Correlation between copy number variations of arm-level result and molecular subtypes
Colon/Rectal Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1J96493
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon/Rectal Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1J96493
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, 89 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_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 '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',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 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'.

  • 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',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  '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'.

  • 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', and 'MRNASEQ_CNMF'.

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

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

  • 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, 89 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
20q gain 0 (0%) 172 1.23e-18
(9.18e-16) 		2.68e-17
(1.99e-14) 		2.22e-46
(1.68e-43) 		9.04e-13
(6.64e-10) 		0.000311
(0.209) 		0.000133
(0.0909) 		9.03e-18
(6.72e-15) 		1.13e-13
(8.32e-11) 		0.463
(1.00) 		0.101
(1.00)
13q gain 0 (0%) 261 1e-07
(7.24e-05) 		2.44e-05
(0.0169) 		1.62e-37
(1.23e-34) 		1.71e-08
(1.24e-05) 		0.0129
(1.00) 		0.0683
(1.00) 		8.54e-09
(6.2e-06) 		6.4e-07
(0.000455) 		0.01
(1.00) 		0.45
(1.00)
20p gain 0 (0%) 287 6.06e-05
(0.0416) 		6.71e-09
(4.88e-06) 		4.25e-22
(3.19e-19) 		7.67e-05
(0.0526) 		0.00725
(1.00) 		0.0222
(1.00) 		3.2e-07
(0.000229) 		3.2e-07
(0.000229) 		0.625
(1.00) 		0.472
(1.00)
14q loss 0 (0%) 432 4.76e-06
(0.00334) 		2.49e-07
(0.000178) 		1.12e-31
(8.43e-29) 		1.97e-07
(0.000142) 		0.000364
(0.244) 		0.012
(1.00) 		1.73e-07
(0.000124) 		0.000705
(0.468) 		0.114
(1.00) 		0.709
(1.00)
18p loss 0 (0%) 251 9.87e-15
(7.29e-12) 		8.51e-12
(6.23e-09) 		4.26e-47
(3.23e-44) 		4.33e-19
(3.24e-16) 		0.012
(1.00) 		0.015
(1.00) 		5.39e-16
(3.99e-13) 		2.73e-11
(2e-08) 		0.065
(1.00) 		0.787
(1.00)
18q loss 0 (0%) 223 1.42e-12
(1.04e-09) 		1.96e-11
(1.44e-08) 		6.8e-51
(5.16e-48) 		8.03e-21
(6.02e-18) 		0.0241
(1.00) 		0.0948
(1.00) 		3.96e-16
(2.93e-13) 		3.68e-09
(2.68e-06) 		0.00938
(1.00) 		0.378
(1.00)
7p gain 0 (0%) 285 0.000443
(0.297) 		0.00887
(1.00) 		1.89e-21
(1.42e-18) 		7.29e-07
