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 subtypes.

Summary

Testing the association between copy number variation 80 arm-level results and 12 molecular subtypes across 559 patients, 56 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 2q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • 12p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 18p gain cnv correlated to 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to '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'.

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

  • 9q loss cnv correlated to 'CN_CNMF'.

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

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

  • 22q loss cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 56 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Chi-square 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
12p gain 202 (36%) 357 7.56e-05
(0.0688) 		1.27e-05
(0.0117) 		0.306
(1.00) 		4.46e-05
(0.0407) 		3.02e-14
(2.88e-11) 		2.39e-09
(2.26e-06) 		0.268
(1.00) 		0.468
(1.00) 		2.75e-05
(0.0252) 		6.01e-05
(0.0549) 		0.166
(1.00) 		0.102
(1.00)
2p gain 125 (22%) 434 5.21e-09
(4.91e-06) 		1.03e-10
(9.72e-08) 		0.615
(1.00) 		1.31e-05
(0.0121) 		2.47e-11
(2.34e-08) 		1.05e-11
(1e-08) 		0.0199
(1.00) 		0.0518
(1.00) 		7.96e-05
(0.0724) 		0.00321
(1.00) 		0.537
(1.00) 		0.0647
(1.00)
20q gain 268 (48%) 291 1.94e-05
(0.0179) 		3.35e-13
(3.19e-10) 		0.585
(1.00) 		4.83e-07
(0.000452) 		1.71e-17
(1.64e-14) 		4.17e-17
(3.99e-14) 		0.671
(1.00) 		0.144
(1.00) 		0.00734
(1.00) 		0.00466
(1.00) 		0.221
(1.00) 		0.91
(1.00)
2q gain 99 (18%) 460 1.53e-06
(0.00142) 		6.48e-07
(0.000605) 		0.648
(1.00) 		0.00255
(1.00) 		1.8e-09
(1.7e-06) 		3.16e-07
(0.000296) 		0.0216
(1.00) 		0.401
(1.00) 		0.000767
(0.683) 		0.000787
(0.699) 		0.543
(1.00) 		0.0778
(1.00)
20p gain 231 (41%) 328 0.00184
(1.00) 		5.58e-07
(0.000522) 		0.218
(1.00) 		1.73e-06
(0.00161) 		2.92e-15
(2.79e-12) 		3.74e-13
(3.56e-10) 		0.515
(1.00) 		0.545
(1.00) 		0.0113
(1.00) 		0.00571
(1.00) 		0.327
(1.00) 		0.657
(1.00)
12q gain 116 (21%) 443 0.00126
(1.00) 		9.11e-06
(0.00842) 		0.566
(1.00) 		0.00196
(1.00) 		1.19e-13
(1.13e-10) 		1.53e-05
(0.0141) 		0.0402
(1.00) 		0.114
(1.00) 		0.00179
(1.00) 		0.000344
(0.309) 		0.0719
(1.00) 		0.0441
(1.00)
5q loss 169 (30%) 390 7.52e-05
(0.0685) 		2.22e-05
(0.0204) 		0.623
(1.00) 		0.000886
(0.785) 		0.000362
(0.325) 		2.81e-07
(0.000263) 		0.0106
(1.00) 		0.116
(1.00) 		0.000547
(0.489) 		0.0927
(1.00) 		0.568
(1.00) 		0.962
(1.00)
6p gain 122 (22%) 437 0.477
(1.00) 		0.0102
(1.00) 		0.875
(1.00) 		0.0159
(1.00) 		8.97e-07
(0.000835) 		9.36e-05
(0.0849) 		0.209
(1.00) 		0.351
(1.00) 		0.18
(1.00) 		0.309
(1.00) 		0.317
(1.00) 		0.211
(1.00)
6q gain 61 (11%) 498 0.829
(1.00) 		0.0168
(1.00) 		0.94
(1.00) 		0.0558
(1.00) 		0.000261
(0.235) 		2.59e-05
(0.0237) 		0.324
(1.00) 		0.634
(1.00) 		0.0143
(1.00) 		0.172
(1.00) 		1
(1.00) 		0.756
(1.00)
7p gain 122 (22%) 437 0.187
(1.00) 		0.136
(1.00) 		0.0569
(1.00) 		0.00888
(1.00) 		1.22e-09
(1.15e-06) 		6.83e-07
(0.000637) 		0.219
(1.00) 		0.307
(1.00) 		0.0472
(1.00) 		0.393
(1.00) 		0.943
(1.00) 		0.688
(1.00)
7q gain 147 (26%) 412 0.0951
(1.00) 		0.326
(1.00) 		0.394
(1.00) 		0.414
(1.00) 		2.06e-07
(0.000193) 		0.000178
(0.161) 		0.17
(1.00) 		0.0937
(1.00) 		0.146
(1.00) 		0.916
(1.00) 		0.283
(1.00) 		0.808
(1.00)
10p gain 133 (24%) 426 0.00729
(1.00) 		3.44e-05
(0.0315) 		0.727
(1.00) 		0.00826
(1.00) 		2.53e-09
(2.39e-06) 		0.00116
