Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1BZ64D4
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/C1BZ64D4
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 80 arm-level results and 12 molecular subtypes across 493 patients, 100 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'METHLYATION_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'METHLYATION_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'METHLYATION_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 18p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF'.

  • Xq gain cnv correlated to 'CN_CNMF'.

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

  • 3p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3q loss cnv correlated to 'METHLYATION_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 6q loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 8q loss cnv correlated to 'CN_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

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

  • 16p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 19q loss cnv correlated to 'METHLYATION_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 100 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 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
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 Fisher's exact test Fisher's exact test
21q loss 0 (0%) 425 1.36e-09
(1.2e-06) 		2.9e-07
(0.00025) 		0.3
(1.00) 		0.0409
(1.00) 		9.06e-10
(8.02e-07) 		2.16e-08
(1.9e-05) 		1.64e-05
(0.0137) 		1.53e-07
(0.000132) 		0.0101
(1.00) 		0.00138
(1.00)
8q gain 0 (0%) 344 0.0641
(1.00) 		0.191
(1.00) 		1.84e-23
(1.65e-20) 		7.33e-09
(6.44e-06) 		0.236
(1.00) 		0.0123
(1.00) 		0.000721
(0.562) 		2.94e-05
(0.0244) 		8.13e-08
(7.07e-05) 		1.45e-07
(0.000126) 		0.000788
(0.61) 		0.00043
(0.34)
7p gain 0 (0%) 334 0.754
(1.00) 		0.523
(1.00) 		3.51e-21
(3.14e-18) 		0.00906
(1.00) 		0.000871
(0.671) 		0.00546
(1.00) 		2.48e-06
(0.00209) 		6.26e-09
(5.51e-06) 		2.92e-05
(0.0243) 		0.00166
(1.00) 		0.00456
(1.00) 		0.00118
(0.897)
12p gain 0 (0%) 434 0.565
(1.00) 		0.132
(1.00) 		4.74e-08
(4.14e-05) 		0.0112
(1.00) 		0.121
(1.00) 		0.0091
(1.00) 		0.000126
(0.103) 		4.98e-06
(0.0042) 		0.000937
(0.719) 		0.0114
(1.00) 		0.000229
(0.184) 		0.00206
(1.00)
4q loss 0 (0%) 446 0.00605
(1.00) 		0.00706
(1.00) 		1.23e-10
(1.09e-07) 		1.58e-06
(0.00135) 		0.819
(1.00) 		0.5
(1.00) 		4.25e-05
(0.0352) 		3.19e-06
(0.00269) 		0.00183
(1.00) 		0.000346
(0.275) 		0.00399
(1.00) 		0.0252
(1.00)
2q gain 0 (0%) 448 0.0302
