Correlation between copy number variations of arm-level result and molecular subtypes
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 577 patients, 113 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'.

  • 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_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_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' and 'METHLYATION_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',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

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

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

  • 4q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 19p loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 20q loss cnv correlated to 'MRNA_CHIERARCHICAL' and '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, 113 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 468 (81%) 109 1e-05
(0.00784) 		1e-05
(0.00784) 		0.00029
(0.196) 		1e-05
(0.00784) 		1e-05
(0.00784) 		1e-05
(0.00784) 		0.00189
(1.00) 		0.00285
(1.00) 		0.0153
(1.00) 		7e-05
(0.0486)
19p gain 226 (39%) 351 1e-05
(0.00784) 		2e-05
(0.0144) 		0.0904
(1.00) 		0.0003
(0.202) 		1e-05
(0.00784) 		1e-05
(0.00784) 		0.00916
(1.00) 		1e-05
(0.00784) 		0.188
(1.00) 		0.655
(1.00)
10q loss 494 (86%) 83 1e-05
(0.00784) 		1e-05
(0.00784) 		0.00612
(1.00) 		0.00011
(0.0756) 		1e-05
(0.00784) 		5e-05
(0.0351) 		7e-05
(0.0486) 		0.00429
(1.00) 		0.26
(1.00) 		0.0218
(1.00)
7q gain 474 (82%) 103 2e-05
(0.0144) 		1e-05
(0.00784) 		0.00146
(0.936) 		0.00017
(0.115) 		1e-05
(0.00784) 		4e-05
(0.0282) 		0.105
(1.00) 		0.0447
(1.00) 		0.0545
(1.00) 		0.00143
(0.919)
20p gain 222 (38%) 355 1e-05
(0.00784) 		1e-05
(0.00784) 		0.00432
(1.00) 		1e-05
(0.00784) 		2e-05
(0.0144) 		9e-05
(0.0619) 		0.0539
(1.00) 		0.00185
(1.00) 		0.794
(1.00) 		0.118
(1.00)
20q gain 220 (38%) 357 1e-05
(0.00784) 		1e-05
(0.00784) 		0.0032
(1.00) 		1e-05
(0.00784) 		1e-05
(0.00784) 		7e-05
(0.0486) 		0.0343
(1.00) 		0.0009
(0.59) 		0.795
(1.00) 		0.119
(1.00)
10p loss 483 (84%) 94 1e-05
(0.00784) 		1e-05
(0.00784) 		0.0104
(1.00) 		7e-05
(0.0486) 		1e-05
(0.00784) 		1e-05
(0.00784) 		0.00232
(1.00) 		0.0274
(1.00) 		0.223
(1.00) 		0.0128
(1.00)
19q gain 199 (34%) 378 1e-05
(0.00784) 		1e-05
(0.00784) 		0.143
(1.00) 		0.0033
(1.00) 		1e-05
(0.00784) 		1e-05
(0.00784) 		0.0461
(1.00) 		0.001
(0.651) 		0.0629
(1.00) 		0.343
(1.00)
5p loss 43 (7%) 534 3e-05
(0.0213) 		2e-05
(0.0144) 		0.00193
(1.00) 		0.0967
(1.00) 		6e-05
(0.0419) 		3e-05
(0.0213) 		0.94
(1.00) 		0.546
(1.00) 		0.343
(1.00) 		0.0516
(1.00)
5q loss 44 (8%) 533 4e-05
(0.0282) 		4e-05
(0.0282) 		0.00086
(0.565) 		0.188
(1.00) 		5e-05
(0.0351) 		1e-05
(0.00784) 		0.943
(1.00) 		0.625
(1.00) 		0.223
(1.00) 		0.043
(1.00)
8q gain 59 (10%) 518 1e-05
(0.00784) 		1e-05
(0.00784) 		0.0402
(1.00) 		0.455
(1.00) 		1e-05
(0.00784) 		0.00048
(0.322) 		0.434
(1.00) 		0.758
(1.00) 		0.123
(1.00) 		0.511
(1.00)
