Correlation between copy number variations of arm-level result and molecular subtypes
Colon/Rectal Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1BR8QCD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1BR8QCD
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 78 arm-level results and 10 molecular subtypes across 575 patients, 86 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'METHLYATION_CNMF'.

  • 2q gain cnv correlated to 'METHLYATION_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 78 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 86 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
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 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
14q loss 143 (25%) 432 3.41e-06
(0.0024) 		2.03e-07
(0.000146) 		1.12e-31
(8.46e-29) 		1.97e-07
(0.000142) 		2.82e-05
(0.0196) 		0.00618
(1.00) 		1.09e-05
(0.0076) 		3.09e-07
(0.000222) 		0.114
(1.00) 		0.709
(1.00)
13q gain 314 (55%) 261 1.31e-07
(9.44e-05) 		2.67e-05
(0.0186) 		1.62e-37
(1.23e-34) 		1.71e-08
(1.24e-05) 		0.012
(1.00) 		0.125
(1.00) 		5.48e-08
(3.97e-05) 		3.75e-10
(2.73e-07) 		0.01
(1.00) 		0.45
(1.00)
20p gain 288 (50%) 287 5.9e-05
(0.0406) 		5.89e-08
(4.26e-05) 		4.25e-22
(3.2e-19) 		7.67e-05
(0.0526) 		0.0303
(1.00) 		0.0924
(1.00) 		1.22e-05
(0.00853) 		4.08e-10
(2.97e-07) 		0.625
(1.00) 		0.472
(1.00)
20q gain 403 (70%) 172 6.95e-19
(5.19e-16) 		2.93e-16
(2.18e-13) 		2.22e-46
(1.69e-43) 		9.04e-13
(6.64e-10) 		0.0011
(0.732) 		0.00113
(0.749) 		2.42e-20
(1.82e-17) 		5.52e-24
(4.16e-21) 		0.463
(1.00) 		0.101
(1.00)
18p loss 324 (56%) 251 2.45e-15
(1.82e-12) 		2.18e-12
(1.6e-09) 		4.26e-47
(3.24e-44) 		4.33e-19
(3.24e-16) 		0.0139
(1.00) 		0.00742
(1.00) 		6.98e-14
(5.16e-11) 		7.3e-14
(5.39e-11) 		0.065
(1.00) 		0.787
(1.00)
18q loss 352 (61%) 223 4.08e-13
(3e-10) 		5.32e-12
(3.9e-09) 		6.8e-51
(5.18e-48) 		8.03e-21
(6.03e-18) 		0.0286
(1.00) 		0.0796
(1.00) 		9.19e-11
(6.71e-08) 		5.51e-14
(4.07e-11) 		0.00938
(1.00) 		0.378
(1.00)
7p gain 290 (50%) 285 0.000291
(0.197) 		0.00824
(1.00) 		1.89e-21
(1.42e-18) 		7.29e-07
(0.00052) 		0.0303
(1.00) 		0.00416
(1.00) 		5.72e-07
(0.000409) 		5.18e-07
(0.000371) 		0.0703
(1.00) 		0.0304
(1.00)
7q gain 255 (44%) 320 0.000406
(0.273) 		0.0393
(1.00) 		6.95e-16
(5.16e-13) 		8.61e-06
(0.00603) 		0.314
(1.00) 		0.0227
(1.00) 		7.49e-07
(0.000533) 		8.39e-06
(0.00588) 		0.245
(1.00) 		0.155
(1.00)
17p loss 252 (44%) 323 0.000159
(0.109) 		0.00124
(0.824) 		5.49e-22
(4.13e-19) 		2.44e-07
(0.000176) 		0.184
(1.00) 		0.538
(1.00) 		0.00344
(1.00) 		0.000188
(0.128) 		0.027
(1.00) 		0.497
(1.00)
11p gain 39 (7%) 536 0.0684
(1.00) 		0.663
(1.00) 		1.71e-05
(0.0119) 		0.000214
(0.146) 		0.815
(1.00) 		0.93
(1.00) 		0.00971
(1.00) 		0.0593
(1.00) 		0.246
(1.00) 		0.882
(1.00)
17q gain 67 (12%) 508 0.0504
(1.00) 		0.0423
(1.00) 		0.000269
(0.182) 		0.00143
(0.946) 		0.278
(1.00) 		0.076
(1.00) 		0.000117
(0.0805) 		0.00212
(1.00) 		0.0785
(1.00) 		0.354
(1.00)
1p loss 68 (12%) 507 0.0576
(1.00) 		0.0028
(1.00) 		7.55e-06
(0.0053) 		3.84e-05
(0.0265) 		0.784
(1.00) 		0.687
(1.00) 		0.0643
(1.00) 		0.0514
(1.00) 		0.193
(1.00) 		0.62
(1.00)
8p loss 145 (25%) 430 0.015
(1.00) 		0.00631
(1.00) 		1.14e-18
(8.52e-16) 		0.000373
(0.252) 		0.0744
(1.00) 		0.184
(1.00) 		4.23e-05
(0.0292) 		0.00286
(1.00) 		0.515
(1.00) 		0.73
(1.00)
9q loss 37 (6%) 538 0.0518
(1.00) 		0.0161
(1.00) 		1.95e-06
(0.00138) 		3.42e-05
(0.0236) 		0.357
(1.00) 		0.294
(1.00) 		0.0314
(1.00) 		0.00628
(1.00) 		0.0491
(1.00) 		0.82
(1.00)
2p gain 60 (10%) 515 0.0149
(1.00) 		0.00232
(1.00) 		0.00816
(1.00) 		0.000256