(0.000518) 		0.22
(1.00) 		0.0313
(1.00) 		3.72e-08
(2.69e-05) 		9.54e-05
(0.0653) 		0.0703
(1.00) 		0.0304
(1.00)
7q gain 0 (0%) 320 0.000644
(0.428) 		0.0134
(1.00) 		6.95e-16
(5.14e-13) 		8.61e-06
(0.00601) 		0.777
(1.00) 		0.18
(1.00) 		8.79e-07
(0.000623) 		1.24e-05
(0.00862) 		0.245
(1.00) 		0.155
(1.00)
17p loss 0 (0%) 323 0.000242
(0.164) 		0.00165
(1.00) 		5.49e-22
(4.12e-19) 		2.44e-07
(0.000175) 		0.317
(1.00) 		0.486
(1.00) 		3.25e-06
(0.00228) 		0.000795
(0.527) 		0.027
(1.00) 		0.497
(1.00)
2p gain 0 (0%) 515 0.0169
(1.00) 		0.00499
(1.00) 		0.00816
(1.00) 		0.000256
(0.172) 		0.0735
(1.00) 		0.357
(1.00) 		0.000224
(0.152) 		0.000137
(0.0937) 		0.216
(1.00) 		0.0209
(1.00)
11p gain 0 (0%) 536 0.063
(1.00) 		0.654
(1.00) 		1.71e-05
(0.0119) 		0.000214
(0.146) 		0.826
(1.00) 		0.764
(1.00) 		0.0491
(1.00) 		0.000153
(0.104) 		0.246
(1.00) 		0.882
(1.00)
2q gain 0 (0%) 516 0.00368
(1.00) 		0.00391
(1.00) 		0.00101
(0.664) 		5.82e-06
(0.00407) 		0.209
(1.00) 		0.806
(1.00) 		0.000234
(0.158) 		0.000824
(0.546) 		0.251
(1.00) 		0.0504
(1.00)
17q gain 0 (0%) 508 0.0455
(1.00) 		0.0639
(1.00) 		0.000269
(0.181) 		0.00143
(0.938) 		0.649
(1.00) 		0.0748
(1.00) 		1.47e-05
(0.0102) 		0.00195
(1.00) 		0.0785
(1.00) 		0.354
(1.00)
1p loss 0 (0%) 507 0.0784
(1.00) 		0.00327
(1.00) 		7.55e-06
(0.00528) 		3.84e-05
(0.0264) 		0.984
(1.00) 		0.821
(1.00) 		0.0764
(1.00) 		0.00823
(1.00) 		0.193
(1.00) 		0.62
(1.00)
9q loss 0 (0%) 538 0.0484
(1.00) 		0.0135
(1.00) 		1.95e-06
(0.00138) 		3.42e-05
(0.0236) 		0.692
(1.00) 		0.209
(1.00) 		0.0214
(1.00) 		0.0167
(1.00) 		0.0491
(1.00) 		0.82
(1.00)
15q loss 0 (0%) 419 0.0144
(1.00) 		0.0117
(1.00) 		2.09e-24
(1.57e-21) 		0.0158
(1.00) 		0.303
(1.00) 		0.832
(1.00) 		1.19e-05
(0.00829) 		0.000572
(0.381) 		0.368
(1.00) 		0.246
(1.00)
3p gain 0 (0%) 539 0.126
(1.00) 		0.433
(1.00) 		0.000181
(0.123) 		0.257
(1.00) 		0.374
(1.00) 		0.77
(1.00) 		0.26
(1.00) 		0.885
(1.00) 		0.208
(1.00) 		0.366
(1.00)
3q gain 0 (0%) 522 0.22
(1.00) 		0.0947
(1.00) 		2.49e-06
(0.00175) 		0.0353
(1.00) 		0.215
(1.00) 		0.655
(1.00) 		0.075
(1.00) 		0.588
(1.00) 		0.111
(1.00) 		0.544
(1.00)
6p gain 0 (0%) 498 0.246
(1.00) 		0.00492
(1.00) 		1.55e-06
(0.00109) 		0.401
(1.00) 		0.704
(1.00) 		0.12
(1.00) 		0.0227
(1.00) 		0.227
(1.00) 		0.848
(1.00) 		0.392
(1.00)
6q gain 0 (0%) 504 0.375
(1.00) 		0.0199
(1.00) 		7.47e-07
(0.000531) 		0.159
(1.00) 		0.317
(1.00) 		0.0418
(1.00) 		0.0607