11p loss 99 (17%) 478 1e-05
(0.00784) 		1e-05
(0.00784) 		0.831
(1.00) 		0.014
(1.00) 		1e-05
(0.00784) 		0.00283
(1.00) 		0.729
(1.00) 		0.159
(1.00) 		0.093
(1.00) 		0.0867
(1.00)
11q loss 93 (16%) 484 2e-05
(0.0144) 		0.00014
(0.0953) 		0.934
(1.00) 		0.0602
(1.00) 		1e-05
(0.00784) 		0.416
(1.00) 		0.936
(1.00) 		0.568
(1.00) 		0.343
(1.00) 		0.536
(1.00)
14q loss 146 (25%) 431 1e-05
(0.00784) 		0.00016
(0.109) 		0.512
(1.00) 		0.539
(1.00) 		1e-05
(0.00784) 		0.0248
(1.00) 		0.813
(1.00) 		0.0922
(1.00) 		0.166
(1.00) 		0.701
(1.00)
15q loss 106 (18%) 471 2e-05
(0.0144) 		1e-05
(0.00784) 		0.00385
(1.00) 		0.00382
(1.00) 		1e-05
(0.00784) 		0.0755
(1.00) 		0.0321
(1.00) 		0.0115
(1.00) 		0.00356
(1.00) 		0.0234
(1.00)
20p loss 19 (3%) 558 0.00013
(0.0888) 		5e-05
(0.0351) 		0.0366
(1.00) 		0.0937
(1.00) 		1e-05
(0.00784) 		0.308
(1.00) 		0.413
(1.00) 		0.456
(1.00) 		0.0104
(1.00) 		0.00206
(1.00)
8p gain 52 (9%) 525 2e-05
(0.0144) 		0.00065
(0.43) 		0.0637
(1.00) 		0.559
(1.00) 		1e-05
(0.00784) 		0.00409
(1.00) 		0.436
(1.00) 		0.755
(1.00) 		0.139
(1.00) 		0.676
(1.00)
10p gain 13 (2%) 564 0.00092
(0.603) 		0.00011
(0.0756) 		0.117
(1.00) 		0.0586
(1.00) 		0.00103
(0.669) 		0.00036
(0.242) 		0.308
(1.00) 		0.561
(1.00)
18p gain 58 (10%) 519 1e-05
(0.00784) 		0.00047
(0.315) 		0.157
(1.00) 		0.365
(1.00) 		1e-05
(0.00784) 		0.00485
(1.00) 		0.422
(1.00) 		0.149
(1.00) 		0.0183
(1.00) 		0.0964
(1.00)
18q gain 58 (10%) 519 1e-05
(0.00784) 		0.00072
(0.475) 		0.157
(1.00) 		0.431
(1.00) 		1e-05
(0.00784) 		0.00557
(1.00) 		0.692
(1.00) 		0.479
(1.00) 		0.0184
(1.00) 		0.114
(1.00)
22q gain 34 (6%) 543 2e-05
(0.0144) 		0.00329
(1.00) 		0.469
(1.00) 		0.218
(1.00) 		7e-05
(0.0486) 		0.143
(1.00) 		0.214
(1.00) 		0.0353
(1.00) 		0.246
(1.00) 		0.194
(1.00)
13q loss 186 (32%) 391 2e-05
(0.0144) 		0.00137
(0.884) 		0.751
(1.00) 		0.588
(1.00) 		1e-05
(0.00784) 		0.011
(1.00) 		0.594
(1.00) 		0.017
(1.00) 		0.0492
(1.00) 		0.4
(1.00)
20q loss 17 (3%) 560 0.00145
(0.931) 		0.00012
(0.0822) 		0.365
(1.00) 		0.266
(1.00) 		1e-05
(0.00784) 		0.309
(1.00) 		0.415
(1.00) 		0.459
(1.00) 		0.0395
(1.00) 		0.0117
(1.00)
1p gain 82 (14%) 495 0.603
(1.00) 		0.13
(1.00) 		0.487
(1.00) 		0.251
(1.00) 		1e-05
(0.00784) 		0.827
(1.00) 		0.501
(1.00) 		0.0845
(1.00) 		0.34
(1.00) 		0.273
(1.00)
1q gain 89 (15%) 488 0.0781
(1.00) 		0.0887
(1.00) 		0.132
(1.00) 		0.628
(1.00) 		1e-05
(0.00784) 		0.528
(1.00) 		0.582
(1.00) 		0.258
(1.00) 		0.826
(1.00) 		0.506
(1.00)
3p gain 58 (10%) 519 0.00063
(0.418) 		0.0289
(1.00) 		0.668
(1.00) 		0.0267
(1.00) 		1e-05
(0.00784) 		0.13
(1.00) 		0.637
(1.00) 		0.342
(1.00) 		0.815
(1.00) 		0.255
(1.00)
3q gain 64 (11%) 513 0.00062
(0.412) 		0.0618
(1.00) 		0.899
(1.00) 		0.064
(1.00) 		1e-05
(0.00784) 		0.0658
(1.00) 		0.714
(1.00) 		0.203
(1.00) 		0.516
(1.00) 		0.15
(1.00)
5p gain 49 (8%) 528 0.114
(1.00) 		0.157
(1.00) 		0.178
(1.00) 		0.345
(1.00) 		5e-05
(0.0351) 		0.233
(1.00) 		0.28
(1.00) 		0.531