(0.174) 		0.287
(1.00) 		0.414
(1.00) 		0.000632
(0.424) 		0.00553
(1.00) 		0.216
(1.00) 		0.0209
(1.00)
2q gain 59 (10%) 516 0.00396
(1.00) 		0.00262
(1.00) 		0.00101
(0.672) 		5.82e-06
(0.00409) 		0.55
(1.00) 		0.497
(1.00) 		0.00218
(1.00) 		0.00233
(1.00) 		0.251
(1.00) 		0.0504
(1.00)
3p gain 36 (6%) 539 0.131
(1.00) 		0.49
(1.00) 		0.000181
(0.124) 		0.257
(1.00) 		0.0827
(1.00) 		0.488
(1.00) 		0.514
(1.00) 		0.484
(1.00) 		0.208
(1.00) 		0.366
(1.00)
3q gain 53 (9%) 522 0.239
(1.00) 		0.138
(1.00) 		2.49e-06
(0.00176) 		0.0353
(1.00) 		0.0277
(1.00) 		0.398
(1.00) 		0.69
(1.00) 		0.269
(1.00) 		0.111
(1.00) 		0.544
(1.00)
6p gain 77 (13%) 498 0.238
(1.00) 		0.00386
(1.00) 		1.55e-06
(0.00109) 		0.401
(1.00) 		0.361
(1.00) 		0.532
(1.00) 		0.0379
(1.00) 		0.178
(1.00) 		0.848
(1.00) 		0.392
(1.00)
6q gain 71 (12%) 504 0.384
(1.00) 		0.0448
(1.00) 		7.47e-07
(0.000532) 		0.159
(1.00) 		0.275
(1.00) 		0.17
(1.00) 		0.0657
(1.00) 		0.409
(1.00) 		0.749
(1.00) 		0.251
(1.00)
8p gain 108 (19%) 467 0.9
(1.00) 		0.653
(1.00) 		1e-08
(7.29e-06) 		0.433
(1.00) 		0.121
(1.00) 		0.0784
(1.00) 		0.708
(1.00) 		0.692
(1.00) 		0.49
(1.00) 		0.891
(1.00)
8q gain 235 (41%) 340 0.0531
(1.00) 		0.589
(1.00) 		1.06e-33
(8e-31) 		0.00942
(1.00) 		0.0445
(1.00) 		0.408
(1.00) 		0.0112
(1.00) 		0.0719
(1.00) 		0.459
(1.00) 		0.633
(1.00)
11q gain 39 (7%) 536 0.105
(1.00) 		0.0458
(1.00) 		1.33e-06
(0.000941) 		0.000911
(0.608) 		0.506
(1.00) 		0.332
(1.00) 		0.000487
(0.328) 		0.00684
(1.00) 		0.559
(1.00) 		0.406
(1.00)
16p gain 96 (17%) 479 0.109
(1.00) 		0.0926
(1.00) 		1.26e-16
(9.39e-14) 		0.0108
(1.00) 		0.426
(1.00) 		0.0283
(1.00) 		0.0352
(1.00) 		0.00634
(1.00) 		0.577
(1.00) 		0.347
(1.00)
16q gain 96 (17%) 479 0.0492
(1.00) 		0.0712
(1.00) 		3.02e-18
(2.25e-15) 		0.00391
(1.00) 		0.19
(1.00) 		0.0155
(1.00) 		0.0102
(1.00) 		0.00534
(1.00) 		0.465
(1.00) 		0.277
(1.00)
19p gain 52 (9%) 523 0.178
(1.00) 		0.299
(1.00) 		5.84e-05
(0.0402) 		0.0236
(1.00) 		0.0656
(1.00) 		0.0771
(1.00) 		0.0217
(1.00) 		0.122
(1.00) 		0.718
(1.00) 		0.745
(1.00)
19q gain 61 (11%) 514 0.0133
(1.00) 		0.0178
(1.00) 		0.0122
(1.00) 		0.0715
(1.00) 		0.00805
(1.00) 		0.0366
(1.00) 		0.0034
(1.00) 		0.000262
(0.178) 		0.832
(1.00) 		0.495
(1.00)
4p loss 122 (21%) 453 0.0598
(1.00) 		0.117
(1.00) 		5.5e-11
(4.02e-08) 		0.0036
(1.00) 		0.35
(1.00) 		0.759
(1.00) 		0.123
(1.00) 		0.0682
(1.00) 		0.045
(1.00) 		0.769
(1.00)
4q loss 113 (20%) 462 0.0752
(1.00) 		0.136
(1.00) 		3.18e-12
(2.33e-09) 		0.00168
(1.00) 		0.392
(1.00) 		0.548
(1.00) 		0.238
(1.00) 		0.0456
(1.00) 		0.0122
(1.00) 		0.564
(1.00)
5q loss 60 (10%) 515 0.0145
(1.00) 		0.0274
(1.00) 		5.53e-07
(0.000396) 		0.0816
(1.00) 		0.431
(1.00) 		0.878
(1.00) 		0.0637
(1.00) 		0.197
(1.00) 		0.963
(1.00) 		0.579
(1.00)
9p loss 39 (7%) 536 0.571
(1.00) 		0.182
(1.00) 		2.9e-05
(0.0201) 		0.00158
(1.00) 		0.188
(1.00) 		0.201
(1.00) 		0.317
(1.00) 		0.377
(1.00) 		0.127
(1.00) 		1
(1.00)
10q loss 46 (8%) 529 0.762
(1.00) 		0.311
(1.00) 		1.44e-06
(0.00102) 		0.153
(1.00) 		0.0239
(1.00) 		0.991
(1.00) 		0.968
(1.00) 		0.286
(1.00) 		0.714
(1.00) 		0.811
(1.00)
12p loss 33 (6%) 542 0.116
(1.00) 		0.188
(1.00) 		5.42e-07
(0.000388) 		0.258
(1.00) 		0.707
(1.00) 		0.664
(1.00) 		0.568
(1.00) 		0.0773
(1.00) 		0.541
(1.00) 		0.222
(1.00)
12q loss 28 (5%) 547 0.136
(1.00) 		0.0476
(1.00) 		1.11e-06
(0.000786) 		0.522
(1.00) 		0.918
(1.00) 		0.866
(1.00) 		0.208
(1.00) 		0.0416
(1.00) 		0.616
(1.00) 		0.681
(1.00)
15q loss 156 (27%) 419 0.00723
(1.00) 		0.00477
(1.00) 		2.09e-24
(1.58e-21) 		0.0158
(1.00) 		0.0218
(1.00) 		0.987