(1.00) 		0.475
(1.00) 		0.189
(1.00) 		0.00498
(1.00) 		0.246
(1.00) 		0.664
(1.00) 		1
(1.00)
13q loss 256 (46%) 303 0.12
(1.00) 		0.74
(1.00) 		0.907
(1.00) 		0.0687
(1.00) 		7.97e-05
(0.0724) 		1.47e-06
(0.00136) 		0.00538
(1.00) 		0.0201
(1.00) 		0.449
(1.00) 		0.576
(1.00) 		0.125
(1.00) 		0.968
(1.00)
15q loss 218 (39%) 341 0.00312
(1.00) 		0.00702
(1.00) 		0.000905
(0.799) 		0.00446
(1.00) 		1.2e-08
(1.13e-05) 		0.000127
(0.115) 		0.494
(1.00) 		0.927
(1.00) 		0.0339
(1.00) 		0.455
(1.00) 		0.0244
(1.00) 		0.51
(1.00)
22q loss 378 (68%) 181 0.00012
(0.109) 		1.8e-05
(0.0166) 		0.056
(1.00) 		0.0363
(1.00) 		0.00283
(1.00) 		0.013
(1.00) 		0.0192
(1.00) 		0.111
(1.00) 		0.0566
(1.00) 		0.262
(1.00) 		0.00429
(1.00) 		0.272
(1.00)
1q gain 154 (28%) 405 0.524
(1.00) 		0.478
(1.00) 		0.772
(1.00) 		0.577
(1.00) 		1.09e-06
(0.00101) 		0.177
(1.00) 		0.482
(1.00) 		0.439
(1.00) 		0.651
(1.00) 		0.969
(1.00) 		0.24
(1.00) 		0.027
(1.00)
3q gain 206 (37%) 353 0.905
(1.00) 		0.00129
(1.00) 		0.801
(1.00) 		0.327
(1.00) 		1.71e-08
(1.61e-05) 		0.00303
(1.00) 		0.594
(1.00) 		0.0979
(1.00) 		0.565
(1.00) 		0.343
(1.00) 		0.379
(1.00) 		0.322
(1.00)
5p gain 142 (25%) 417 0.604
(1.00) 		0.196
(1.00) 		0.629
(1.00) 		0.614
(1.00) 		2.33e-06
(0.00216) 		0.395
(1.00) 		0.144
(1.00) 		0.19
(1.00) 		0.505
(1.00) 		0.982
(1.00) 		0.013
(1.00) 		0.486
(1.00)
18p gain 73 (13%) 486 0.0047
(1.00) 		0.000695
(0.619) 		0.924
(1.00) 		0.156
(1.00) 		0.0011
(0.972) 		3.85e-05
(0.0352) 		0.0022
(1.00) 		0.0601
(1.00) 		0.154
(1.00) 		0.253
(1.00) 		0.261
(1.00) 		0.634
(1.00)
19p gain 99 (18%) 460 0.0174
(1.00) 		0.0145
(1.00) 		0.582
(1.00) 		0.178
(1.00) 		7.52e-09
(7.09e-06) 		0.00069
(0.616) 		0.0388
(1.00) 		0.0248
(1.00) 		0.645
(1.00) 		0.586
(1.00) 		0.632
(1.00) 		0.83
(1.00)
19q gain 91 (16%) 468 0.0226
(1.00) 		0.047
(1.00) 		0.624
(1.00) 		0.16
(1.00) 		7.97e-07
(0.000743) 		0.000585
(0.522) 		0.0527
(1.00) 		0.0436
(1.00) 		0.291
(1.00) 		0.789
(1.00) 		0.313
(1.00) 		0.623
(1.00)
21q gain 67 (12%) 492 0.666
(1.00) 		0.0322
(1.00) 		0.986
(1.00) 		0.906
(1.00) 		4.21e-06
(0.0039) 		0.000335
(0.302) 		0.249
(1.00) 		0.0632
(1.00) 		0.369
(1.00) 		0.519
(1.00) 		0.11
(1.00) 		0.742
(1.00)
9q loss 235 (42%) 324 0.00133
(1.00) 		0.000371
(0.333) 		0.142
(1.00) 		0.00651
(1.00) 		3.32e-15
(3.17e-12) 		0.00105
(0.922) 		0.559
(1.00) 		0.999
(1.00) 		0.013
(1.00) 		0.515
(1.00) 		0.119
(1.00) 		0.0522
(1.00)
1p gain 101 (18%) 458 0.0968
(1.00) 		0.447
(1.00) 		0.0931
(1.00) 		0.513
(1.00) 		0.0967
(1.00) 		0.932
(1.00) 		0.21
(1.00) 		0.23
(1.00) 		0.463
(1.00) 		0.329
(1.00) 		0.0731
(1.00) 		0.0121
(1.00)
3p gain 106 (19%) 453 0.407
(1.00) 		0.118
(1.00) 		0.102
(1.00) 		0.619
(1.00) 		0.0253
(1.00) 		0.865
(1.00) 		0.11
(1.00) 		0.244
(1.00) 		0.426
(1.00) 		0.897
(1.00) 		0.588
(1.00) 		0.379
(1.00)
4p gain 30 (5%) 529 0.888
(1.00) 		0.499
(1.00) 		0.0047
(1.00) 		0.688
(1.00) 		0.114
(1.00) 		0.0926
(1.00) 		0.0899
(1.00) 		0.362
(1.00) 		0.865
(1.00) 		0.626
(1.00) 		0.324
(1.00) 		0.00869
(1.00)
4q gain 17 (3%) 542 0.904
(1.00) 		0.904
(1.00) 		0.703
(1.00) 		0.788
(1.00) 		0.286
(1.00) 		0.0514
(1.00) 		0.0596
(1.00) 		0.271
(1.00) 		0.835
(1.00) 		0.302
(1.00) 		0.0336
(1.00) 		0.187
(1.00)
5q gain 32 (6%) 527 0.0365
(1.00) 		0.118
(1.00) 		0.499
(1.00) 		0.356
(1.00) 		0.783
(1.00) 		0.274
(1.00) 		0.124
(1.00) 		0.684
(1.00) 		0.299
(1.00) 		0.368
(1.00) 		0.00291
(1.00) 		0.447
(1.00)
8p gain 86 (15%) 473 0.355
(1.00) 		0.125
(1.00) 		0.977
(1.00) 		0.0131
