) 		0.232
(1.00) 		0.175
(1.00) 		0.322
(1.00) 		0.0155
(1.00) 		0.619
(1.00) 		0.73
(1.00)
12p loss 59 (11%) 501 0.0349
(1.00) 		0.0237
(1.00) 		0.543
(1.00) 		0.549
(1.00) 		0.00124
(0.82) 		0.812
(1.00) 		0.154
(1.00) 		0.2
(1.00) 		0.889
(1.00) 		0.907
(1.00)
16p loss 62 (11%) 498 0.286
(1.00) 		0.348
(1.00) 		0.665
(1.00) 		0.856
(1.00) 		0.00295
(1.00) 		0.231
(1.00) 		0.442
(1.00) 		0.518
(1.00) 		0.532
(1.00) 		0.532
(1.00)
16q loss 81 (14%) 479 0.0612
(1.00) 		0.263
(1.00) 		0.461
(1.00) 		0.843
(1.00) 		0.00393
(1.00) 		0.588
(1.00) 		0.0487
(1.00) 		0.276
(1.00) 		0.669
(1.00) 		0.618
(1.00)
18q loss 61 (11%) 499 0.238
(1.00) 		0.0695
(1.00) 		0.63
(1.00) 		0.143
(1.00) 		0.00663
(1.00) 		0.344
(1.00) 		0.0302
(1.00) 		0.00426
(1.00) 		0.395
(1.00) 		0.303
(1.00)
19p loss 26 (5%) 534 0.0055
(1.00) 		0.0215
(1.00) 		0.186
(1.00) 		0.0913
(1.00) 		0.00558
(1.00) 		0.00395
(1.00) 		0.0361
(1.00) 		0.665
(1.00) 		0.839
(1.00) 		0.229
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 6.39e-13 (Fisher's exact test), Q value = 4.9e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
1P GAIN MUTATED 51 13 18
1P GAIN WILD-TYPE 99 207 172

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

'1q gain' versus 'CN_CNMF'

P value = 1.83e-16 (Fisher's exact test), Q value = 1.4e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
1Q GAIN MUTATED 57 11 20
1Q GAIN WILD-TYPE 93 209 170

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

'2p gain' versus 'CN_CNMF'

P value = 4.87e-05 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
2P GAIN MUTATED 22 7 7
2P GAIN WILD-TYPE 128 213 183

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

'2q gain' versus 'CN_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.077

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
2Q GAIN MUTATED 21 7 7
2Q GAIN WILD-TYPE 129 213 183

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

'3p gain' versus 'CN_CNMF'

P value = 5.36e-08 (Fisher's exact test), Q value = 4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
3P GAIN MUTATED 33 7 17
3P GAIN WILD-TYPE 117 213 173

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

'3q gain' versus 'CN_CNMF'

P value = 6.89e-07 (Fisher's exact test), Q value = 0.00051

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
3Q GAIN MUTATED 34 10 19
3Q GAIN WILD-TYPE 116 210 171

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

'5p gain' versus 'CN_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
5P GAIN MUTATED 28 7 13
5P GAIN WILD-TYPE 122 213 177

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

'5q gain' versus 'CN_CNMF'

P value = 2.98e-06 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
5Q GAIN MUTATED 25 6 9
5Q GAIN WILD-TYPE 125 214 181

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

'7p gain' versus 'MRNA_CNMF'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.0014

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 65 129 82
7P GAIN WILD-TYPE 12 31 23 31

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

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.81e-07 (Fisher's exact test), Q value = 5e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
7P GAIN MUTATED 99 116 196
7P GAIN WILD-TYPE 18 55 24

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

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1.34e-08 (Fisher's exact test), Q value = 1e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
7P GAIN MUTATED 161 124 160
7P GAIN WILD-TYPE 16 60 25

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

'7p gain' versus 'CN_CNMF'

P value = 5.66e-10 (Fisher's exact test), Q value = 4.3e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
7P GAIN MUTATED 134 196 125
7P GAIN WILD-TYPE 16 24 65

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

'7q gain' versus 'MRNA_CNMF'

P value = 8.72e-07 (Fisher's exact test), Q value = 0.00064

Table S13.  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 62 130 87
7Q GAIN WILD-TYPE 12 34 22 26

Figure S13.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 5.31e-08 (Fisher's exact test), Q value = 4e-05

Table S14.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
7Q GAIN MUTATED 130 199 131
7Q GAIN WILD-TYPE 20 21 59

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'8p gain' versus 'MRNA_CNMF'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.037

Table S15.  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 S15.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.3e-09 (Fisher's exact test), Q value = 9.8e-07