(1.00) 		0.128
(1.00) 		0.227
(1.00)
5q gain 41 (7%) 536 0.141
(1.00) 		0.234
(1.00) 		0.116
(1.00) 		0.0549
(1.00) 		0.00014
(0.0953) 		0.117
(1.00) 		0.39
(1.00) 		0.296
(1.00) 		0.169
(1.00) 		0.405
(1.00)
9p gain 47 (8%) 530 0.00359
(1.00) 		0.0313
(1.00) 		0.702
(1.00) 		0.432
(1.00) 		2e-05
(0.0144) 		0.545
(1.00) 		0.8
(1.00) 		0.367
(1.00) 		0.429
(1.00) 		0.113
(1.00)
9q gain 71 (12%) 506 0.0802
(1.00) 		0.0709
(1.00) 		0.578
(1.00) 		0.167
(1.00) 		3e-05
(0.0213) 		0.198
(1.00) 		0.318
(1.00) 		0.387
(1.00) 		0.67
(1.00) 		0.0774
(1.00)
12p gain 60 (10%) 517 0.67
(1.00) 		0.793
(1.00) 		0.641
(1.00) 		0.164
(1.00) 		8e-05
(0.0551) 		0.9
(1.00) 		0.236
(1.00) 		0.662
(1.00) 		0.00392
(1.00) 		0.0752
(1.00)
15q gain 24 (4%) 553 0.0609
(1.00) 		0.108
(1.00) 		0.566
(1.00) 		0.133
(1.00) 		6e-05
(0.0419) 		0.279
(1.00) 		0.534
(1.00) 		0.339
(1.00) 		0.0343
(1.00) 		0.387
(1.00)
16p gain 38 (7%) 539 0.00826
(1.00) 		0.0659
(1.00) 		0.412
(1.00) 		0.273
(1.00) 		1e-05
(0.00784) 		0.0312
(1.00) 		0.612
(1.00) 		0.474
(1.00) 		1
(1.00) 		1
(1.00)
16q gain 37 (6%) 540 0.0182
(1.00) 		0.00581
(1.00) 		0.358
(1.00) 		0.0664
(1.00) 		6e-05
(0.0419) 		0.026
(1.00) 		0.758
(1.00) 		0.418
(1.00) 		0.419
(1.00) 		0.736
(1.00)
17p gain 48 (8%) 529 0.00048
(0.322) 		0.0204
(1.00) 		0.0783
(1.00) 		0.04
(1.00) 		5e-05
(0.0351) 		0.0327
(1.00) 		0.149
(1.00) 		0.238
(1.00) 		0.336
(1.00) 		0.39
(1.00)
17q gain 60 (10%) 517 0.00112
(0.726) 		0.0451
(1.00) 		0.129
(1.00) 		0.0703
(1.00) 		1e-05
(0.00784) 		0.0379
(1.00) 		0.088
(1.00) 		0.108
(1.00) 		0.945
(1.00) 		0.615
(1.00)
21q gain 64 (11%) 513 0.00121
(0.783) 		0.00736
(1.00) 		0.0108
(1.00) 		0.00422
(1.00) 		0.00019
(0.129) 		0.00182
(1.00) 		0.315
(1.00) 		0.0261
(1.00) 		0.0178
(1.00) 		0.334
(1.00)
2p loss 32 (6%) 545 0.0307
(1.00) 		0.0282
(1.00) 		0.263
(1.00) 		0.771
(1.00) 		1e-05
(0.00784) 		0.618
(1.00) 		1
(1.00) 		0.428
(1.00) 		0.244
(1.00) 		0.226
(1.00)
2q loss 32 (6%) 545 0.0298
(1.00) 		0.0284
(1.00) 		0.262
(1.00) 		0.77
(1.00) 		1e-05
(0.00784) 		0.616
(1.00) 		0.896
(1.00) 		0.249
(1.00) 		0.0823
(1.00) 		0.0733
(1.00)
3p loss 40 (7%) 537 0.91
(1.00) 		0.788
(1.00) 		0.718
(1.00) 		0.151
(1.00) 		6e-05
(0.0419) 		0.202
(1.00) 		0.236
(1.00) 		0.901
(1.00) 		0.638
(1.00) 		0.231
(1.00)
3q loss 34 (6%) 543 0.229
(1.00) 		0.129
(1.00) 		0.514
(1.00) 		0.678
(1.00) 		1e-05
(0.00784) 		0.0344
(1.00) 		0.785
(1.00) 		0.321
(1.00) 		0.888
(1.00) 		0.18
(1.00)
4q loss 56 (10%) 521 0.00098
(0.639) 		0.00058
(0.386) 		0.0189
(1.00) 		0.154
(1.00) 		0.00019
(0.129) 		0.00092
(0.603) 		0.732
(1.00) 		0.479
(1.00) 		0.561
(1.00) 		1
(1.00)
6p loss 86 (15%) 491 0.569
(1.00) 		0.332
(1.00) 		0.773
(1.00) 		0.706
(1.00) 		1e-05
(0.00784) 		0.572
(1.00) 		0.795
(1.00) 		0.3
(1.00) 		0.869
(1.00) 		0.595
(1.00)
6q loss 125 (22%) 452 0.939
(1.00) 		0.579
(1.00) 		0.563
(1.00) 		0.941
(1.00) 		1e-05
(0.00784) 		0.653
(1.00) 		0.969
(1.00) 		0.647
(1.00) 		0.495