(1.00) 		0.357
(1.00) 		0.00137
(0.906) 		0.368
(1.00) 		0.246
(1.00)
19p loss 20 (3%) 555 0.489
(1.00) 		0.604
(1.00) 		1.46e-05
(0.0102) 		0.0244
(1.00) 		0.756
(1.00) 		0.724
(1.00) 		0.69
(1.00) 		0.525
(1.00) 		0.235
(1.00) 		0.371
(1.00)
19q loss 18 (3%) 557 0.489
(1.00) 		0.604
(1.00) 		0.000235
(0.16) 		0.0965
(1.00) 		0.57
(1.00) 		0.646
(1.00) 		0.69
(1.00) 		0.525
(1.00) 		0.424
(1.00) 		0.0976
(1.00)
20p loss 47 (8%) 528 0.181
(1.00) 		0.228
(1.00) 		4.56e-07
(0.000328) 		0.039
(1.00) 		0.206
(1.00) 		0.584
(1.00) 		0.0353
(1.00) 		0.177
(1.00) 		0.554
(1.00) 		0.486
(1.00)
21q loss 114 (20%) 461 0.0471
(1.00) 		0.223
(1.00) 		3.64e-05
(0.0252) 		0.0555
(1.00) 		0.332
(1.00) 		0.531
(1.00) 		0.614
(1.00) 		0.287
(1.00) 		0.118
(1.00) 		0.342
(1.00)
22q loss 122 (21%) 453 0.0567
(1.00) 		0.00484
(1.00) 		7.8e-14
(5.75e-11) 		0.352
(1.00) 		0.194
(1.00) 		0.464
(1.00) 		0.335
(1.00) 		0.0196
(1.00) 		0.0662
(1.00) 		0.1
(1.00)
1p gain 15 (3%) 560 0.404
(1.00) 		0.112
(1.00) 		0.932
(1.00) 		0.497
(1.00) 		0.224
(1.00) 		0.0213
(1.00) 		0.864
(1.00) 		0.829
(1.00) 		0.111
(1.00) 		0.911
(1.00)
1q gain 80 (14%) 495 0.509
(1.00) 		0.927
(1.00) 		0.0158
(1.00) 		0.926
(1.00) 		0.137
(1.00) 		0.477
(1.00) 		0.00343
(1.00) 		0.681
(1.00) 		0.0729
(1.00) 		0.978
(1.00)
4p gain 6 (1%) 569 0.0622
(1.00) 		0.226
(1.00) 		0.17
(1.00) 		0.081
(1.00) 		0.137
(1.00) 		0.0525
(1.00)
4q gain 7 (1%) 568 0.703
(1.00) 		0.321
(1.00) 		0.25
(1.00) 		0.787
(1.00) 		0.568
(1.00) 		0.732
(1.00) 		0.435
(1.00) 		0.745
(1.00) 		0.383
(1.00) 		0.809
(1.00)
5p gain 60 (10%) 515 0.117
(1.00) 		0.681
(1.00) 		0.0015
(0.992) 		0.178
(1.00) 		0.172
(1.00) 		0.949
(1.00) 		0.0611
(1.00) 		0.0544
(1.00) 		0.784
(1.00) 		0.354
(1.00)
5q gain 33 (6%) 542 0.456
(1.00) 		0.617
(1.00) 		0.00356
(1.00) 		0.356
(1.00) 		0.661
(1.00) 		0.639
(1.00) 		0.432
(1.00) 		0.463
(1.00) 		0.818
(1.00) 		0.483
(1.00)
9p gain 79 (14%) 496 0.491
(1.00) 		0.907
(1.00) 		0.178
(1.00) 		0.79
(1.00) 		0.407
(1.00) 		0.446
(1.00) 		0.0435
(1.00) 		0.0519
(1.00) 		0.78
(1.00) 		0.781
(1.00)
9q gain 64 (11%) 511 0.47
(1.00) 		0.857
(1.00) 		0.214
(1.00) 		0.433
(1.00) 		0.187
(1.00) 		0.226
(1.00) 		0.0965
(1.00) 		0.0677
(1.00) 		0.408
(1.00) 		0.739
(1.00)
10p gain 28 (5%) 547 0.0804
(1.00) 		1
(1.00) 		0.00981
(1.00) 		0.0125
(1.00) 		0.887
(1.00) 		0.835
(1.00) 		0.449
(1.00) 		0.674
(1.00) 		0.616
(1.00) 		0.496
(1.00)
10q gain 13 (2%) 562 0.689
(1.00) 		0.595
(1.00) 		0.193
(1.00) 		0.0437
(1.00) 		0.721
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.795
(1.00) 		0.694
(1.00) 		0.902
(1.00)
12p gain 93 (16%) 482 0.354
(1.00) 		0.872
(1.00) 		0.256
(1.00) 		0.0171
(1.00) 		0.556
(1.00) 		0.142
(1.00) 		0.0536
(1.00) 		0.0665
(1.00) 		0.22
(1.00) 		0.112
(1.00)
12q gain 78 (14%) 497 0.233
(1.00) 		0.801
(1.00) 		0.0986
(1.00) 		0.00193
(1.00) 		0.893
(1.00) 		0.145
(1.00) 		0.146
(1.00) 		0.157
(1.00) 		0.222
(1.00) 		0.166
(1.00)
14q gain 19 (3%) 556 0.493
(1.00) 		0.48
(1.00) 		0.0301
(1.00) 		0.709
(1.00) 		0.352
(1.00) 		0.277
(1.00) 		0.169
(1.00) 		0.0699
(1.00) 		1
(1.00) 		0.371
(1.00)
15q gain 7 (1%) 568 0.515
(1.00) 		0.882
(1.00) 		0.0247
(1.00) 		0.0606
(1.00) 		0.87
(1.00) 		0.374
(1.00)
17p gain 13 (2%) 562 0.779
(1.00) 		0.00789
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.373
(1.00) 		0.673
(1.00) 		0.308
(1.00) 		0.48
(1.00) 		0.694
(1.00) 		0.902
(1.00)
18p gain 21 (4%) 554 0.19
(1.00) 		0.014
(1.00) 		0.00061
(0.409) 		0.00955
(1.00) 		0.365
(1.00) 		0.713
(1.00) 		0.0311
(1.00) 		0.00817
(1.00) 		0.568
(1.00) 		0.397
(1.00)
18q gain 12 (2%) 563 0.172
(1.00) 		0.00729