(1.00) 		0.575
(1.00) 		0.749
(1.00) 		0.251
(1.00)
8p gain 0 (0%) 467 0.946
(1.00) 		0.746
(1.00) 		1e-08
(7.27e-06) 		0.433
(1.00) 		0.28
(1.00) 		0.215
(1.00) 		0.181
(1.00) 		0.44
(1.00) 		0.49
(1.00) 		0.891
(1.00)
8q gain 0 (0%) 340 0.0693
(1.00) 		0.621
(1.00) 		1.06e-33
(7.98e-31) 		0.00942
(1.00) 		0.15
(1.00) 		0.33
(1.00) 		0.0011
(0.721) 		0.0265
(1.00) 		0.459
(1.00) 		0.633
(1.00)
11q gain 0 (0%) 536 0.102
(1.00) 		0.0316
(1.00) 		1.33e-06
(0.000939) 		0.000911
(0.601) 		0.497
(1.00) 		0.651
(1.00) 		0.0356
(1.00) 		0.00526
(1.00) 		0.559
(1.00) 		0.406
(1.00)
16p gain 0 (0%) 479 0.0975
(1.00) 		0.0844
(1.00) 		1.26e-16
(9.37e-14) 		0.0108
(1.00) 		0.941
(1.00) 		0.0295
(1.00) 		0.0228
(1.00) 		0.136
(1.00) 		0.577
(1.00) 		0.347
(1.00)
16q gain 0 (0%) 479 0.0433
(1.00) 		0.0683
(1.00) 		3.02e-18
(2.25e-15) 		0.00391
(1.00) 		0.991
(1.00) 		0.0182
(1.00) 		0.0198
(1.00) 		0.0602
(1.00) 		0.465
(1.00) 		0.277
(1.00)
19p gain 0 (0%) 523 0.167
(1.00) 		0.228
(1.00) 		5.84e-05
(0.0401) 		0.0236
(1.00) 		0.598
(1.00) 		0.0285
(1.00) 		0.423
(1.00) 		0.474
(1.00) 		0.718
(1.00) 		0.745
(1.00)
4p loss 0 (0%) 453 0.106
(1.00) 		0.105
(1.00) 		5.5e-11
(4.01e-08) 		0.0036
(1.00) 		0.693
(1.00) 		0.889
(1.00) 		0.0062
(1.00) 		0.0572
(1.00) 		0.045
(1.00) 		0.769
(1.00)
4q loss 0 (0%) 462 0.0962
(1.00) 		0.0638
(1.00) 		3.18e-12
(2.33e-09) 		0.00168
(1.00) 		0.606
(1.00) 		0.81
(1.00) 		0.00213
(1.00) 		0.0535
(1.00) 		0.0122
(1.00) 		0.564
(1.00)
5q loss 0 (0%) 515 0.0163
(1.00) 		0.0917
(1.00) 		5.53e-07
(0.000394) 		0.0816
(1.00) 		0.186
(1.00) 		0.812
(1.00) 		0.0211
(1.00) 		0.0985
(1.00) 		0.963
(1.00) 		0.579
(1.00)
8p loss 0 (0%) 430 0.0117
(1.00) 		0.00463
(1.00) 		1.14e-18
(8.53e-16) 		0.000373
(0.25) 		0.28
(1.00) 		0.0393
(1.00) 		0.11
(1.00) 		0.152
(1.00) 		0.515
(1.00) 		0.73
(1.00)
9p loss 0 (0%) 536 0.564
(1.00) 		0.12
(1.00) 		2.9e-05
(0.02) 		0.00158
(1.00) 		0.247
(1.00) 		0.147
(1.00) 		0.102
(1.00) 		0.0221
(1.00) 		0.127
(1.00) 		1
(1.00)
10q loss 0 (0%) 529 0.34
(1.00) 		0.568
(1.00) 		1.44e-06
(0.00101) 		0.153
(1.00) 		0.0204
(1.00) 		0.772
(1.00) 		0.102
(1.00) 		0.231
(1.00) 		0.714
(1.00) 		0.811
(1.00)
12p loss 0 (0%) 542 0.114
(1.00) 		0.264
(1.00) 		5.42e-07
(0.000387) 		0.258
(1.00) 		0.694
(1.00) 		0.373
(1.00) 		0.201
(1.00) 		0.46
(1.00) 		0.541
(1.00) 		0.222
(1.00)
12q loss 0 (0%) 547 0.131
(1.00) 		0.0524
(1.00) 		1.11e-06
(0.000784) 		0.522
(1.00) 		0.885