(1.00) 		0.293
(1.00)
12q loss 57 (10%) 520 0.14
(1.00) 		0.0983
(1.00) 		0.444
(1.00) 		0.653
(1.00) 		0.0003
(0.202) 		0.553
(1.00) 		0.182
(1.00) 		0.391
(1.00) 		1
(1.00) 		0.663
(1.00)
17p loss 65 (11%) 512 0.0194
(1.00) 		0.0202
(1.00) 		0.65
(1.00) 		0.581
(1.00) 		1e-05
(0.00784) 		0.129
(1.00) 		0.214
(1.00) 		0.351
(1.00) 		0.3
(1.00) 		0.704
(1.00)
17q loss 41 (7%) 536 0.00504
(1.00) 		0.0602
(1.00) 		0.212
(1.00) 		0.0472
(1.00) 		1e-05
(0.00784) 		0.0363
(1.00) 		0.687
(1.00) 		0.48
(1.00) 		0.147
(1.00) 		0.107
(1.00)
18p loss 71 (12%) 506 0.0473
(1.00) 		0.0318
(1.00) 		0.361
(1.00) 		0.221
(1.00) 		1e-05
(0.00784) 		0.506
(1.00) 		0.0637
(1.00) 		0.0059
(1.00) 		0.134
(1.00) 		0.597
(1.00)
18q loss 62 (11%) 515 0.147
(1.00) 		0.00732
(1.00) 		0.62
(1.00) 		0.239
(1.00) 		0.00013
(0.0888) 		0.479
(1.00) 		0.00916
(1.00) 		0.00351
(1.00) 		0.418
(1.00) 		0.12
(1.00)
19p loss 27 (5%) 550 0.00062
(0.412) 		0.00092
(0.603) 		0.0584
(1.00) 		0.435
(1.00) 		0.0134
(1.00) 		0.00012
(0.0822) 		0.0198
(1.00) 		0.0108
(1.00) 		0.853
(1.00) 		0.668
(1.00)
22q loss 181 (31%) 396 0.651
(1.00) 		0.562
(1.00) 		0.198
(1.00) 		0.875
(1.00) 		1e-05
(0.00784) 		0.0736
(1.00) 		0.909
(1.00) 		0.135
(1.00) 		0.202
(1.00) 		0.0925
(1.00)
xq loss 106 (18%) 471 0.0189
(1.00) 		0.0157
(1.00) 		0.112
(1.00) 		0.106
(1.00) 		1e-05
(0.00784) 		0.00587
(1.00) 		0.903
(1.00) 		0.683
(1.00) 		0.414
(1.00) 		0.961
(1.00)
2p gain 37 (6%) 540 0.467
(1.00) 		0.734
(1.00) 		0.252
(1.00) 		0.225
(1.00) 		0.0024
(1.00) 		0.392
(1.00) 		0.808
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.54
(1.00)
2q gain 36 (6%) 541 0.649
(1.00) 		0.912
(1.00) 		0.0981
(1.00) 		0.278
(1.00) 		0.00154
(0.986) 		0.39
(1.00) 		0.985
(1.00) 		0.611
(1.00) 		0.766
(1.00) 		0.179
(1.00)
4p gain 36 (6%) 541 0.241
(1.00) 		0.615
(1.00) 		0.486
(1.00) 		0.521
(1.00) 		0.00066
(0.436) 		0.458
(1.00) 		0.757
(1.00) 		0.55
(1.00) 		0.614
(1.00) 		0.792
(1.00)
4q gain 33 (6%) 544 0.309
(1.00) 		0.318
(1.00) 		0.496
(1.00) 		0.541
(1.00) 		0.00552
(1.00) 		0.266
(1.00) 		0.926
(1.00) 		0.684
(1.00) 		0.364
(1.00) 		0.657
(1.00)
6p gain 24 (4%) 553 0.0121
(1.00) 		0.117
(1.00) 		0.875
(1.00) 		0.162
(1.00) 		0.158
(1.00) 		0.0824
(1.00) 		0.811
(1.00) 		0.583
(1.00) 		1
(1.00) 		1
(1.00)
6q gain 23 (4%) 554 0.00141
(0.908) 		0.0362
(1.00) 		0.787
(1.00) 		0.104
(1.00) 		0.0249
(1.00) 		0.00575
(1.00) 		0.931
(1.00) 		0.529
(1.00) 		0.813
(1.00) 		1
(1.00)
10q gain 3 (1%) 574 0.555
(1.00) 		1
(1.00) 		0.0528
(1.00) 		0.794
(1.00) 		0.196
(1.00) 		0.19
(1.00)
11p gain 17 (3%) 560 0.906
(1.00) 		0.881
(1.00) 		0.247
(1.00) 		0.945
(1.00) 		0.197
(1.00) 		0.0857
(1.00) 		0.868
(1.00) 		0.529
(1.00) 		0.697
(1.00) 		1
(1.00)
11q gain 14 (2%) 563 0.187
(1.00) 		0.0647
(1.00) 		0.216
(1.00) 		0.36
(1.00) 		0.15
(1.00) 		0.00057
(0.38) 		0.868
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12q gain 49 (8%) 528 0.517
(1.00) 		0.955
(1.00) 		0.538
(1.00) 		0.00986