(1.00) 		0.0253
(1.00) 		2.09e-06
(0.00177) 		9.64e-08
(8.38e-05) 		0.117
(1.00) 		0.178
(1.00) 		0.000296
(0.237) 		0.00706
(1.00) 		0.00221
(1.00) 		0.00636
(1.00) 		0.00155
(1.00) 		0.00515
(1.00)
7q gain 0 (0%) 381 0.388
(1.00) 		0.702
(1.00) 		3.13e-10
(2.77e-07) 		0.0172
(1.00) 		0.0318
(1.00) 		0.166
(1.00) 		5.43e-05
(0.0448) 		1.02e-06
(0.000875) 		0.0316
(1.00) 		0.0915
(1.00) 		0.0369
(1.00) 		0.0352
(1.00)
20p gain 0 (0%) 430 0.0235
(1.00) 		0.0127
(1.00) 		1.88e-06
(0.00159) 		4.43e-05
(0.0366) 		0.153
(1.00) 		0.916
(1.00) 		0.002
(1.00) 		4.06e-05
(0.0337) 		0.012
(1.00) 		0.00507
(1.00) 		0.0132
(1.00) 		0.0345
(1.00)
20q gain 0 (0%) 415 0.00237
(1.00) 		0.00219
(1.00) 		3.11e-07
(0.000268) 		7.35e-08
(6.4e-05) 		0.00827
(1.00) 		0.26
(1.00) 		0.000462
(0.364) 		0.000183
(0.148) 		0.00195
(1.00) 		0.00135
(1.00) 		0.0243
(1.00) 		0.00795
(1.00)
5q loss 0 (0%) 433 0.0235
(1.00) 		0.0127
(1.00) 		1.84e-06
(0.00156) 		4.4e-07
(0.000378) 		0.129
(1.00) 		0.257
(1.00) 		0.000117
(0.0958) 		0.00101
(0.777) 		0.00919
(1.00) 		0.0165
(1.00) 		0.00363
(1.00) 		0.00779
(1.00)
15q loss 0 (0%) 395 0.405
(1.00) 		0.219
(1.00) 		7.75e-14
(6.93e-11) 		1.1e-07
(9.56e-05) 		0.46
(1.00) 		0.236
(1.00) 		0.0153
(1.00) 		0.000378
(0.299) 		0.000315
(0.251) 		0.000342
(0.273) 		0.0124
(1.00) 		0.000177
(0.143)
19p loss 0 (0%) 374 0.649
(1.00) 		0.688
(1.00) 		5.57e-05
(0.0458) 		1.68e-13
(1.5e-10) 		0.614
(1.00) 		0.651
(1.00) 		2.41e-05
(0.02) 		0.00132
(1.00) 		0.00263
(1.00) 		0.0131
(1.00) 		0.00753
(1.00) 		0.0521
(1.00)
22q loss 0 (0%) 396 0.308
(1.00) 		0.321
(1.00) 		4.23e-11
(3.76e-08) 		7.29e-06
(0.00612) 		0.0218
(1.00) 		0.00614
(1.00) 		0.00504
(1.00) 		0.00267
(1.00) 		0.00707
(1.00) 		0.00186
(1.00) 		0.00996
(1.00) 		0.000111
(0.0906)
2p gain 0 (0%) 443 0.0312
(1.00) 		0.0151
(1.00) 		2.28e-08
(2e-05) 		1.15e-07
(9.97e-05) 		0.021
(1.00) 		0.0137
(1.00) 		0.00237
(1.00) 		0.000478
(0.375) 		0.00932
(1.00) 		0.00745
(1.00) 		0.0345
(1.00) 		0.00518
(1.00)
11q gain 0 (0%) 442 0.12
(1.00) 		0.157
(1.00) 		0.000187
(0.151) 		0.00145
(1.00) 		0.0128
(1.00) 		0.0771
(1.00) 		0.00393
(1.00) 		0.000135
(0.109) 		0.00328
(1.00) 		0.0118
(1.00) 		0.0247
(1.00) 		0.06
(1.00)
12q gain 0 (0%) 445 0.565
(1.00) 		0.132
(1.00) 		8.62e-06
(0.00722) 		0.0234
(1.00) 		0.103
(1.00) 		0.00863
(1.00) 		0.000706
(0.55) 		0.000161
(0.13) 		0.0392
(1.00) 		0.0629
(1.00) 		0.00517
(1.00) 		0.0338
(1.00)
14q gain 0 (0%) 434 5.1e-07
(0.000438) 		0.000206
(0.165) 		0.281
(1.00) 		0.339
(1.00) 		0.151