(1.00) 		0.499
(1.00) 		0.923
(1.00) 		0.704
(1.00) 		0.201
(1.00) 		0.436
(1.00) 		0.379
(1.00) 		0.373
(1.00) 		0.336
(1.00)
8q gain 203 (36%) 356 0.119
(1.00) 		0.417
(1.00) 		0.17
(1.00) 		0.0883
(1.00) 		0.0147
(1.00) 		0.92
(1.00) 		0.54
(1.00) 		0.103
(1.00) 		0.00297
(1.00) 		0.411
(1.00) 		0.561
(1.00) 		0.928
(1.00)
9p gain 61 (11%) 498 0.0325
(1.00) 		0.505
(1.00) 		0.28
(1.00) 		0.319
(1.00) 		0.0486
(1.00) 		0.0224
(1.00) 		0.231
(1.00) 		0.293
(1.00) 		0.897
(1.00) 		0.748
(1.00) 		0.174
(1.00) 		0.674
(1.00)
9q gain 26 (5%) 533 0.397
(1.00) 		0.275
(1.00) 		0.104
(1.00) 		0.619
(1.00) 		0.104
(1.00) 		0.163
(1.00) 		0.664
(1.00) 		0.0635
(1.00) 		0.568
(1.00) 		0.851
(1.00) 		0.826
(1.00) 		0.849
(1.00)
10q gain 68 (12%) 491 0.0085
(1.00) 		0.00254
(1.00) 		0.945
(1.00) 		0.0328
(1.00) 		0.0497
(1.00) 		0.0338
(1.00) 		0.567
(1.00) 		0.339
(1.00) 		0.0468
(1.00) 		0.137
(1.00) 		0.612
(1.00) 		0.618
(1.00)
11p gain 41 (7%) 518 0.427
(1.00) 		0.543
(1.00) 		0.302
(1.00) 		0.397
(1.00) 		0.0888
(1.00) 		0.0153
(1.00) 		0.0377
(1.00) 		0.0174
(1.00) 		0.0753
(1.00) 		0.109
(1.00) 		0.162
(1.00) 		0.467
(1.00)
11q gain 60 (11%) 499 0.359
(1.00) 		0.811
(1.00) 		0.896
(1.00) 		0.0128
(1.00) 		0.000886
(0.785) 		0.0015
(1.00) 		0.408
(1.00) 		0.648
(1.00) 		0.291
(1.00) 		0.0331
(1.00) 		0.348
(1.00) 		0.534
(1.00)
13q gain 39 (7%) 520 0.0168
(1.00) 		0.221
(1.00) 		0.889
(1.00) 		0.00174
(1.00) 		0.0189
(1.00) 		0.000375
(0.336) 		0.924
(1.00) 		0.716
(1.00) 		0.411
(1.00) 		0.496
(1.00) 		0.157
(1.00) 		0.401
(1.00)
14q gain 34 (6%) 525 0.011
(1.00) 		0.0521
(1.00) 		0.348
(1.00) 		0.0546
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.109
(1.00) 		0.0433
(1.00) 		0.165
(1.00) 		0.1
(1.00) 		0.423
(1.00) 		0.483
(1.00)
15q gain 24 (4%) 535 0.382
(1.00) 		0.64
(1.00) 		0.337
(1.00) 		0.459
(1.00) 		0.261
(1.00) 		0.508
(1.00) 		0.106
(1.00) 		0.789
(1.00) 		1
(1.00) 		1
(1.00) 		0.703
(1.00) 		0.377
(1.00)
16p gain 32 (6%) 527 0.0552
(1.00) 		0.0164
(1.00) 		0.78
(1.00) 		0.385
(1.00) 		0.0912
(1.00) 		0.169
(1.00) 		0.785
(1.00) 		0.0651
(1.00) 		1
(1.00) 		1
(1.00) 		0.923
(1.00) 		0.569
(1.00)
16q gain 16 (3%) 543 0.0183
(1.00) 		0.000961
(0.847) 		0.219
(1.00) 		0.491
(1.00) 		0.506
(1.00) 		0.0475
(1.00) 		0.326
(1.00) 		0.0888
(1.00) 		0.128
(1.00) 		0.159
(1.00)
17p gain 10 (2%) 549 0.433
(1.00) 		0.129
(1.00) 		0.509
(1.00) 		0.27
(1.00) 		0.441
(1.00) 		0.215
(1.00) 		0.396
(1.00) 		0.611
(1.00) 		0.353
(1.00) 		0.577
(1.00) 		0.571
(1.00) 		0.328
(1.00)
17q gain 23 (4%) 536 0.729
(1.00) 		0.285
(1.00) 		0.271
(1.00) 		0.245
(1.00) 		0.214
(1.00) 		0.353
(1.00) 		0.897
(1.00) 		0.795
(1.00) 		0.636
(1.00) 		0.571
(1.00) 		0.662
(1.00) 		0.321
(1.00)
18q gain 41 (7%) 518 0.282
(1.00) 		0.518
(1.00) 		0.603
(1.00) 		0.408
(1.00) 		0.00604
(1.00) 		0.00621
(1.00) 		0.0994
(1.00) 		0.406
(1.00) 		0.837
(1.00) 		0.623
(1.00) 		0.0799
(1.00) 		0.467
(1.00)
22q gain 9 (2%) 550 0.379
(1.00) 		0.833
(1.00) 		0.692
(1.00) 		0.641
(1.00) 		0.0863
(1.00) 		0.84
(1.00) 		0.397
(1.00) 		1
(1.00) 		0.835
(1.00) 		0.532
(1.00) 		0.172
(1.00) 		0.457
(1.00)
Xq gain 33 (6%) 526 0.244
(1.00) 		0.0366
(1.00) 		0.923
(1.00) 		0.503
(1.00) 		0.0357
(1.00) 		0.16
(1.00) 		0.0822
(1.00) 		0.31
(1.00) 		0.764
(1.00) 		0.198
(1.00) 		0.451
(1.00) 		0.135
(1.00)
1p loss 35 (6%) 524 0.00443
(1.00) 		0.0112
(1.00) 		0.284
(1.00) 		0.49
(1.00) 		0.741
(1.00) 		0.202
(1.00) 		0.606
(1.00) 		0.282
(1.00) 		0.783
(1.00) 		0.455
(1.00) 		0.968
(1.00) 		0.612