(1.00) 		0.0016
(1.00) 		0.591
(1.00) 		0.312
(1.00) 		0.3
(1.00) 		0.0221
(1.00) 		0.124
(1.00)
13q gain 10 (2%) 567 0.0531
(1.00) 		0.494
(1.00) 		0.179
(1.00) 		0.826
(1.00) 		0.0568
(1.00) 		1
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.426
(1.00) 		1
(1.00)
14q gain 22 (4%) 555 0.429
(1.00) 		0.782
(1.00) 		0.0103
(1.00) 		0.806
(1.00) 		0.39
(1.00) 		0.508
(1.00) 		0.473
(1.00) 		0.857
(1.00) 		0.425
(1.00) 		0.326
(1.00)
xq gain 16 (3%) 561 0.255
(1.00) 		0.947
(1.00) 		0.985
(1.00) 		0.362
(1.00) 		0.952
(1.00) 		0.718
(1.00) 		0.79
(1.00) 		1
(1.00) 		0.0398
(1.00) 		0.263
(1.00)
1p loss 16 (3%) 561 0.636
(1.00) 		0.827
(1.00) 		0.941
(1.00) 		0.198
(1.00) 		0.0218
(1.00) 		0.582
(1.00) 		0.339
(1.00) 		0.181
(1.00) 		0.111
(1.00) 		0.018
(1.00)
1q loss 15 (3%) 562 0.831
(1.00) 		0.978
(1.00) 		0.857
(1.00) 		0.363
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.339
(1.00) 		0.208
(1.00) 		0.515
(1.00) 		0.0839
(1.00)
4p loss 55 (10%) 522 0.0796
(1.00) 		0.00323
(1.00) 		0.0329
(1.00) 		0.226
(1.00) 		0.00274
(1.00) 		0.00199
(1.00) 		0.294
(1.00) 		0.122
(1.00) 		0.744
(1.00) 		1
(1.00)
7p loss 8 (1%) 569 0.0223
(1.00) 		0.0344
(1.00) 		0.458
(1.00) 		0.0422
(1.00) 		0.0158
(1.00)
7q loss 6 (1%) 571 0.101
(1.00) 		0.299
(1.00) 		0.942
(1.00) 		0.125
(1.00) 		0.0987
(1.00)
8p loss 58 (10%) 519 0.544
(1.00) 		0.441
(1.00) 		0.181
(1.00) 		0.78
(1.00) 		0.261
(1.00) 		0.65
(1.00) 		0.906
(1.00) 		0.95
(1.00) 		0.575
(1.00) 		0.392
(1.00)
8q loss 42 (7%) 535 0.621
(1.00) 		0.152
(1.00) 		0.0224
(1.00) 		0.808
(1.00) 		0.103
(1.00) 		0.137
(1.00) 		0.858
(1.00) 		0.655
(1.00) 		0.461
(1.00) 		0.146
(1.00)
9p loss 202 (35%) 375 0.0074
(1.00) 		0.108
(1.00) 		0.551
(1.00) 		0.484
(1.00) 		0.599
(1.00) 		0.48
(1.00) 		0.621
(1.00) 		0.0468
(1.00) 		0.0222
(1.00) 		0.00873
(1.00)
9q loss 94 (16%) 483 0.37
(1.00) 		0.0985
(1.00) 		0.0731
(1.00) 		0.276
(1.00) 		0.548
(1.00) 		0.574
(1.00) 		0.362
(1.00) 		0.117
(1.00) 		0.751
(1.00) 		0.181
(1.00)
12p loss 58 (10%) 519 0.0961
(1.00) 		0.0954
(1.00) 		0.559
(1.00) 		0.832
(1.00) 		0.00616
(1.00) 		0.599
(1.00) 		0.154
(1.00) 		0.0581
(1.00) 		1
(1.00) 		0.662
(1.00)
16p loss 63 (11%) 514 0.287
(1.00) 		0.852
(1.00) 		0.661
(1.00) 		0.735
(1.00) 		0.0343
(1.00) 		0.0593
(1.00) 		0.451
(1.00) 		0.19
(1.00) 		0.565
(1.00) 		0.649
(1.00)
16q loss 83 (14%) 494 0.0603
(1.00) 		0.428
(1.00) 		0.467
(1.00) 		0.898
(1.00) 		0.0128
(1.00) 		0.367
(1.00) 		0.0489
(1.00) 		0.0183
(1.00) 		0.662
(1.00) 		0.6
(1.00)
19q loss 35 (6%) 542 0.00056
(0.374) 		0.00497
(1.00) 		0.413
(1.00) 		0.152
(1.00) 		0.00106
(0.688) 		0.00079
(0.521) 		0.0801
(1.00) 		0.337
(1.00) 		0.93
(1.00) 		0.513
(1.00)
21q loss 42 (7%) 535 0.0215
(1.00) 		0.00134
(0.866) 		0.0531
(1.00) 		0.263
(1.00) 		0.0008
(0.526) 		0.00177
(1.00) 		0.0121
(1.00) 		0.0837
(1.00) 		0.827
(1.00) 		1
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
1P GAIN MUTATED 50 15 17
1P GAIN WILD-TYPE 112 203 180