(1.00) 		0.619
(1.00) 		0.143
(1.00) 		0.189
(1.00) 		0.616
(1.00) 		0.681
(1.00)
19p loss 0 (0%) 555 0.49
(1.00) 		0.598
(1.00) 		1.46e-05
(0.0102) 		0.0244
(1.00) 		0.579
(1.00) 		0.705
(1.00) 		0.00155
(1.00) 		0.00289
(1.00) 		0.235
(1.00) 		0.371
(1.00)
19q loss 0 (0%) 557 0.49
(1.00) 		0.598
(1.00) 		0.000235
(0.159) 		0.0965
(1.00) 		0.625
(1.00) 		0.912
(1.00) 		0.00155
(1.00) 		0.00289
(1.00) 		0.424
(1.00) 		0.0976
(1.00)
20p loss 0 (0%) 528 0.169
(1.00) 		0.18
(1.00) 		4.56e-07
(0.000326) 		0.039
(1.00) 		0.77
(1.00) 		0.365
(1.00) 		0.577
(1.00) 		0.391
(1.00) 		0.554
(1.00) 		0.486
(1.00)
21q loss 0 (0%) 461 0.0588
(1.00) 		0.319
(1.00) 		3.64e-05
(0.0251) 		0.0555
(1.00) 		0.328
(1.00) 		0.31
(1.00) 		0.235
(1.00) 		0.392
(1.00) 		0.118
(1.00) 		0.342
(1.00)
22q loss 0 (0%) 453 0.0679
(1.00) 		0.0038
(1.00) 		7.8e-14
(5.75e-11) 		0.352
(1.00) 		0.419
(1.00) 		0.264
(1.00) 		0.0676
(1.00) 		0.0646
(1.00) 		0.0662
(1.00) 		0.1
(1.00)
1p gain 0 (0%) 560 0.406
(1.00) 		0.102
(1.00) 		0.932
(1.00) 		0.497
(1.00) 		0.497
(1.00) 		0.128
(1.00) 		0.178
(1.00) 		0.33
(1.00) 		0.111
(1.00) 		0.911
(1.00)
1q gain 0 (0%) 495 0.484
(1.00) 		0.855
(1.00) 		0.0158
(1.00) 		0.926
(1.00) 		0.255
(1.00) 		0.15
(1.00) 		0.128
(1.00) 		0.0758
(1.00) 		0.0729
(1.00) 		0.978
(1.00)
4p gain 0 (0%) 569 0.0622
(1.00) 		0.226
(1.00) 		0.184
(1.00) 		0.339
(1.00) 		0.137
(1.00) 		0.0525
(1.00)
4q gain 0 (0%) 568 0.704
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.787
(1.00) 		0.732
(1.00) 		0.645
(1.00) 		0.383
(1.00) 		0.809
(1.00)
5p gain 0 (0%) 515 0.113
(1.00) 		0.708
(1.00) 		0.0015
(0.985) 		0.178
(1.00) 		0.795
(1.00) 		0.863
(1.00) 		0.401
(1.00) 		0.4
(1.00) 		0.784
(1.00) 		0.354
(1.00)
5q gain 0 (0%) 542 0.457
(1.00) 		0.534
(1.00) 		0.00356
(1.00) 		0.356
(1.00) 		0.742
(1.00) 		0.557
(1.00) 		0.73
(1.00) 		0.446
(1.00) 		0.818
(1.00) 		0.483
(1.00)
9p gain 0 (0%) 496 0.42
(1.00) 		0.843
(1.00) 		0.178
(1.00) 		0.79
(1.00) 		0.91
(1.00) 		0.204
(1.00) 		0.539
(1.00) 		0.855
(1.00) 		0.78
(1.00) 		0.781
(1.00)
9q gain 0 (0%) 511 0.476
(1.00) 		0.923
(1.00) 		0.214
(1.00) 		0.433
(1.00) 		0.612
(1.00) 		0.0336
(1.00) 		0.989
(1.00) 		0.691
(1.00) 		0.408
(1.00) 		0.739
(1.00)
10p gain 0 (0%) 547 0.137
(1.00) 		0.846
(1.00) 		0.00981
(1.00) 		0.0125
(1.00) 		0.673
(1.00) 		0.857
(1.00) 		0.617
(1.00) 		0.0446
(1.00) 		0.616
(1.00) 		0.496
(1.00)
10q gain 0 (0%) 562 0.691
(1.00) 		0.589
(1.00) 		0.193