(1.00)
1q loss 22 (4%) 537 0.018
(1.00) 		0.00428
(1.00) 		0.00412
(1.00) 		0.347
(1.00) 		0.267
(1.00) 		0.496
(1.00) 		0.278
(1.00) 		0.174
(1.00) 		0.8
(1.00) 		0.426
(1.00) 		0.454
(1.00) 		0.512
(1.00)
2p loss 26 (5%) 533 0.761
(1.00) 		0.871
(1.00) 		0.905
(1.00) 		0.181
(1.00) 		0.651
(1.00) 		0.422
(1.00) 		0.322
(1.00) 		0.72
(1.00) 		0.202
(1.00) 		0.284
(1.00) 		0.666
(1.00) 		0.715
(1.00)
2q loss 30 (5%) 529 0.789
(1.00) 		0.53
(1.00) 		0.816
(1.00) 		0.0858
(1.00) 		0.794
(1.00) 		0.166
(1.00) 		0.306
(1.00) 		0.859
(1.00) 		0.55
(1.00) 		0.253
(1.00) 		0.649
(1.00) 		0.346
(1.00)
3p loss 60 (11%) 499 0.0608
(1.00) 		0.0112
(1.00) 		0.867
(1.00) 		0.0391
(1.00) 		0.00132
(1.00) 		0.0732
(1.00) 		0.836
(1.00) 		0.583
(1.00) 		0.0234
(1.00) 		0.0517
(1.00) 		0.506
(1.00) 		0.315
(1.00)
3q loss 23 (4%) 536 0.239
(1.00) 		0.0866
(1.00) 		0.964
(1.00) 		0.182
(1.00) 		0.177
(1.00) 		0.203
(1.00) 		0.936
(1.00) 		0.445
(1.00) 		0.0802
(1.00) 		0.151
(1.00) 		0.667
(1.00) 		0.501
(1.00)
4p loss 254 (45%) 305 0.116
(1.00) 		0.0826
(1.00) 		0.454
(1.00) 		0.0373
(1.00) 		0.059
(1.00) 		0.964
(1.00) 		0.168
(1.00) 		0.235
(1.00) 		0.448
(1.00) 		0.0564
(1.00) 		0.0419
(1.00) 		0.0369
(1.00)
4q loss 294 (53%) 265 0.0627
(1.00) 		0.0243
(1.00) 		0.215
(1.00) 		0.023
(1.00) 		0.0105
(1.00) 		0.914
(1.00) 		0.209
(1.00) 		0.147
(1.00) 		0.538
(1.00) 		0.0429
(1.00) 		0.0718
(1.00) 		0.00293
(1.00)
5p loss 84 (15%) 475 0.28
(1.00) 		0.088
(1.00) 		0.289
(1.00) 		0.1
(1.00) 		0.0523
(1.00) 		0.00703
(1.00) 		0.0492
(1.00) 		0.329
(1.00) 		0.000899
(0.794) 		0.405
(1.00) 		0.931
(1.00) 		0.497
(1.00)
6p loss 121 (22%) 438 0.991
(1.00) 		0.0765
(1.00) 		0.682
(1.00) 		0.822
(1.00) 		0.0589
(1.00) 		0.036
(1.00) 		0.213
(1.00) 		0.483
(1.00) 		0.502
(1.00) 		0.135
(1.00) 		0.231
(1.00) 		0.866
(1.00)
6q loss 192 (34%) 367 0.928
(1.00) 		0.0182
(1.00) 		0.77
(1.00) 		0.793
(1.00) 		0.112
(1.00) 		0.00985
(1.00) 		0.272
(1.00) 		0.526
(1.00) 		0.402
(1.00) 		0.128
(1.00) 		0.562
(1.00) 		0.681
(1.00)
7p loss 91 (16%) 468 0.683
(1.00) 		0.336
(1.00) 		0.184
(1.00) 		0.304
(1.00) 		0.151
(1.00) 		0.199
(1.00) 		0.647
(1.00) 		0.749
(1.00) 		0.826
(1.00) 		0.29
(1.00) 		0.0421
(1.00) 		0.598
(1.00)
7q loss 48 (9%) 511 0.337
(1.00) 		0.855
(1.00) 		0.431
(1.00) 		0.652
(1.00) 		0.304
(1.00) 		0.0203
(1.00) 		0.29
(1.00) 		0.545
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.0557
(1.00) 		0.198
(1.00)
8p loss 229 (41%) 330 0.699
(1.00) 		0.601
(1.00) 		0.54
(1.00) 		0.909
(1.00) 		0.00215
(1.00) 		0.133
(1.00) 		0.257
(1.00) 		0.284
(1.00) 		0.642
(1.00) 		0.55
(1.00) 		0.782
(1.00) 		1
(1.00)
8q loss 62 (11%) 497 0.0489
(1.00) 		0.0245
(1.00) 		0.116
(1.00) 		0.121
(1.00) 		0.000342
(0.308) 		0.0429
(1.00) 		0.147
(1.00) 		0.2
(1.00) 		0.0128
(1.00) 		0.047
(1.00) 		0.562
(1.00) 		0.477
(1.00)
9p loss 207 (37%) 352 0.000773
(0.687) 		0.00643
(1.00) 		0.771
(1.00) 		0.0612
(1.00) 		0.000852
(0.756) 		0.000469
(0.42) 		0.676
(1.00) 		0.812
(1.00) 		0.538
(1.00) 		0.342
(1.00) 		0.0219
(1.00) 		0.212
(1.00)
10p loss 63 (11%) 496 0.303
(1.00) 		0.538
(1.00) 		0.381
(1.00) 		0.793
(1.00) 		0.521
(1.00) 		0.67
(1.00) 		0.285
(1.00) 		0.0737
(1.00) 		0.776
(1.00) 		0.494
(1.00) 		0.15
(1.00) 		0.751
(1.00)
10q loss 87 (16%) 472 0.474
(1.00) 		0.38
(1.00) 		0.144
(1.00) 		0.836
(1.00) 		0.282
(1.00) 		0.512
(1.00) 		0.398
(1.00) 		0.138
(1.00) 		0.803
(1.00) 		0.165
(1.00) 		0.195
(1.00) 		0.754
(1.00)
11p loss 142 (25%) 417 0.00609
(1.00) 		0.00524
(1.00) 		0.0964