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 = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
1Q GAIN MUTATED 57 13 19
1Q GAIN WILD-TYPE 105 205 178

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

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3P GAIN MUTATED 37 5 16
3P GAIN WILD-TYPE 125 213 181

Figure S3.  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 = 0.0078

Table S4.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3Q GAIN MUTATED 38 7 19
3Q GAIN WILD-TYPE 124 211 178

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

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

Table S5.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5P GAIN MUTATED 27 7 15
5P GAIN WILD-TYPE 135 211 182

Figure S5.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.095

Table S6.  Gene #10: '5q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5Q GAIN MUTATED 23 6 12
5Q GAIN WILD-TYPE 139 212 185

Figure S6.  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 = 0.0078

Table S7.  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 S7.  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 = 0.0078

Table S8.  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 S8.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'MIR_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.2

Table S9.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
7P GAIN MUTATED 139 136 64 105
7P GAIN WILD-TYPE 17 47 23 15

Figure S9.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S10.  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 S10.  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 = 0.0078

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
7P GAIN MUTATED 145 196 127
7P GAIN WILD-TYPE 17 22 70

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
7P GAIN MUTATED 82 93 46
7P GAIN WILD-TYPE 7 15 32

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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 = 0.0078

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 = 0.00017 (Fisher's exact test), Q value = 0.12

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 = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
7Q GAIN MUTATED 141 199 134
7Q GAIN WILD-TYPE 21 19 63

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

'7q gain' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
7Q GAIN MUTATED 81 91 50
7Q GAIN WILD-TYPE 8 17 28

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

'8p gain' versus 'MRNA_CNMF'

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

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 = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
8P GAIN MUTATED 35 4 13
8P GAIN WILD-TYPE 127 214 184

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 = 0.0078

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 = 1e-05 (Fisher's exact test), Q value = 0.0078

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 = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
8Q GAIN MUTATED 34 6 19
8Q GAIN WILD-TYPE 128 212 178

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

'9p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
9P GAIN MUTATED 27 7 13
9P GAIN WILD-TYPE 135 211 184

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

'9q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
9Q GAIN MUTATED 36 14 21
9Q GAIN WILD-TYPE 126 204 176

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

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

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'

'10p gain' versus 'METHLYATION_CNMF'

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

Table S27.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
10P GAIN MUTATED 1 0 7
10P GAIN WILD-TYPE 88 108 71

Figure S27.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.055

Table S28.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
12P GAIN MUTATED 31 11 18
12P GAIN WILD-TYPE 131 207 179