(1.00) 		0.269
(1.00) 		0.314
(1.00) 		0.105
(1.00) 		0.134
(1.00)
21q gain 19 (3%) 556 0.435
(1.00) 		0.401
(1.00) 		0.00268
(1.00) 		0.709
(1.00) 		0.214
(1.00) 		0.219
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.143
(1.00)
22q gain 7 (1%) 568 0.689
(1.00) 		0.00789
(1.00) 		0.234
(1.00) 		0.466
(1.00) 		0.908
(1.00) 		0.493
(1.00) 		0.14
(1.00) 		0.48
(1.00) 		0.459
(1.00) 		0.596
(1.00)
Xq gain 17 (3%) 558 0.145
(1.00) 		0.644
(1.00) 		0.0167
(1.00) 		0.338
(1.00) 		0.141
(1.00) 		0.344
(1.00) 		0.759
(1.00) 		0.869
(1.00) 		0.482
(1.00) 		0.705
(1.00)
1q loss 25 (4%) 550 0.404
(1.00) 		0.0115
(1.00) 		0.0823
(1.00) 		0.0315
(1.00) 		0.65
(1.00) 		0.825
(1.00) 		0.148
(1.00) 		0.332
(1.00) 		0.425
(1.00) 		0.725
(1.00)
2p loss 10 (2%) 565 1
(1.00) 		0.485
(1.00) 		0.0735
(1.00) 		0.00349
(1.00) 		0.78
(1.00) 		0.232
(1.00) 		0.0186
(1.00) 		0.0151
(1.00) 		0.0133
(1.00)
2q loss 8 (1%) 567 0.741
(1.00) 		0.456
(1.00) 		0.548
(1.00) 		0.0792
(1.00) 		0.374
(1.00) 		0.198
(1.00) 		0.0127
(1.00) 		0.0584
(1.00) 		0.0455
(1.00)
3p loss 35 (6%) 540 0.938
(1.00) 		0.451
(1.00) 		0.831
(1.00) 		0.835
(1.00) 		0.927
(1.00) 		0.917
(1.00) 		0.376
(1.00) 		0.89
(1.00) 		0.105
(1.00) 		0.729
(1.00)
3q loss 17 (3%) 558 0.618
(1.00) 		0.736
(1.00) 		0.757
(1.00) 		0.0157
(1.00) 		0.134
(1.00) 		0.44
(1.00) 		0.773
(1.00) 		0.632
(1.00) 		0.74
(1.00) 		0.772
(1.00)
5p loss 34 (6%) 541 0.261
(1.00) 		0.297
(1.00) 		0.000544
(0.366) 		0.0341
(1.00) 		0.306
(1.00) 		0.505
(1.00) 		0.787
(1.00) 		0.88
(1.00) 		0.969
(1.00) 		0.829
(1.00)
6p loss 18 (3%) 557 0.11
(1.00) 		0.0962
(1.00) 		0.026
(1.00) 		0.277
(1.00) 		0.476
(1.00) 		0.855
(1.00) 		0.0723
(1.00) 		0.149
(1.00) 		0.602
(1.00) 		0.923
(1.00)
6q loss 33 (6%) 542 0.452
(1.00) 		0.433
(1.00) 		0.0983
(1.00) 		1
(1.00) 		0.0928
(1.00) 		0.668
(1.00) 		0.247
(1.00) 		0.457
(1.00) 		0.262
(1.00) 		0.298
(1.00)
7q loss 3 (1%) 572 0.212
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.764
(1.00) 		1
(1.00)
8q loss 12 (2%) 563 0.602
(1.00) 		0.741
(1.00) 		0.0828
(1.00) 		0.58
(1.00) 		0.0207
(1.00) 		0.6
(1.00) 		0.221
(1.00) 		0.226
(1.00) 		0.159
(1.00) 		0.271
(1.00)
10p loss 40 (7%) 535 0.884
(1.00) 		0.521
(1.00) 		0.000862
(0.577) 		0.419
(1.00) 		0.0821
(1.00) 		0.621
(1.00) 		0.954
(1.00) 		0.262
(1.00) 		0.132
(1.00) 		0.591
(1.00)
11p loss 40 (7%) 535 0.745
(1.00) 		0.948
(1.00) 		0.00977
(1.00) 		0.706
(1.00) 		0.179
(1.00) 		0.277
(1.00) 		0.0808
(1.00) 		0.39
(1.00) 		0.113
(1.00) 		0.359
(1.00)
11q loss 51 (9%) 524 0.975
(1.00) 		0.952
(1.00) 		0.00166
(1.00) 		0.232
(1.00) 		0.841
(1.00) 		0.25
(1.00) 		0.253
(1.00) 		0.178
(1.00) 		0.129
(1.00) 		0.835
(1.00)
13q loss 12 (2%) 563 0.294
(1.00) 		0.115
(1.00) 		0.0495
(1.00) 		0.226
(1.00) 		0.425
(1.00) 		0.0932
(1.00) 		0.28
(1.00) 		0.232
(1.00) 		0.726
(1.00) 		0.403
(1.00)
16p loss 15 (3%) 560 0.254
(1.00) 		0.349
(1.00) 		0.0995
(1.00) 		0.226
(1.00) 		0.57
(1.00) 		0.646
(1.00) 		0.441
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.911
(1.00)
16q loss 17 (3%) 558 0.0132
(1.00) 		0.194
(1.00) 		0.00221
(1.00) 		0.492
(1.00) 		0.526
(1.00) 		0.758
(1.00) 		0.739
(1.00) 		0.831
(1.00) 		0.134
(1.00) 		0.257
(1.00)
17q loss 45 (8%) 530 0.776
(1.00) 		0.441
(1.00) 		0.0023
(1.00) 		0.857
(1.00) 		0.923
(1.00) 		0.97
(1.00) 		0.253
(1.00) 		0.121
(1.00) 		0.116
(1.00) 		0.635
(1.00)
Xq loss 11 (2%) 564 0.764
(1.00) 		0.84
(1.00) 		0.339
(1.00) 		0.446
(1.00) 		0.0148
(1.00) 		0.402
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.515
(1.00) 		0.652
(1.00)
'2p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.17