(1.00) 		0.262
(1.00) 		0.0867
(1.00) 		0.00941
(1.00) 		0.666
(1.00) 		0.137
(1.00) 		0.0361
(1.00) 		0.142
(1.00) 		0.882
(1.00) 		0.508
(1.00)
11q loss 105 (19%) 454 0.147
(1.00) 		0.462
(1.00) 		0.00992
(1.00) 		0.26
(1.00) 		0.219
(1.00) 		0.148
(1.00) 		0.895
(1.00) 		0.292
(1.00) 		0.124
(1.00) 		0.222
(1.00) 		0.261
(1.00) 		0.114
(1.00)
12p loss 50 (9%) 509 0.294
(1.00) 		0.0891
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.00585
(1.00) 		0.248
(1.00) 		0.884
(1.00) 		0.0613
(1.00) 		0.245
(1.00) 		0.541
(1.00) 		0.297
(1.00) 		0.229
(1.00)
12q loss 74 (13%) 485 0.192
(1.00) 		0.00199
(1.00) 		0.389
(1.00) 		0.277
(1.00) 		0.00297
(1.00) 		0.129
(1.00) 		0.832
(1.00) 		0.0971
(1.00) 		0.167
(1.00) 		0.0457
(1.00) 		0.248
(1.00) 		0.644
(1.00)
14q loss 162 (29%) 397 0.0689
(1.00) 		0.13
(1.00) 		0.922
(1.00) 		0.906
(1.00) 		0.00404
(1.00) 		0.0177
(1.00) 		0.301
(1.00) 		0.223
(1.00) 		0.0399
(1.00) 		0.682
(1.00) 		0.354
(1.00) 		0.143
(1.00)
16p loss 263 (47%) 296 0.976
(1.00) 		0.911
(1.00) 		0.293
(1.00) 		0.806
(1.00) 		0.0603
(1.00) 		0.115
(1.00) 		0.766
(1.00) 		0.69
(1.00) 		0.575
(1.00) 		0.618
(1.00) 		0.32
(1.00) 		0.713
(1.00)
16q loss 350 (63%) 209 0.968
(1.00) 		0.814
(1.00) 		0.038
(1.00) 		0.297
(1.00) 		0.0155
(1.00) 		0.0832
(1.00) 		0.842
(1.00) 		0.932
(1.00) 		0.495
(1.00) 		0.682
(1.00) 		0.312
(1.00) 		0.346
(1.00)
17p loss 420 (75%) 139 0.167
(1.00) 		0.0601
(1.00) 		0.944
(1.00) 		0.626
(1.00) 		0.121
(1.00) 		0.0558
(1.00) 		0.43
(1.00) 		0.146
(1.00) 		0.203
(1.00) 		0.253
(1.00) 		0.301
(1.00) 		0.47
(1.00)
17q loss 323 (58%) 236 0.00548
(1.00) 		0.00638
(1.00) 		0.0201
(1.00) 		0.528
(1.00) 		0.266
(1.00) 		0.165
(1.00) 		0.323
(1.00) 		0.201
(1.00) 		0.011
(1.00) 		0.05
(1.00) 		0.000364
(0.327) 		0.326
(1.00)
18p loss 182 (33%) 377 0.887
(1.00) 		0.814
(1.00) 		0.326
(1.00) 		0.472
(1.00) 		0.29
(1.00) 		0.0094
(1.00) 		0.8
(1.00) 		0.297
(1.00) 		0.0389
(1.00) 		0.583
(1.00) 		0.886
(1.00) 		0.853
(1.00)
18q loss 228 (41%) 331 0.275
(1.00) 		0.814
(1.00) 		0.712
(1.00) 		0.657
(1.00) 		0.571
(1.00) 		0.378
(1.00) 		0.88
(1.00) 		0.184
(1.00) 		0.00185
(1.00) 		0.145
(1.00) 		0.736
(1.00) 		0.493
(1.00)
19p loss 140 (25%) 419 0.427
(1.00) 		0.821
(1.00) 		0.0544
(1.00) 		0.125
(1.00) 		0.224
(1.00) 		0.134
(1.00) 		0.0166
(1.00) 		0.502
(1.00) 		0.647
(1.00) 		0.16
(1.00) 		0.556
(1.00) 		0.296
(1.00)
19q loss 140 (25%) 419 0.0853
(1.00) 		0.309
(1.00) 		0.178
(1.00) 		0.157
(1.00) 		0.112
(1.00) 		0.819
(1.00) 		0.04
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.249
(1.00) 		0.154
(1.00) 		0.128
(1.00)
20p loss 37 (7%) 522 0.304
(1.00) 		0.529
(1.00) 		0.625
(1.00) 		0.361
(1.00) 		0.0534
(1.00) 		0.0447
(1.00) 		0.416
(1.00) 		0.284
(1.00) 		0.0151
(1.00) 		0.0328
(1.00) 		0.0287
(1.00) 		0.145
(1.00)
20q loss 21 (4%) 538 0.717
(1.00) 		0.188
(1.00) 		0.276
(1.00) 		0.737
(1.00) 		0.247
(1.00) 		0.546
(1.00) 		0.271
(1.00) 		0.0993
(1.00) 		0.245
(1.00) 		0.44
(1.00) 		0.434
(1.00) 		0.0722
(1.00)
21q loss 148 (26%) 411 0.343
(1.00) 		0.248
(1.00) 		0.31
(1.00) 		0.0634
(1.00) 		0.97
(1.00) 		0.0449
(1.00) 		0.0939
(1.00) 		0.173
(1.00) 		0.602
(1.00) 		0.763
(1.00) 		0.21
(1.00) 		0.886
(1.00)
Xq loss 102 (18%) 457 0.0884
(1.00) 		0.175
(1.00) 		0.0337
(1.00) 		0.124
(1.00) 		0.155
(1.00) 		0.379
(1.00) 		0.735
(1.00) 		0.417
(1.00) 		0.395
(1.00) 		0.615
(1.00) 		0.951
(1.00) 		0.361
(1.00)
'1q gain mutation analysis' versus 'CN_CNMF'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.001