Figure S28.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S29.  Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
15Q GAIN MUTATED 15 1 8
15Q GAIN WILD-TYPE 147 217 189

Figure S29.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S30.  Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
16P GAIN MUTATED 25 4 9
16P GAIN WILD-TYPE 137 214 188

Figure S30.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S31.  Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
16Q GAIN MUTATED 22 5 10
16Q GAIN WILD-TYPE 140 213 187

Figure S31.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17P GAIN MUTATED 27 9 12
17P GAIN WILD-TYPE 135 209 185

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 = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17Q GAIN MUTATED 34 12 14
17Q GAIN WILD-TYPE 128 206 183

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 = 0.0078

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 = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18P GAIN MUTATED 34 3 21
18P GAIN WILD-TYPE 128 215 176

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 = 0.0078

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 = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18Q GAIN MUTATED 37 4 17
18Q GAIN WILD-TYPE 125 214 180

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 = 0.0078

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 34 91 21
19P GAIN WILD-TYPE 95 62 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 = 2e-05 (Fisher's exact test), Q value = 0.014

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 25 58 53
19P GAIN WILD-TYPE 86 77 42 105

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

'19p gain' versus 'MIR_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S40.  Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
19P GAIN MUTATED 94 50 68
19P GAIN WILD-TYPE 199 74 61

Figure S40.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S41.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
19P GAIN MUTATED 45 137 44
19P GAIN WILD-TYPE 117 81 153

Figure S41.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S42.  Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
19P GAIN MUTATED 28 68 12
19P GAIN WILD-TYPE 61 40 66

Figure S42.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S43.  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 S43.  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 = 0.0078

Table S44.  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 S44.  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 = 0.0078

Table S45.  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 46
19Q GAIN WILD-TYPE 93 84 45 112

Figure S45.  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 = 0.0078

Table S46.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
19Q GAIN MUTATED 39 127 33
19Q GAIN WILD-TYPE 123 91 164

Figure S46.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S47.  Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
19Q GAIN MUTATED 25 62 6
19Q GAIN WILD-TYPE 64 46 72

Figure S47.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S48.  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 S48.  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 = 0.0078

Table S49.  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 S49.  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 = 0.0078

Table S50.  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 S50.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

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

Table S51.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20P GAIN MUTATED 61 108 53
20P GAIN WILD-TYPE 101 110 144

Figure S51.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

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

Table S52.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
20P GAIN MUTATED 35 57 17
20P GAIN WILD-TYPE 54 51 61

Figure S52.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S53.  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 S53.  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 = 0.0078

Table S54.  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 S54.  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 = 0.0078

Table S55.  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 S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S56.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20Q GAIN MUTATED 59 107 54
20Q GAIN WILD-TYPE 103 111 143

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
20Q GAIN MUTATED 34 57 16
20Q GAIN WILD-TYPE 55 51 62

Figure S57.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S58.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
21Q GAIN MUTATED 30 11 23
21Q GAIN WILD-TYPE 132 207 174

Figure S58.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'22q gain' versus 'MRNA_CNMF'

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

Table S59.  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 S59.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'CN_CNMF'

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

Table S60.  Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
22Q GAIN MUTATED 19 3 12
22Q GAIN WILD-TYPE 143 215 185

Figure S60.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S61.  Gene #43: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
2P LOSS MUTATED 21 2 9
2P LOSS WILD-TYPE 141 216 188

Figure S61.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S62.  Gene #44: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
2Q LOSS MUTATED 21 2 9
2Q LOSS WILD-TYPE 141 216 188

Figure S62.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S63.  Gene #45: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3P LOSS MUTATED 21 4 15
3P LOSS WILD-TYPE 141 214 182

Figure S63.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S64.  Gene #46: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
3Q LOSS MUTATED 20 2 12
3Q LOSS WILD-TYPE 142 216 185

Figure S64.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S65.  Gene #48: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
4Q LOSS MUTATED 29 11 16
4Q LOSS WILD-TYPE 133 207 181

Figure S65.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'MRNA_CNMF'

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

Table S66.  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 S66.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S67.  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 S67.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S68.  Gene #49: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5P LOSS MUTATED 21 4 18
5P LOSS WILD-TYPE 141 214 179

Figure S68.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

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

Table S69.  Gene #49: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
5P LOSS MUTATED 1 5 15
5P LOSS WILD-TYPE 88 103 63

Figure S69.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNA_CNMF'

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

Table S70.  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 S70.  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 S71.  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 S71.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

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

Table S72.  Gene #50: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
5Q LOSS MUTATED 21 5 18
5Q LOSS WILD-TYPE 141 213 179