Table S1.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
2P GAIN MUTATED 28 9 3
2P GAIN WILD-TYPE 115 104 88

Figure S1.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.82e-06 (Fisher's exact test), Q value = 0.0041

Table S2.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
2Q GAIN MUTATED 28 8 1
2Q GAIN WILD-TYPE 115 105 90

Figure S2.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'3p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.12

Table S3.  Gene #5: '3p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
3P GAIN MUTATED 25 7 4 0
3P GAIN WILD-TYPE 175 227 96 41

Figure S3.  Get High-res Image Gene #5: '3p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3q gain mutation analysis' versus 'CN_CNMF'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.0018

Table S4.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
3Q GAIN MUTATED 35 7 9 2
3Q GAIN WILD-TYPE 165 227 91 39

Figure S4.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p gain mutation analysis' versus 'CN_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0011

Table S5.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
6P GAIN MUTATED 46 15 8 8
6P GAIN WILD-TYPE 154 219 92 33

Figure S5.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 7.47e-07 (Fisher's exact test), Q value = 0.00053

Table S6.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
6Q GAIN MUTATED 43 12 8 8
6Q GAIN WILD-TYPE 157 222 92 33

Figure S6.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'MRNA_CNMF'

P value = 0.000291 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
7P GAIN MUTATED 38 12 35 10
7P GAIN WILD-TYPE 25 33 35 29

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

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.89e-21 (Fisher's exact test), Q value = 1.4e-18

Table S8.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
7P GAIN MUTATED 144 62 59 25
7P GAIN WILD-TYPE 56 172 41 16