Table S1.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
1Q GAIN MUTATED 35 41 78
1Q GAIN WILD-TYPE 128 168 109

Figure S1.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'2p gain mutation analysis' versus 'MRNA_CNMF'

P value = 5.21e-09 (Fisher's exact test), Q value = 4.9e-06

Table S2.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
2P GAIN MUTATED 76 23 26
2P GAIN WILD-TYPE 139 190 103

Figure S2.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'2p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.03e-10 (Fisher's exact test), Q value = 9.7e-08

Table S3.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
2P GAIN MUTATED 34 77 14
2P GAIN WILD-TYPE 199 122 111

Figure S3.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2p gain mutation analysis' versus 'MIR_CHIERARCHICAL'

P value = 1.31e-05 (Chi-square test), Q value = 0.012

Table S4.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
2P GAIN MUTATED 11 17 24 20 12 41
2P GAIN WILD-TYPE 54 98 101 79 45 53

Figure S4.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 2.47e-11 (Fisher's exact test), Q value = 2.3e-08

Table S5.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
2P GAIN MUTATED 24 26 75
2P GAIN WILD-TYPE 139 183 112

Figure S5.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'2p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.05e-11 (Fisher's exact test), Q value = 1e-08

Table S6.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
2P GAIN MUTATED 69 32 24
2P GAIN WILD-TYPE 98 139 196

Figure S6.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'2p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.96e-05 (Fisher's exact test), Q value = 0.072