(1.00) 		0.0311
(1.00) 		0.003
(1.00) 		0.000893
(0.687) 		0.00796
(1.00) 		0.005
(1.00)
17p gain 0 (0%) 464 4.76e-06
(0.00402) 		0.000135
(0.11) 		0.399
(1.00) 		0.551
(1.00) 		0.584
(1.00) 		0.204
(1.00) 		0.0482
(1.00) 		0.416
(1.00) 		0.658
(1.00) 		0.133
(1.00)
17q gain 0 (0%) 413 0.0447
(1.00) 		0.702
(1.00) 		4.62e-10
(4.09e-07) 		4.36e-07
(0.000375) 		0.828
(1.00) 		0.554
(1.00) 		0.148
(1.00) 		0.0562
(1.00) 		0.0296
(1.00) 		0.0332
(1.00) 		0.337
(1.00) 		0.0109
(1.00)
18p gain 0 (0%) 449 3.57e-07
(0.000308) 		0.00121
(0.919) 		0.03
(1.00) 		0.129
(1.00) 		0.0519
(1.00) 		0.0161
(1.00) 		0.0268
(1.00) 		0.00323
(1.00) 		0.0345
(1.00) 		0.000241
(0.193)
1p loss 0 (0%) 464 2.16e-05
(0.018) 		6.26e-06
(0.00526) 		0.783
(1.00) 		0.221
(1.00) 		0.00054
(0.424) 		0.267
(1.00) 		0.965
(1.00) 		0.198
(1.00) 		0.694
(1.00) 		0.0834
(1.00)
3p loss 0 (0%) 397 0.208
(1.00) 		0.176
(1.00) 		1.86e-06
(0.00158) 		1.05e-09
(9.29e-07) 		0.23
(1.00) 		0.156
(1.00) 		0.00213
(1.00) 		0.0211
(1.00) 		0.0188
(1.00) 		0.0413
(1.00) 		0.0243
(1.00) 		0.0893
(1.00)
8p loss 0 (0%) 371 0.104
(1.00) 		0.173
(1.00) 		1.72e-20
(1.54e-17) 		0.000134
(0.109) 		0.149
(1.00) 		0.0833
(1.00) 		0.0632
(1.00) 		0.000793
(0.614) 		0.0269
(1.00) 		0.0291
(1.00) 		0.028
(1.00) 		0.00085
(0.657)
9p loss 0 (0%) 351 0.0512
(1.00) 		0.0702
(1.00) 		5.55e-05
(0.0457) 		7.61e-07
(0.000652) 		0.128
(1.00) 		0.0616
(1.00) 		0.185
(1.00) 		0.031
(1.00) 		0.918
(1.00) 		0.304
(1.00) 		0.723
(1.00) 		0.444
(1.00)
9q loss 0 (0%) 373 0.203
(1.00) 		0.222
(1.00) 		1.04e-06
(0.000889) 		5.15e-08
(4.49e-05) 		0.626
(1.00) 		0.183
(1.00) 		0.0351
(1.00) 		0.0106
(1.00) 		0.16
(1.00) 		0.154
(1.00) 		0.195
(1.00) 		0.0262
(1.00)
10p loss 0 (0%) 455 0.901
(1.00) 		0.818
(1.00) 		2.07e-05
(0.0172) 		0.00151
(1.00) 		0.109
(1.00) 		0.129
(1.00) 		0.231
(1.00) 		0.15
(1.00) 		0.0145
(1.00) 		0.00258
(1.00) 		0.00123
(0.934) 		0.000132
(0.108)
13q loss 0 (0%) 378 0.142
(1.00) 		0.145
(1.00) 		6.37e-27
(5.72e-24) 		7.41e-06
(0.00622) 		0.404
(1.00) 		0.0249
(1.00) 		0.0613
(1.00) 		0.0306
(1.00) 		0.0264
(1.00) 		0.0848
(1.00) 		0.248
(1.00) 		0.102
(1.00)
16p loss 0 (0%) 454 7.15e-05
(0.0587) 		1.75e-05
(0.0146) 		0.339
(1.00) 		0.721
(1.00) 		0.00905
(1.00) 		0.039
(1.00) 		0.0453
(1.00) 		0.094
(1.00) 		0.041
(1.00) 		0.0622
(1.00)
16q loss 0 (0%) 436 0.0159
(1.00) 		1
(1.00) 		6.8e-09
(5.98e-06) 		8.24e-05
(0.0676) 		0.0216
(1.00) 		0.326
(1.00) 		0.0196
(1.00) 		0.0903
(1.00) 		0.0233
(1.00) 		0.254
(1.00) 		0.000986
(0.756) 		0.00581