(1.00) 		0.0437
(1.00) 		0.597
(1.00) 		0.288
(1.00) 		0.448
(1.00) 		0.0762
(1.00) 		0.694
(1.00) 		0.902
(1.00)
12p gain 0 (0%) 482 0.362
(1.00) 		0.818
(1.00) 		0.256
(1.00) 		0.0171
(1.00) 		0.629
(1.00) 		0.205
(1.00) 		0.0232
(1.00) 		0.0134
(1.00) 		0.22
(1.00) 		0.112
(1.00)
12q gain 0 (0%) 497 0.315
(1.00) 		0.721
(1.00) 		0.0986
(1.00) 		0.00193
(1.00) 		0.91
(1.00) 		0.339
(1.00) 		0.0353
(1.00) 		0.0154
(1.00) 		0.222
(1.00) 		0.166
(1.00)
14q gain 0 (0%) 556 0.495
(1.00) 		0.55
(1.00) 		0.0301
(1.00) 		0.709
(1.00) 		0.724
(1.00) 		0.397
(1.00) 		0.0605
(1.00) 		0.048
(1.00) 		1
(1.00) 		0.371
(1.00)
15q gain 0 (0%) 568 0.515
(1.00) 		0.882
(1.00) 		0.133
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.244
(1.00) 		0.87
(1.00) 		0.374
(1.00)
17p gain 0 (0%) 562 0.78
(1.00) 		0.00605
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.552
(1.00) 		0.721
(1.00) 		0.0157
(1.00) 		0.009
(1.00) 		0.694
(1.00) 		0.902
(1.00)
18p gain 0 (0%) 554 0.192
(1.00) 		0.0168
(1.00) 		0.00061
(0.406) 		0.00955
(1.00) 		0.514
(1.00) 		0.897
(1.00) 		0.133
(1.00) 		0.391
(1.00) 		0.568
(1.00) 		0.397
(1.00)
18q gain 0 (0%) 563 0.172
(1.00) 		0.00729
(1.00) 		0.648
(1.00) 		0.468
(1.00) 		0.122
(1.00) 		0.858
(1.00) 		0.105
(1.00) 		0.134
(1.00)
19q gain 0 (0%) 514 0.0123
(1.00) 		0.0249
(1.00) 		0.0122
(1.00) 		0.0715
(1.00) 		0.233
(1.00) 		0.0383
(1.00) 		0.507
(1.00) 		0.512
(1.00) 		0.832
(1.00) 		0.495
(1.00)
21q gain 0 (0%) 556 0.436
(1.00) 		0.381
(1.00) 		0.00268
(1.00) 		0.709
(1.00) 		0.48
(1.00) 		0.0895
(1.00) 		0.619
(1.00) 		0.834
(1.00) 		0.686
(1.00) 		0.143
(1.00)
22q gain 0 (0%) 568 0.691
(1.00) 		0.00605
(1.00) 		0.234
(1.00) 		0.466
(1.00) 		0.685
(1.00) 		0.47
(1.00) 		0.689
(1.00) 		0.499
(1.00) 		0.459
(1.00) 		0.596
(1.00)
Xq gain 0 (0%) 558 0.147
(1.00) 		0.735
(1.00) 		0.0167
(1.00) 		0.338
(1.00) 		0.244
(1.00) 		0.313
(1.00) 		0.846
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.705
(1.00)
1q loss 0 (0%) 550 0.558
(1.00) 		0.0215
(1.00) 		0.0823
(1.00) 		0.0315
(1.00) 		0.825
(1.00) 		0.949
(1.00) 		0.158
(1.00) 		0.324
(1.00) 		0.425
(1.00) 		0.725
(1.00)
2p loss 0 (0%) 565 1
(1.00) 		0.435
(1.00) 		0.0735
(1.00) 		0.0168
(1.00) 		0.658
(1.00) 		0.0151
(1.00) 		0.0133
(1.00)
2q loss 0 (0%) 567 0.741
(1.00) 		0.444
(1.00) 		0.548
(1.00) 		0.157
(1.00) 		0.299
(1.00) 		0.0584
(1.00) 		0.0455
(1.00)
3p loss 0 (0%) 540 0.938
(1.00) 		0.53
(1.00) 		0.831
(1.00) 		0.835