Table S7.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 70 91
2P GAIN MUTATED 20 7 35
2P GAIN WILD-TYPE 78 63 56

Figure S7.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

'2q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.53e-06 (Fisher's exact test), Q value = 0.0014

Table S8.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
2Q GAIN MUTATED 61 21 17
2Q GAIN WILD-TYPE 154 192 112

Figure S8.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'2q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.48e-07 (Fisher's exact test), Q value = 6e-04

Table S9.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
2Q GAIN MUTATED 26 59 14
2Q GAIN WILD-TYPE 207 140 111

Figure S9.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.7e-06

Table S10.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
2Q GAIN MUTATED 17 21 61
2Q GAIN WILD-TYPE 146 188 126

Figure S10.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'2q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.16e-07 (Fisher's exact test), Q value = 3e-04

Table S11.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
2Q GAIN MUTATED 53 22 24
2Q GAIN WILD-TYPE 114 149 196

Figure S11.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'3q gain mutation analysis' versus 'CN_CNMF'

P value = 1.71e-08 (Fisher's exact test), Q value = 1.6e-05

Table S12.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
3Q GAIN MUTATED 42 63 101
3Q GAIN WILD-TYPE 121 146 86

Figure S12.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 2.33e-06 (Fisher's exact test), Q value = 0.0022

Table S13.  Gene #9: '5p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
5P GAIN MUTATED 19 61 62
5P GAIN WILD-TYPE 144 148 125

Figure S13.  Get High-res Image Gene #9: '5p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'6p gain mutation analysis' versus 'CN_CNMF'

P value = 8.97e-07 (Fisher's exact test), Q value = 0.00084

Table S14.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
6P GAIN MUTATED 16 45 61
6P GAIN WILD-TYPE 147 164 126

Figure S14.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'6p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.36e-05 (Fisher's exact test), Q value = 0.085

Table S15.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
6P GAIN MUTATED 56 26 40
6P GAIN WILD-TYPE 111 145 180

Figure S15.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.24

Table S16.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
6Q GAIN MUTATED 7 21 33
6Q GAIN WILD-TYPE 156 188 154

Figure S16.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'6q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.59e-05 (Fisher's exact test), Q value = 0.024

Table S17.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
6Q GAIN MUTATED 34 9 18
6Q GAIN WILD-TYPE 133 162 202

Figure S17.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 1.2e-06

Table S18.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
7P GAIN MUTATED 24 27 71
7P GAIN WILD-TYPE 139 182 116

Figure S18.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.83e-07 (Fisher's exact test), Q value = 0.00064

Table S19.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
7P GAIN MUTATED 61 25 36
7P GAIN WILD-TYPE 106 146 184

Figure S19.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 2.06e-07 (Fisher's exact test), Q value = 0.00019

Table S20.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
7Q GAIN MUTATED 30 40 77
7Q GAIN WILD-TYPE 133 169 110

Figure S20.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000178 (Fisher's exact test), Q value = 0.16

Table S21.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
7Q GAIN MUTATED 64 34 49
7Q GAIN WILD-TYPE 103 137 171

Figure S21.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'10p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.031

Table S22.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
10P GAIN MUTATED 54 65 14
10P GAIN WILD-TYPE 179 134 111

Figure S22.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'10p gain mutation analysis' versus 'CN_CNMF'

P value = 2.53e-09 (Fisher's exact test), Q value = 2.4e-06

Table S23.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
10P GAIN MUTATED 20 39 74
10P GAIN WILD-TYPE 143 170 113

Figure S23.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'12p gain mutation analysis' versus 'MRNA_CNMF'

P value = 7.56e-05 (Fisher's exact test), Q value = 0.069

Table S24.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
12P GAIN MUTATED 102 60 40
12P GAIN WILD-TYPE 113 153 89

Figure S24.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'12p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.012

Table S25.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
12P GAIN MUTATED 70 98 34
12P GAIN WILD-TYPE 163 101 91

Figure S25.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'12p gain mutation analysis' versus 'MIR_CHIERARCHICAL'

P value = 4.46e-05 (Chi-square test), Q value = 0.041

Table S26.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
12P GAIN MUTATED 21 31 42 28 25 54
12P GAIN WILD-TYPE 44 84 83 71 32 40

Figure S26.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 3.02e-14 (Fisher's exact test), Q value = 2.9e-11

Table S27.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
12P GAIN MUTATED 37 55 110
12P GAIN WILD-TYPE 126 154 77

Figure S27.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'12p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.39e-09 (Fisher's exact test), Q value = 2.3e-06

Table S28.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
12P GAIN MUTATED 93 53 56
12P GAIN WILD-TYPE 74 118 164

Figure S28.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.75e-05 (Fisher's exact test), Q value = 0.025

Table S29.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 70 91
12P GAIN MUTATED 24 20 50
12P GAIN WILD-TYPE 74 50 41

Figure S29.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.01e-05 (Fisher's exact test), Q value = 0.055

Table S30.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 106 50
12P GAIN MUTATED 24 55 15
12P GAIN WILD-TYPE 79 51 35

Figure S30.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #10: 'MRNASEQ_CHIERARCHICAL'

'12q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.11e-06 (Fisher's exact test), Q value = 0.0084