Figure S72.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S73.  Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
5Q LOSS MUTATED 0 5 17
5Q LOSS WILD-TYPE 89 103 61

Figure S73.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S74.  Gene #51: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
6P LOSS MUTATED 51 13 22
6P LOSS WILD-TYPE 111 205 175

Figure S74.  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 = 0.0078

Table S75.  Gene #52: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
6Q LOSS MUTATED 62 30 33
6Q LOSS WILD-TYPE 100 188 164

Figure S75.  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 = 0.0078

Table S76.  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 S76.  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 = 0.0078

Table S77.  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 S77.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CHIERARCHICAL'

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

Table S78.  Gene #59: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10P LOSS MUTATED 227 109 120
10P LOSS WILD-TYPE 66 15 9

Figure S78.  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 = 0.0078

Table S79.  Gene #59: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
10P LOSS MUTATED 150 212 121
10P LOSS WILD-TYPE 12 6 76

Figure S79.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S80.  Gene #59: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
10P LOSS MUTATED 79 99 46
10P LOSS WILD-TYPE 10 9 32

Figure S80.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S81.  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 S81.  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 = 0.0078

Table S82.  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 S82.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

Table S83.  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 S83.  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 = 0.0078

Table S84.  Gene #60: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
10Q LOSS MUTATED 150 214 130
10Q LOSS WILD-TYPE 12 4 67

Figure S84.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

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

Table S85.  Gene #60: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
10Q LOSS MUTATED 78 102 56
10Q LOSS WILD-TYPE 11 6 22

Figure S85.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

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

Table S86.  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 S86.  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 = 0.0078

Table S87.  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 S87.  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 = 0.0078

Table S88.  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 S88.  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 = 0.0078

Table S89.  Gene #61: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
11P LOSS MUTATED 59 8 32
11P LOSS WILD-TYPE 103 210 165

Figure S89.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'MRNA_CNMF'

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

Table S90.  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 S90.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.095

Table S91.  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 S91.  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 = 0.0078

Table S92.  Gene #62: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
11Q LOSS MUTATED 58 10 25
11Q LOSS WILD-TYPE 104 208 172

Figure S92.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S93.  Gene #64: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
12Q LOSS MUTATED 28 10 19
12Q LOSS WILD-TYPE 134 208 178

Figure S93.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

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

Table S94.  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 S94.  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 = 0.0078

Table S95.  Gene #65: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
13Q LOSS MUTATED 112 20 54
13Q LOSS WILD-TYPE 50 198 143

Figure S95.  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 = 0.0078

Table S96.  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 S96.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S97.  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 35 10 47
14Q LOSS WILD-TYPE 105 67 90 111

Figure S97.  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 = 0.0078

Table S98.  Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
14Q LOSS MUTATED 82 12 52
14Q LOSS WILD-TYPE 80 206 145

Figure S98.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MRNA_CNMF'

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

Table S99.  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 S99.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S100.  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 S100.  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 = 0.0078

Table S101.  Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
15Q LOSS MUTATED 58 20 28
15Q LOSS WILD-TYPE 104 198 169

Figure S101.  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 = 0.0078

Table S102.  Gene #70: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17P LOSS MUTATED 37 5 23
17P LOSS WILD-TYPE 125 213 174

Figure S102.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S103.  Gene #71: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
17Q LOSS MUTATED 24 4 13
17Q LOSS WILD-TYPE 138 214 184

Figure S103.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S104.  Gene #72: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18P LOSS MUTATED 34 12 25
18P LOSS WILD-TYPE 128 206 172

Figure S104.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S105.  Gene #73: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
18Q LOSS MUTATED 29 10 23
18Q LOSS WILD-TYPE 133 208 174

Figure S105.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.082

Table S106.  Gene #74: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
19P LOSS MUTATED 3 0 10
19P LOSS WILD-TYPE 86 108 68

Figure S106.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p loss' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S107.  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 S107.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S108.  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 S108.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S109.  Gene #76: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20P LOSS MUTATED 14 0 5
20P LOSS WILD-TYPE 148 218 192

Figure S109.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.082

Table S110.  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 S110.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S111.  Gene #77: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
20Q LOSS MUTATED 14 1 2
20Q LOSS WILD-TYPE 148 217 195

Figure S111.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0078

Table S112.  Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
22Q LOSS MUTATED 79 47 55
22Q LOSS WILD-TYPE 83 171 142

Figure S112.  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 = 0.0078

Table S113.  Gene #80: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
XQ LOSS MUTATED 56 25 25
XQ LOSS WILD-TYPE 106 193 172

Figure S113.  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 = 577

  • 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.

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)
Made with Nozzle