(1.00) 		0.703
(1.00) 		0.536
(1.00) 		0.441
(1.00) 		0.157
(1.00) 		0.105
(1.00) 		0.729
(1.00)
3q loss 0 (0%) 558 0.618
(1.00) 		0.816
(1.00) 		0.757
(1.00) 		0.0157
(1.00) 		0.0903
(1.00) 		0.398
(1.00) 		0.385
(1.00) 		0.184
(1.00) 		0.74
(1.00) 		0.772
(1.00)
5p loss 0 (0%) 541 0.291
(1.00) 		0.433
(1.00) 		0.000544
(0.364) 		0.0341
(1.00) 		0.556
(1.00) 		0.449
(1.00) 		0.234
(1.00) 		0.0352
(1.00) 		0.969
(1.00) 		0.829
(1.00)
6p loss 0 (0%) 557 0.117
(1.00) 		0.0742
(1.00) 		0.026
(1.00) 		0.277
(1.00) 		0.611
(1.00) 		0.641
(1.00) 		0.89
(1.00) 		0.601
(1.00) 		0.602
(1.00) 		0.923
(1.00)
6q loss 0 (0%) 542 0.457
(1.00) 		0.338
(1.00) 		0.0983
(1.00) 		1
(1.00) 		0.132
(1.00) 		0.145
(1.00) 		0.737
(1.00) 		0.677
(1.00) 		0.262
(1.00) 		0.298
(1.00)
7q loss 0 (0%) 572 0.212
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.764
(1.00) 		1
(1.00)
8q loss 0 (0%) 563 0.603
(1.00) 		0.639
(1.00) 		0.0828
(1.00) 		0.58
(1.00) 		0.0237
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.159
(1.00) 		0.271
(1.00)
10p loss 0 (0%) 535 0.704
(1.00) 		0.401
(1.00) 		0.000862
(0.57) 		0.419
(1.00) 		0.053
(1.00) 		0.682
(1.00) 		0.409
(1.00) 		0.532
(1.00) 		0.132
(1.00) 		0.591
(1.00)
11p loss 0 (0%) 535 0.797
(1.00) 		1
(1.00) 		0.00977
(1.00) 		0.706
(1.00) 		0.322
(1.00) 		0.201
(1.00) 		0.0716
(1.00) 		0.0838
(1.00) 		0.113
(1.00) 		0.359
(1.00)
11q loss 0 (0%) 524 0.975
(1.00) 		0.858
(1.00) 		0.00166
(1.00) 		0.232
(1.00) 		0.731
(1.00) 		0.292
(1.00) 		0.0997
(1.00) 		0.509
(1.00) 		0.129
(1.00) 		0.835
(1.00)
13q loss 0 (0%) 563 0.324
(1.00) 		0.108
(1.00) 		0.0495
(1.00) 		0.226
(1.00) 		0.0716
(1.00) 		0.108
(1.00) 		0.236
(1.00) 		0.668
(1.00) 		0.726
(1.00) 		0.403
(1.00)
16p loss 0 (0%) 560 0.256
(1.00) 		0.598
(1.00) 		0.0995
(1.00) 		0.226
(1.00) 		0.561
(1.00) 		0.646
(1.00) 		0.589
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.911
(1.00)
16q loss 0 (0%) 558 0.0131
(1.00) 		0.506
(1.00) 		0.00221
(1.00) 		0.492
(1.00) 		0.459
(1.00) 		0.748
(1.00) 		0.0911
(1.00) 		0.121
(1.00) 		0.134
(1.00) 		0.257
(1.00)
17q loss 0 (0%) 530 0.762
(1.00) 		0.558
(1.00) 		0.0023
(1.00) 		0.857
(1.00) 		0.576
(1.00) 		0.587
(1.00) 		0.101
(1.00) 		0.105
(1.00) 		0.116
(1.00) 		0.635
(1.00)
Xq loss 0 (0%) 564 0.765
(1.00) 		0.839
(1.00) 		0.339
(1.00) 		0.446
(1.00) 		0.108
(1.00) 		0.495
(1.00) 		0.0157
(1.00) 		0.0674
(1.00) 		0.515
(1.00) 		0.652
(1.00)
'2p gain' versus 'METHLYATION_CNMF'