Table S31.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
12Q GAIN MUTATED 34 64 18
12Q GAIN WILD-TYPE 199 135 107

Figure S31.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'12q gain mutation analysis' versus 'CN_CNMF'

P value = 1.19e-13 (Fisher's exact test), Q value = 1.1e-10

Table S32.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
12Q GAIN MUTATED 26 17 73
12Q GAIN WILD-TYPE 137 192 114

Figure S32.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'12q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.014

Table S33.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
12Q GAIN MUTATED 56 25 35
12Q GAIN WILD-TYPE 111 146 185

Figure S33.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'18p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.035

Table S34.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
18P GAIN MUTATED 38 11 24
18P GAIN WILD-TYPE 129 160 196

Figure S34.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 7.52e-09 (Fisher's exact test), Q value = 7.1e-06

Table S35.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
19P GAIN MUTATED 18 21 60
19P GAIN WILD-TYPE 145 188 127

Figure S35.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 7.97e-07 (Fisher's exact test), Q value = 0.00074

Table S36.  Gene #35: '19q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
19Q GAIN MUTATED 16 22 53
19Q GAIN WILD-TYPE 147 187 134

Figure S36.  Get High-res Image Gene #35: '19q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.58e-07 (Fisher's exact test), Q value = 0.00052

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
20P GAIN MUTATED 91 108 31
20P GAIN WILD-TYPE 142 91 94

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

'20p gain mutation analysis' versus 'MIR_CHIERARCHICAL'

P value = 1.73e-06 (Chi-square test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
20P GAIN MUTATED 24 41 37 36 30 61
20P GAIN WILD-TYPE 41 74 88 63 27 33

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

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 2.92e-15 (Fisher's exact test), Q value = 2.8e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
20P GAIN MUTATED 44 65 122
20P GAIN WILD-TYPE 119 144 65

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

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.74e-13 (Fisher's exact test), Q value = 3.6e-10

Table S40.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
20P GAIN MUTATED 109 59 63
20P GAIN WILD-TYPE 58 112 157

Figure S40.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.018

Table S41.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
20Q GAIN MUTATED 127 78 62
20Q GAIN WILD-TYPE 88 135 67

Figure S41.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.35e-13 (Fisher's exact test), Q value = 3.2e-10

Table S42.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
20Q GAIN MUTATED 110 129 28
20Q GAIN WILD-TYPE 123 70 97

Figure S42.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MIR_CHIERARCHICAL'

P value = 4.83e-07 (Chi-square test), Q value = 0.00045

Table S43.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 65 115 125 99 57 94
20Q GAIN MUTATED 26 46 48 43 34 69
20Q GAIN WILD-TYPE 39 69 77 56 23 25

Figure S43.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 1.71e-17 (Fisher's exact test), Q value = 1.6e-14

Table S44.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
20Q GAIN MUTATED 49 82 137
20Q GAIN WILD-TYPE 114 127 50

Figure S44.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.17e-17 (Fisher's exact test), Q value = 4e-14

Table S45.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
20Q GAIN MUTATED 126 68 74
20Q GAIN WILD-TYPE 41 103 146

Figure S45.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'21q gain mutation analysis' versus 'CN_CNMF'

P value = 4.21e-06 (Fisher's exact test), Q value = 0.0039

Table S46.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
21Q GAIN MUTATED 10 16 41
21Q GAIN WILD-TYPE 153 193 146

Figure S46.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'5q loss mutation analysis' versus 'MRNA_CNMF'

P value = 7.52e-05 (Fisher's exact test), Q value = 0.068

Table S47.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
5Q LOSS MUTATED 88 54 27
5Q LOSS WILD-TYPE 127 159 102

Figure S47.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'5q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.02

Table S48.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
5Q LOSS MUTATED 51 84 34
5Q LOSS WILD-TYPE 182 115 91

Figure S48.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'5q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.81e-07 (Fisher's exact test), Q value = 0.00026

Table S49.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
5Q LOSS MUTATED 77 33 59
5Q LOSS WILD-TYPE 90 138 161

Figure S49.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 3.32e-15 (Fisher's exact test), Q value = 3.2e-12

Table S50.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
9Q LOSS MUTATED 59 54 122
9Q LOSS WILD-TYPE 104 155 65

Figure S50.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 7.97e-05 (Fisher's exact test), Q value = 0.072

Table S51.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
13Q LOSS MUTATED 52 112 92
13Q LOSS WILD-TYPE 111 97 95

Figure S51.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'13q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.0014

Table S52.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
13Q LOSS MUTATED 75 54 127
13Q LOSS WILD-TYPE 92 117 93

Figure S52.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 1.2e-08 (Fisher's exact test), Q value = 1.1e-05

Table S53.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 209 187
15Q LOSS MUTATED 49 63 106
15Q LOSS WILD-TYPE 114 146 81

Figure S53.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'15q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.11

Table S54.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 171 220
15Q LOSS MUTATED 86 50 82
15Q LOSS WILD-TYPE 81 121 138

Figure S54.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.11

Table S55.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 213 129
22Q LOSS MUTATED 168 129 80
22Q LOSS WILD-TYPE 47 84 49

Figure S55.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'22q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.017

Table S56.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 199 125
22Q LOSS MUTATED 134 156 87
22Q LOSS WILD-TYPE 99 43 38

Figure S56.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 559

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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