Table S16.  Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
8P GAIN MUTATED 32 4 15
8P GAIN WILD-TYPE 118 216 175

Figure S16.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 5.51e-06 (Fisher's exact test), Q value = 0.004

Table S17.  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 S17.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000265 (Fisher's exact test), Q value = 0.18

Table S18.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
8Q GAIN MUTATED 7 32 15
8Q GAIN WILD-TYPE 110 139 205

Figure S18.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 8.96e-08 (Fisher's exact test), Q value = 6.7e-05

Table S19.  Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
8Q GAIN MUTATED 31 6 21
8Q GAIN WILD-TYPE 119 214 169

Figure S19.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 3.5e-05 (Fisher's exact test), Q value = 0.025

Table S20.  Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
9P GAIN MUTATED 25 7 15
9P GAIN WILD-TYPE 125 213 175

Figure S20.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.022

Table S21.  Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
9Q GAIN MUTATED 34 14 24
9Q GAIN WILD-TYPE 116 206 166

Figure S21.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 5.24e-05 (Fisher's exact test), Q value = 0.037

Table S22.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
12P GAIN MUTATED 30 12 16
12P GAIN WILD-TYPE 120 208 174

Figure S22.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 6.28e-05 (Fisher's exact test), Q value = 0.044

Table S23.  Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
15Q GAIN MUTATED 14 1 9
15Q GAIN WILD-TYPE 136 219 181

Figure S23.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.017

Table S24.  Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
16P GAIN MUTATED 21 4 12
16P GAIN WILD-TYPE 129 216 178

Figure S24.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.24

Table S25.  Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
16Q GAIN MUTATED 19 5 12
16Q GAIN WILD-TYPE 131 215 178

Figure S25.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.012

Table S26.  Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
17P GAIN MUTATED 26 8 11
17P GAIN WILD-TYPE 124 212 179

Figure S26.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 6.42e-06 (Fisher's exact test), Q value = 0.0046

Table S27.  Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
17Q GAIN MUTATED 31 11 14
17Q GAIN WILD-TYPE 119 209 176

Figure S27.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 4.13e-07 (Fisher's exact test), Q value = 0.00031

Table S28.  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 S28.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 3.56e-10 (Fisher's exact test), Q value = 2.7e-07

Table S29.  Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
18P GAIN MUTATED 31 3 24
18P GAIN WILD-TYPE 119 217 166

Figure S29.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'MRNA_CNMF'

P value = 5.07e-07 (Fisher's exact test), Q value = 0.00038

Table S30.  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 5 16
18Q GAIN WILD-TYPE 138 72 147 97

Figure S30.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 9.9e-11 (Fisher's exact test), Q value = 7.5e-08

Table S31.  Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
18Q GAIN MUTATED 33 3 21
18Q GAIN WILD-TYPE 117 217 169

Figure S31.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'MRNA_CNMF'

P value = 9.83e-11 (Fisher's exact test), Q value = 7.5e-08

Table S32.  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 S32.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.0011

Table S33.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
19P GAIN MUTATED 67 46 86
19P GAIN WILD-TYPE 50 125 134

Figure S33.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.000154 (Fisher's exact test), Q value = 0.11

Table S34.  Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
19P GAIN MUTATED 89 53 71
19P GAIN WILD-TYPE 88 131 114

Figure S34.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.55e-14 (Fisher's exact test), Q value = 1.2e-11

Table S35.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
19P GAIN MUTATED 44 131 45
19P GAIN WILD-TYPE 106 89 145

Figure S35.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.011

Table S36.  Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
19P GAIN MUTATED 39 8 28
19P GAIN WILD-TYPE 25 25 76

Figure S36.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 2.93e-12 (Fisher's exact test), Q value = 2.2e-09

Table S37.  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 15
19Q GAIN WILD-TYPE 101 68 67 98

Figure S37.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.36e-09 (Fisher's exact test), Q value = 4.8e-06

Table S38.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
19Q GAIN MUTATED 62 32 80
19Q GAIN WILD-TYPE 55 139 140

Figure S38.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 3.49e-16 (Fisher's exact test), Q value = 2.7e-13

Table S39.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
19Q GAIN MUTATED 35 122 36
19Q GAIN WILD-TYPE 115 98 154

Figure S39.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 6.47e-05 (Fisher's exact test), Q value = 0.045

Table S40.  Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 33 104
19Q GAIN MUTATED 33 6 22
19Q GAIN WILD-TYPE 31 27 82

Figure S40.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 1.45e-07 (Fisher's exact test), Q value = 0.00011

Table S41.  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 S41.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.97e-09 (Fisher's exact test), Q value = 2.2e-06