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

Table S1.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.15

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
2P GAIN CNV 1 20 4 3
2P GAIN WILD-TYPE 37 61 52 63

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.094

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
2P GAIN CNV 9 1 18
2P GAIN WILD-TYPE 86 66 61

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

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

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

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

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.16

Table S5.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
2Q GAIN CNV 2 19 3 2
2Q GAIN WILD-TYPE 36 62 53 64

Figure S5.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'CN_CNMF'

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

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

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

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

'3q gain' versus 'CN_CNMF'

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

Table S7.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S7.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

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

Table S8.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S8.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

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

Table S9.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S9.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

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

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

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

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

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

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

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.72e-08 (Fisher's exact test), Q value = 2.7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
7P GAIN CNV 22 61 31 17
7P GAIN WILD-TYPE 16 20 25 49

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.54e-05 (Fisher's exact test), Q value = 0.065

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
7P GAIN CNV 53 23 55
7P GAIN WILD-TYPE 42 44 24

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.95e-16 (Fisher's exact test), Q value = 5.1e-13

Table S14.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

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

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 8.79e-07 (Fisher's exact test), Q value = 0.00062

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
7Q GAIN CNV 17 56 24 16
7Q GAIN WILD-TYPE 21 25 32 50

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0086

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
7Q GAIN CNV 43 18 52
7Q GAIN WILD-TYPE 52 49 27

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

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

Table S18.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S18.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

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

Table S19.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S19.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

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

Table S20.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S20.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

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

Table S21.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S21.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
11P GAIN CNV 3 0 12
11P GAIN WILD-TYPE 92 67 67

Figure S22.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

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

Table S23.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S23.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 1e-07 (Fisher's exact test), Q value = 7.2e-05

Table S24.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
13Q GAIN CNV 13 46 48 13
13Q GAIN WILD-TYPE 32 16 21 26

Figure S24.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.017

Table S25.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
13Q GAIN CNV 19 76 25
13Q GAIN WILD-TYPE 42 38 15

Figure S25.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

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

Table S26.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S26.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

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

Table S27.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S27.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 8.54e-09 (Fisher's exact test), Q value = 6.2e-06

Table S28.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
13Q GAIN CNV 25 57 28 14
13Q GAIN WILD-TYPE 13 24 28 52

Figure S28.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-07 (Fisher's exact test), Q value = 0.00046

Table S29.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
13Q GAIN CNV 53 17 54
13Q GAIN WILD-TYPE 42 50 25

Figure S29.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

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

Table S30.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S30.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

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

Table S31.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S31.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

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

Table S32.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S32.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.01

Table S33.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
17Q GAIN CNV 5 22 2 2
17Q GAIN WILD-TYPE 33 59 54 64

Figure S33.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

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

Table S34.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S34.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 6.06e-05 (Fisher's exact test), Q value = 0.042

Table S35.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
20P GAIN CNV 14 39 47 14
20P GAIN WILD-TYPE 31 23 22 25

Figure S35.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.71e-09 (Fisher's exact test), Q value = 4.9e-06

Table S36.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
20P GAIN CNV 13 71 30
20P GAIN WILD-TYPE 48 43 10

Figure S36.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

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

Table S37.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S37.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

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

Table S38.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S38.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00023

Table S39.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
20P GAIN CNV 19 48 26 10
20P GAIN WILD-TYPE 19 33 30 56

Figure S39.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00023

Table S40.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
20P GAIN CNV 46 11 46
20P GAIN WILD-TYPE 49 56 33

Figure S40.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1.23e-18 (Fisher's exact test), Q value = 9.2e-16

Table S41.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
20Q GAIN CNV 15 61 62 18
20Q GAIN WILD-TYPE 30 1 7 21

Figure S41.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.68e-17 (Fisher's exact test), Q value = 2e-14

Table S42.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
20Q GAIN CNV 18 102 36
20Q GAIN WILD-TYPE 43 12 4

Figure S42.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S43.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S43.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

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

Table S44.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S44.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.21

Table S45.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 115 184 33 119
20Q GAIN CNV 85 141 23 64
20Q GAIN WILD-TYPE 30 43 10 55

Figure S45.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.091

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 248 92 35
20Q GAIN CNV 62 182 50 19
20Q GAIN WILD-TYPE 14 66 42 16

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 9.03e-18 (Fisher's exact test), Q value = 6.7e-15

Table S47.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
20Q GAIN CNV 27 74 41 15
20Q GAIN WILD-TYPE 11 7 15 51

Figure S47.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-13 (Fisher's exact test), Q value = 8.3e-11