Figure S8.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.29e-07 (Fisher's exact test), Q value = 0.00052

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
7P GAIN MUTATED 102 52 36
7P GAIN WILD-TYPE 41 61 55

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

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.72e-07 (Fisher's exact test), Q value = 0.00041

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
7P GAIN MUTATED 62 16 20 20
7P GAIN WILD-TYPE 32 42 47 16

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

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.18e-07 (Fisher's exact test), Q value = 0.00037

Table S11.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
7P GAIN MUTATED 15 92 11
7P GAIN WILD-TYPE 44 62 31

Figure S11.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 6.95e-16 (Fisher's exact test), Q value = 5.2e-13

Table S12.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
7Q GAIN MUTATED 126 56 52 21
7Q GAIN WILD-TYPE 74 178 48 20

Figure S12.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.61e-06 (Fisher's exact test), Q value = 0.006

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
7Q GAIN MUTATED 88 47 28
7Q GAIN WILD-TYPE 55 66 63

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

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.49e-07 (Fisher's exact test), Q value = 0.00053

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
7Q GAIN MUTATED 56 12 19 20
7Q GAIN WILD-TYPE 38 46 48 16

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

'7q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.39e-06 (Fisher's exact test), Q value = 0.0059

Table S15.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
7Q GAIN MUTATED 13 83 11
7Q GAIN WILD-TYPE 46 71 31

Figure S15.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 1e-08 (Fisher's exact test), Q value = 7.3e-06

Table S16.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8P GAIN MUTATED 26 29 39 14
8P GAIN WILD-TYPE 174 205 61 27

Figure S16.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 1.06e-33 (Fisher's exact test), Q value = 8e-31

Table S17.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8Q GAIN MUTATED 78 44 88 25
8Q GAIN WILD-TYPE 122 190 12 16

Figure S17.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p gain mutation analysis' versus 'CN_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.012

Table S18.  Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
11P GAIN MUTATED 26 4 5 4
11P GAIN WILD-TYPE 174 230 95 37

Figure S18.  Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S19.  Gene #21: '11p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
11P GAIN MUTATED 20 2 3
11P GAIN WILD-TYPE 123 111 88

Figure S19.  Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00094

Table S20.  Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
11Q GAIN MUTATED 24 3 5 7
11Q GAIN WILD-TYPE 176 231 95 34

Figure S20.  Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.31e-07 (Fisher's exact test), Q value = 9.4e-05

Table S21.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
13Q GAIN MUTATED 46 13 49 13
13Q GAIN WILD-TYPE 17 32 21 26

Figure S21.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'13q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.67e-05 (Fisher's exact test), Q value = 0.019

Table S22.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 61 112
13Q GAIN MUTATED 30 19 72
13Q GAIN WILD-TYPE 14 42 40

Figure S22.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 1.62e-37 (Fisher's exact test), Q value = 1.2e-34

Table S23.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
13Q GAIN MUTATED 175 64 56 19
13Q GAIN WILD-TYPE 25 170 44 22

Figure S23.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.71e-08 (Fisher's exact test), Q value = 1.2e-05

Table S24.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
13Q GAIN MUTATED 106 46 40
13Q GAIN WILD-TYPE 37 67 51

Figure S24.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.48e-08 (Fisher's exact test), Q value = 4e-05

Table S25.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
13Q GAIN MUTATED 68 18 24 24
13Q GAIN WILD-TYPE 26 40 43 12

Figure S25.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.75e-10 (Fisher's exact test), Q value = 2.7e-07

Table S26.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
13Q GAIN MUTATED 14 106 14
13Q GAIN WILD-TYPE 45 48 28

Figure S26.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 9.4e-14

Table S27.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
16P GAIN MUTATED 66 7 16 7
16P GAIN WILD-TYPE 134 227 84 34

Figure S27.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 3.02e-18 (Fisher's exact test), Q value = 2.3e-15

Table S28.  Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
16Q GAIN MUTATED 68 6 16 6
16Q GAIN WILD-TYPE 132 228 84 35

Figure S28.  Get High-res Image Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.18

Table S29.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
17Q GAIN MUTATED 36 13 15 3
17Q GAIN WILD-TYPE 164 221 85 38

Figure S29.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.08

Table S30.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
17Q GAIN MUTATED 19 1 2 6
17Q GAIN WILD-TYPE 75 57 65 30

Figure S30.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.04

Table S31.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19P GAIN MUTATED 29 7 10 6
19P GAIN WILD-TYPE 171 227 90 35

Figure S31.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000262 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #35: '19q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
19Q GAIN MUTATED 0 22 9
19Q GAIN WILD-TYPE 59 132 33

Figure S32.  Get High-res Image Gene #35: '19q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain mutation analysis' versus 'MRNA_CNMF'

P value = 5.9e-05 (Fisher's exact test), Q value = 0.041

Table S33.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
20P GAIN MUTATED 39 14 48 14
20P GAIN WILD-TYPE 24 31 22 25

Figure S33.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.89e-08 (Fisher's exact test), Q value = 4.3e-05

Table S34.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 61 112
20P GAIN MUTATED 32 14 69
20P GAIN WILD-TYPE 12 47 43

Figure S34.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 4.25e-22 (Fisher's exact test), Q value = 3.2e-19

Table S35.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20P GAIN MUTATED 130 67 52 39
20P GAIN WILD-TYPE 70 167 48 2