Table S42.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
20P GAIN MUTATED 70 40 82
20P GAIN WILD-TYPE 47 131 138

Figure S42.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00078

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
20P GAIN MUTATED 86 44 82
20P GAIN WILD-TYPE 91 140 103

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 8.78e-05 (Fisher's exact test), Q value = 0.061

Table S44.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
20P GAIN MUTATED 57 107 53
20P GAIN WILD-TYPE 93 113 137

Figure S44.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 9.04e-08 (Fisher's exact test), Q value = 6.7e-05

Table S45.  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 S45.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 7.31e-09 (Fisher's exact test), Q value = 5.5e-06

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
20Q GAIN MUTATED 69 40 82
20Q GAIN WILD-TYPE 48 131 138

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 5.44e-06 (Fisher's exact test), Q value = 0.0039

Table S47.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
20Q GAIN MUTATED 84 45 81
20Q GAIN WILD-TYPE 93 139 104

Figure S47.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.13

Table S48.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
20Q GAIN MUTATED 55 106 54
20Q GAIN WILD-TYPE 95 114 136

Figure S48.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.000228 (Fisher's exact test), Q value = 0.16

Table S49.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
21Q GAIN MUTATED 27 11 24
21Q GAIN WILD-TYPE 123 209 166

Figure S49.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'22q gain' versus 'MRNA_CNMF'

P value = 2.32e-06 (Fisher's exact test), Q value = 0.0017

Table S50.  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 S50.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.15

Table S51.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
22Q GAIN MUTATED 0 18 13
22Q GAIN WILD-TYPE 117 153 207

Figure S51.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 6.39e-05 (Fisher's exact test), Q value = 0.045

Table S52.  Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
22Q GAIN MUTATED 18 3 13
22Q GAIN WILD-TYPE 132 217 177

Figure S52.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.022

Table S53.  Gene #43: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
2P LOSS MUTATED 17 2 11
2P LOSS WILD-TYPE 133 218 179

Figure S53.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.022

Table S54.  Gene #44: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
2Q LOSS MUTATED 17 2 11
2Q LOSS WILD-TYPE 133 218 179

Figure S54.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.22

Table S55.  Gene #45: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
3P LOSS MUTATED 19 5 15
3P LOSS WILD-TYPE 131 215 175

Figure S55.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 5.79e-06 (Fisher's exact test), Q value = 0.0042

Table S56.  Gene #46: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
3Q LOSS MUTATED 19 2 12
3Q LOSS WILD-TYPE 131 218 178

Figure S56.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'MRNA_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.013

Table S57.  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 S57.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CNMF'

P value = 3.87e-05 (Fisher's exact test), Q value = 0.027

Table S58.  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 S58.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 3.48e-13 (Fisher's exact test), Q value = 2.7e-10

Table S59.  Gene #51: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
6P LOSS MUTATED 51 11 22
6P LOSS WILD-TYPE 99 209 168

Figure S59.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1.78e-10 (Fisher's exact test), Q value = 1.3e-07

Table S60.  Gene #52: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
6Q LOSS MUTATED 62 27 32
6Q LOSS WILD-TYPE 88 193 158

Figure S60.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'MRNA_CNMF'

P value = 6.19e-08 (Fisher's exact test), Q value = 4.6e-05

Table S61.  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 S61.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.86e-05 (Fisher's exact test), Q value = 0.02

Table S62.  Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
10P LOSS MUTATED 108 124 188
10P LOSS WILD-TYPE 9 47 32

Figure S62.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0013

Table S63.  Gene #59: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
10P LOSS MUTATED 157 132 167
10P LOSS WILD-TYPE 20 52 18

Figure S63.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 4.86e-21 (Fisher's exact test), Q value = 3.7e-18

Table S64.  Gene #59: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
10P LOSS MUTATED 137 212 118
10P LOSS WILD-TYPE 13 8 72

Figure S64.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 4.48e-08 (Fisher's exact test), Q value = 3.4e-05

Table S65.  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 68 145 87
10Q LOSS WILD-TYPE 15 28 7 26

Figure S65.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00094

Table S66.  Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
10Q LOSS MUTATED 113 129 190
10Q LOSS WILD-TYPE 4 42 30

Figure S66.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 8.68e-05 (Fisher's exact test), Q value = 0.06

Table S67.  Gene #60: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 184 185
10Q LOSS MUTATED 160 140 167
10Q LOSS WILD-TYPE 17 44 18

Figure S67.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 3.79e-23 (Fisher's exact test), Q value = 2.9e-20

Table S68.  Gene #60: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
10Q LOSS MUTATED 138 217 123
10Q LOSS WILD-TYPE 12 3 67