Table S48.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
20Q GAIN CNV 69 19 69
20Q GAIN WILD-TYPE 26 48 10

Figure S48.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

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

Table S49.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S49.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.026

Table S50.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S50.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

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

Table S51.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S51.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

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

Table S52.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S52.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 5.53e-07 (Fisher's exact test), Q value = 0.00039

Table S53.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S53.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

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

Table S54.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S54.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

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

Table S55.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S55.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

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

Table S56.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S56.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S57.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'CN_CNMF'

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

Table S58.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S58.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

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

Table S59.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S59.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00078

Table S60.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S60.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 4.76e-06 (Fisher's exact test), Q value = 0.0033

Table S61.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
14Q LOSS CNV 7 28 26 2
14Q LOSS WILD-TYPE 38 34 43 37

Figure S61.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.49e-07 (Fisher's exact test), Q value = 0.00018

Table S62.  Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
14Q LOSS CNV 3 42 18
14Q LOSS WILD-TYPE 58 72 22

Figure S62.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.12e-31 (Fisher's exact test), Q value = 8.4e-29

Table S63.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S63.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

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

Table S64.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S64.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.000364 (Fisher's exact test), Q value = 0.24

Table S65.  Gene #65: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 115 184 33 119
14Q LOSS CNV 30 64 4 18
14Q LOSS WILD-TYPE 85 120 29 101

Figure S65.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.73e-07 (Fisher's exact test), Q value = 0.00012

Table S66.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
14Q LOSS CNV 9 33 10 2
14Q LOSS WILD-TYPE 29 48 46 64

Figure S66.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'CN_CNMF'

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

Table S67.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S67.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0083

Table S68.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
15Q LOSS CNV 11 30 13 3
15Q LOSS WILD-TYPE 27 51 43 63

Figure S68.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.16

Table S69.  Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
17P LOSS CNV 14 36 41 10
17P LOSS WILD-TYPE 31 26 28 29

Figure S69.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

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

Table S70.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S70.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

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

Table S71.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S71.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 3.25e-06 (Fisher's exact test), Q value = 0.0023

Table S72.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
17P LOSS CNV 21 45 21 11
17P LOSS WILD-TYPE 17 36 35 55

Figure S72.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 9.87e-15 (Fisher's exact test), Q value = 7.3e-12

Table S73.  Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
18P LOSS CNV 11 53 52 10
18P LOSS WILD-TYPE 34 9 17 29

Figure S73.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.51e-12 (Fisher's exact test), Q value = 6.2e-09

Table S74.  Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
18P LOSS CNV 13 81 32
18P LOSS WILD-TYPE 48 33 8

Figure S74.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

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

Table S75.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S75.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

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

Table S76.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S76.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 5.39e-16 (Fisher's exact test), Q value = 4e-13

Table S77.  Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
18P LOSS CNV 20 66 33 9
18P LOSS WILD-TYPE 18 15 23 57

Figure S77.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-11 (Fisher's exact test), Q value = 2e-08

Table S78.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
18P LOSS CNV 56 13 59
18P LOSS WILD-TYPE 39 54 20

Figure S78.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 1e-09

Table S79.  Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
18Q LOSS CNV 15 54 54 12
18Q LOSS WILD-TYPE 30 8 15 27

Figure S79.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-11 (Fisher's exact test), Q value = 1.4e-08

Table S80.  Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
18Q LOSS CNV 16 86 33
18Q LOSS WILD-TYPE 45 28 7

Figure S80.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

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

Table S81.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S81.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

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

Table S82.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S82.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3.96e-16 (Fisher's exact test), Q value = 2.9e-13

Table S83.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
18Q LOSS CNV 26 68 34 11
18Q LOSS WILD-TYPE 12 13 22 55

Figure S83.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.68e-09 (Fisher's exact test), Q value = 2.7e-06

Table S84.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
18Q LOSS CNV 58 19 62
18Q LOSS WILD-TYPE 37 48 17

Figure S84.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S85.  Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S85.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

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

Table S86.  Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S86.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'CN_CNMF'

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

Table S87.  Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S87.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

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

Table S88.  Gene #76: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S88.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

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

Table S89.  Gene #77: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S89.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #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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