Figure S35.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.053

Table S36.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
20P GAIN MUTATED 89 42 37
20P GAIN WILD-TYPE 54 71 54

Figure S36.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.0085

Table S37.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
20P GAIN MUTATED 61 16 29 24
20P GAIN WILD-TYPE 33 42 38 12

Figure S37.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-10 (Fisher's exact test), Q value = 3e-07

Table S38.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
20P GAIN MUTATED 10 101 19
20P GAIN WILD-TYPE 49 53 23

Figure S38.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNA_CNMF'

P value = 6.95e-19 (Fisher's exact test), Q value = 5.2e-16

Table S39.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
20Q GAIN MUTATED 62 15 63 18
20Q GAIN WILD-TYPE 1 30 7 21

Figure S39.  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 = 2.93e-16 (Fisher's exact test), Q value = 2.2e-13

Table S40.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 61 112
20Q GAIN MUTATED 40 19 99
20Q GAIN WILD-TYPE 4 42 13

Figure S40.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 2.22e-46 (Fisher's exact test), Q value = 1.7e-43

Table S41.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20Q GAIN MUTATED 193 91 79 40
20Q GAIN WILD-TYPE 7 143 21 1

Figure S41.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.04e-13 (Fisher's exact test), Q value = 6.6e-10

Table S42.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
20Q GAIN MUTATED 128 57 53
20Q GAIN WILD-TYPE 15 56 38

Figure S42.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.42e-20 (Fisher's exact test), Q value = 1.8e-17

Table S43.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
20Q GAIN MUTATED 91 20 36 33
20Q GAIN WILD-TYPE 3 38 31 3

Figure S43.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.52e-24 (Fisher's exact test), Q value = 4.2e-21

Table S44.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
20Q GAIN MUTATED 13 142 25
20Q GAIN WILD-TYPE 46 12 17

Figure S44.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0053

Table S45.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
1P LOSS MUTATED 39 14 6 9
1P LOSS WILD-TYPE 161 220 94 32

Figure S45.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.027

Table S46.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
1P LOSS MUTATED 29 4 6
1P LOSS WILD-TYPE 114 109 85

Figure S46.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 5.5e-11 (Fisher's exact test), Q value = 4e-08

Table S47.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
4P LOSS MUTATED 70 21 17 14
4P LOSS WILD-TYPE 130 213 83 27

Figure S47.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 3.18e-12 (Fisher's exact test), Q value = 2.3e-09

Table S48.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
4Q LOSS MUTATED 68 16 17 12
4Q LOSS WILD-TYPE 132 218 83 29

Figure S48.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 5.53e-07 (Fisher's exact test), Q value = 4e-04

Table S49.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
5Q LOSS MUTATED 31 6 17 6
5Q LOSS WILD-TYPE 169 228 83 35

Figure S49.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 1.14e-18 (Fisher's exact test), Q value = 8.5e-16

Table S50.  Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8P LOSS MUTATED 88 17 31 9
8P LOSS WILD-TYPE 112 217 69 32

Figure S50.  Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.029

Table S51.  Gene #54: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
8P LOSS MUTATED 38 6 13 15
8P LOSS WILD-TYPE 56 52 54 21

Figure S51.  Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.02

Table S52.  Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
9P LOSS MUTATED 26 4 7 2
9P LOSS WILD-TYPE 174 230 93 39

Figure S52.  Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0014

Table S53.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
9Q LOSS MUTATED 28 4 3 2
9Q LOSS WILD-TYPE 172 230 97 39

Figure S53.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.024

Table S54.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
9Q LOSS MUTATED 19 1 2
9Q LOSS WILD-TYPE 124 112 89

Figure S54.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.001

Table S55.  Gene #59: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
10Q LOSS MUTATED 16 6 13 11
10Q LOSS WILD-TYPE 184 228 87 30

Figure S55.  Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12p loss mutation analysis' versus 'CN_CNMF'

P value = 5.42e-07 (Fisher's exact test), Q value = 0.00039

Table S56.  Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
12P LOSS MUTATED 21 2 3 7
12P LOSS WILD-TYPE 179 232 97 34

Figure S56.  Get High-res Image Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q loss mutation analysis' versus 'CN_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00079

Table S57.  Gene #63: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
12Q LOSS MUTATED 19 2 1 6
12Q LOSS WILD-TYPE 181 232 99 35

Figure S57.  Get High-res Image Gene #63: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'MRNA_CNMF'

P value = 3.41e-06 (Fisher's exact test), Q value = 0.0024

Table S58.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
14Q LOSS MUTATED 29 7 26 2
14Q LOSS WILD-TYPE 34 38 44 37

Figure S58.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'14q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00015

Table S59.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 61 112
14Q LOSS MUTATED 20 3 41
14Q LOSS WILD-TYPE 24 58 71

Figure S59.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 1.12e-31 (Fisher's exact test), Q value = 8.5e-29

Table S60.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
14Q LOSS MUTATED 109 20 6 8
14Q LOSS WILD-TYPE 91 214 94 33

Figure S60.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.97e-07 (Fisher's exact test), Q value = 0.00014

Table S61.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
14Q LOSS MUTATED 53 12 12
14Q LOSS WILD-TYPE 90 101 79

Figure S61.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'RPPA_CNMF'