Figure S68.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.14

Table S69.  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 49 42 44 41
10Q LOSS WILD-TYPE 5 16 0 4

Figure S69.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'11p loss' versus 'MRNA_CNMF'

P value = 5.43e-07 (Fisher's exact test), Q value = 4e-04

Table S70.  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 21
11P LOSS WILD-TYPE 120 64 143 92

Figure S70.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.97e-05 (Fisher's exact test), Q value = 0.042

Table S71.  Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
11P LOSS MUTATED 8 45 36
11P LOSS WILD-TYPE 109 126 184

Figure S71.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 4.38e-15 (Fisher's exact test), Q value = 3.4e-12

Table S72.  Gene #61: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
11P LOSS MUTATED 54 9 33
11P LOSS WILD-TYPE 96 211 157

Figure S72.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.0094

Table S73.  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 16
11Q LOSS WILD-TYPE 116 68 142 97

Figure S73.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.1e-14 (Fisher's exact test), Q value = 2.4e-11

Table S74.  Gene #62: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
11Q LOSS MUTATED 54 11 25
11Q LOSS WILD-TYPE 96 209 165

Figure S74.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.02

Table S75.  Gene #64: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
12Q LOSS MUTATED 28 9 20
12Q LOSS WILD-TYPE 122 211 170

Figure S75.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.017

Table S76.  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 S76.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.13

Table S77.  Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
13Q LOSS MUTATED 20 65 78
13Q LOSS WILD-TYPE 97 106 142

Figure S77.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1.42e-21 (Fisher's exact test), Q value = 1.1e-18

Table S78.  Gene #65: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
13Q LOSS MUTATED 90 27 65
13Q LOSS WILD-TYPE 60 193 125

Figure S78.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.0012

Table S79.  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 33 17 39
14Q LOSS WILD-TYPE 101 63 135 74

Figure S79.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1.26e-29 (Fisher's exact test), Q value = 9.8e-27

Table S80.  Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
14Q LOSS MUTATED 83 9 49
14Q LOSS WILD-TYPE 67 211 141

Figure S80.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MRNA_CNMF'

P value = 3.38e-05 (Fisher's exact test), Q value = 0.024

Table S81.  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 S81.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.29e-06 (Fisher's exact test), Q value = 0.0031

Table S82.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 171 220
15Q LOSS MUTATED 8 50 37
15Q LOSS WILD-TYPE 109 121 183

Figure S82.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2.47e-08 (Fisher's exact test), Q value = 1.8e-05

Table S83.  Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
15Q LOSS MUTATED 50 20 29
15Q LOSS WILD-TYPE 100 200 161

Figure S83.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.012

Table S84.  Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 41 33
15Q LOSS MUTATED 1 1 12
15Q LOSS WILD-TYPE 34 40 21

Figure S84.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1.19e-09 (Fisher's exact test), Q value = 9e-07

Table S85.  Gene #70: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
17P LOSS MUTATED 34 5 24
17P LOSS WILD-TYPE 116 215 166

Figure S85.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.0035

Table S86.  Gene #71: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
17Q LOSS MUTATED 23 4 15
17Q LOSS WILD-TYPE 127 216 175

Figure S86.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.13

Table S87.  Gene #72: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
18P LOSS MUTATED 30 13 25
18P LOSS WILD-TYPE 120 207 165

Figure S87.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.15

Table S88.  Gene #75: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
19Q LOSS MUTATED 13 3 18
19Q LOSS WILD-TYPE 137 217 172

Figure S88.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

'20p loss' versus 'MRNA_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.15

Table S89.  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 S89.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 9.12e-06 (Fisher's exact test), Q value = 0.0066

Table S90.  Gene #76: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
20P LOSS MUTATED 13 0 5
20P LOSS WILD-TYPE 137 220 185

Figure S90.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0098

Table S91.  Gene #77: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
20Q LOSS MUTATED 13 1 2
20Q LOSS WILD-TYPE 137 219 188

Figure S91.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 9.66e-05 (Fisher's exact test), Q value = 0.067

Table S92.  Gene #78: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
21Q LOSS MUTATED 22 6 12
21Q LOSS WILD-TYPE 128 214 178

Figure S92.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #5: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.012

Table S93.  Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
22Q LOSS MUTATED 68 49 56
22Q LOSS WILD-TYPE 82 171 134

Figure S93.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 4.42e-08 (Fisher's exact test), Q value = 3.3e-05

Table S94.  Gene #80: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 220 190
XQ LOSS MUTATED 52 28 22
XQ LOSS WILD-TYPE 98 192 168

Figure S94.  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 = 560

  • 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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