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

Table S62.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 158 18 120
14Q LOSS MUTATED 26 57 1 16
14Q LOSS WILD-TYPE 68 101 17 104

Figure S62.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0076

Table S63.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
14Q LOSS MUTATED 41 6 12 13
14Q LOSS WILD-TYPE 53 52 55 23

Figure S63.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.09e-07 (Fisher's exact test), Q value = 0.00022

Table S64.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
14Q LOSS MUTATED 5 62 5
14Q LOSS WILD-TYPE 54 92 37

Figure S64.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 2.09e-24 (Fisher's exact test), Q value = 1.6e-21

Table S65.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
15Q LOSS MUTATED 88 16 26 26
15Q LOSS WILD-TYPE 112 218 74 15

Figure S65.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.11

Table S66.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
17P LOSS MUTATED 38 14 41 10
17P LOSS WILD-TYPE 25 31 29 29

Figure S66.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 5.49e-22 (Fisher's exact test), Q value = 4.1e-19

Table S67.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
17P LOSS MUTATED 128 46 57 21
17P LOSS WILD-TYPE 72 188 43 20

Figure S67.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.44e-07 (Fisher's exact test), Q value = 0.00018

Table S68.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
17P LOSS MUTATED 86 35 27
17P LOSS WILD-TYPE 57 78 64

Figure S68.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.13

Table S69.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
17P LOSS MUTATED 15 87 18
17P LOSS WILD-TYPE 44 67 24

Figure S69.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.45e-15 (Fisher's exact test), Q value = 1.8e-12

Table S70.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
18P LOSS MUTATED 55 11 52 10
18P LOSS WILD-TYPE 8 34 18 29

Figure S70.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.18e-12 (Fisher's exact test), Q value = 1.6e-09

Table S71.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 61 112
18P LOSS MUTATED 37 13 78
18P LOSS WILD-TYPE 7 48 34

Figure S71.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 4.26e-47 (Fisher's exact test), Q value = 3.2e-44

Table S72.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
18P LOSS MUTATED 176 53 62 33
18P LOSS WILD-TYPE 24 181 38 8

Figure S72.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.33e-19 (Fisher's exact test), Q value = 3.2e-16

Table S73.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
18P LOSS MUTATED 120 38 35
18P LOSS WILD-TYPE 23 75 56

Figure S73.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.98e-14 (Fisher's exact test), Q value = 5.2e-11

Table S74.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
18P LOSS MUTATED 78 17 26 29
18P LOSS WILD-TYPE 16 41 41 7

Figure S74.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.3e-14 (Fisher's exact test), Q value = 5.4e-11

Table S75.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
18P LOSS MUTATED 12 118 20
18P LOSS WILD-TYPE 47 36 22

Figure S75.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.08e-13 (Fisher's exact test), Q value = 3e-10

Table S76.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 45 70 39
18Q LOSS MUTATED 56 15 54 12
18Q LOSS WILD-TYPE 7 30 16 27

Figure S76.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.32e-12 (Fisher's exact test), Q value = 3.9e-09

Table S77.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 61 112
18Q LOSS MUTATED 38 16 83
18Q LOSS WILD-TYPE 6 45 29

Figure S77.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 6.8e-51 (Fisher's exact test), Q value = 5.2e-48

Table S78.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
18Q LOSS MUTATED 180 59 77 36
18Q LOSS WILD-TYPE 20 175 23 5

Figure S78.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.03e-21 (Fisher's exact test), Q value = 6e-18

Table S79.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
18Q LOSS MUTATED 128 45 38
18Q LOSS WILD-TYPE 15 68 53

Figure S79.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.19e-11 (Fisher's exact test), Q value = 6.7e-08

Table S80.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 94 58 67 36
18Q LOSS MUTATED 80 23 30 29
18Q LOSS WILD-TYPE 14 35 37 7

Figure S80.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.51e-14 (Fisher's exact test), Q value = 4.1e-11

Table S81.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 154 42
18Q LOSS MUTATED 14 124 24
18Q LOSS WILD-TYPE 45 30 18

Figure S81.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss mutation analysis' versus 'CN_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.01

Table S82.  Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19P LOSS MUTATED 7 1 5 7
19P LOSS WILD-TYPE 193 233 95 34

Figure S82.  Get High-res Image Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.16

Table S83.  Gene #74: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19Q LOSS MUTATED 6 1 6 5
19Q LOSS WILD-TYPE 194 233 94 36

Figure S83.  Get High-res Image Gene #74: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 4.56e-07 (Fisher's exact test), Q value = 0.00033

Table S84.  Gene #75: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20P LOSS MUTATED 27 5 15 0
20P LOSS WILD-TYPE 173 229 85 41

Figure S84.  Get High-res Image Gene #75: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.025

Table S85.  Gene #76: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
21Q LOSS MUTATED 58 28 16 12
21Q LOSS WILD-TYPE 142 206 84 29

Figure S85.  Get High-res Image Gene #76: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 7.8e-14 (Fisher's exact test), Q value = 5.7e-11

Table S86.  Gene #77: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
22Q LOSS MUTATED 76 20 13 13
22Q LOSS WILD-TYPE 124 214 87 28

Figure S86.  Get High-res Image Gene #77: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 575

  • Number of significantly arm-level cnvs = 78

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] 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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