(1.00)
1p gain 0 (0%) 435 1
(1.00) 		1
(1.00) 		1.63e-07
(0.00014) 		0.0115
(1.00) 		0.182
(1.00) 		0.0217
(1.00) 		0.203
(1.00) 		0.339
(1.00) 		0.687
(1.00) 		0.84
(1.00) 		0.903
(1.00) 		0.718
(1.00)
1q gain 0 (0%) 302 0.465
(1.00) 		0.885
(1.00) 		0.0337
(1.00) 		3.24e-08
(2.84e-05) 		0.01
(1.00) 		0.127
(1.00) 		0.409
(1.00) 		0.703
(1.00) 		0.856
(1.00) 		0.834
(1.00) 		0.102
(1.00) 		0.315
(1.00)
4p gain 0 (0%) 463 0.554
(1.00) 		0.418
(1.00) 		0.000114
(0.0929) 		0.00774
(1.00) 		0.35
(1.00) 		0.022
(1.00) 		0.518
(1.00) 		0.115
(1.00) 		0.463
(1.00) 		0.332
(1.00) 		0.832
(1.00) 		0.224
(1.00)
5p gain 0 (0%) 309 0.487
(1.00) 		0.419
(1.00) 		5.03e-12
(4.48e-09) 		0.163
(1.00) 		0.836
(1.00) 		0.941
(1.00) 		0.512
(1.00) 		0.0609
(1.00) 		0.232
(1.00) 		0.211
(1.00) 		0.593
(1.00) 		0.437
(1.00)
6p gain 0 (0%) 420 0.292
(1.00) 		0.0507
(1.00) 		0.00917
(1.00) 		3.02e-06
(0.00256) 		0.00372
(1.00) 		0.25
(1.00) 		0.055
(1.00) 		0.213
(1.00) 		0.207
(1.00) 		0.437
(1.00) 		0.203
(1.00) 		0.405
(1.00)
8p gain 0 (0%) 432 1
(1.00) 		0.418
(1.00) 		7.74e-11
(6.88e-08) 		0.00117
(0.889) 		0.68
(1.00) 		0.107
(1.00) 		0.00786
(1.00) 		0.0276
(1.00) 		0.339
(1.00) 		0.076
(1.00) 		0.406
(1.00) 		0.855
(1.00)
10p gain 0 (0%) 442 0.00243
(1.00) 		0.000147
(0.119) 		0.299
(1.00) 		0.226
(1.00) 		0.00115
(0.876) 		0.00921
(1.00) 		0.0326
(1.00) 		0.208
(1.00) 		0.0123
(1.00) 		0.298
(1.00)
13q gain 0 (0%) 477 0.192
(1.00) 		0.157
(1.00) 		0.565
(1.00) 		4.53e-05
(0.0374) 		0.0708
(1.00) 		0.0712
(1.00) 		0.0703
(1.00) 		0.349
(1.00) 		0.561
(1.00) 		0.406
(1.00) 		0.928
(1.00) 		0.492
(1.00)
18q gain 0 (0%) 466 2.24e-06
(0.0019) 		0.000885
(0.681) 		0.0866
(1.00) 		0.0369
(1.00) 		0.00949
(1.00) 		0.000369
(0.293) 		0.214
(1.00) 		0.0128
(1.00) 		0.0622
(1.00) 		0.0136
(1.00)
21q gain 0 (0%) 450 0.192
(1.00) 		0.157
(1.00) 		0.000224
(0.18) 		0.029
(1.00) 		0.205
(1.00) 		0.129
(1.00) 		0.171
(1.00) 		0.122
(1.00) 		0.0219
(1.00) 		0.07
(1.00) 		0.767
(1.00) 		0.418
(1.00)
Xq gain 0 (0%) 476 0.75
(1.00) 		0.591
(1.00) 		8.37e-05
(0.0685) 		0.646
(1.00) 		0.396
(1.00) 		0.107
(1.00) 		0.119
(1.00) 		0.662
(1.00) 		0.245
(1.00) 		0.422
(1.00) 		0.365
(1.00) 		0.0908
(1.00)
3q loss 0 (0%) 437 0.554
(1.00) 		0.418
(1.00) 		0.000368
(0.293) 		2.02e-09
(1.78e-06) 		0.552
(1.00) 		1
(1.00) 		0.0246
(1.00) 		0.244
(1.00) 		0.185
(1.00) 		0.395
(1.00) 		0.0326
(1.00) 		0.183
(1.00)
4p loss 0 (0%) 453 1.22e-05
(0.0102) 		0.00794
(1.00) 		0.354
(1.00) 		0.657
(1.00) 		0.00045
(0.354) 		0.000485
(0.381) 		0.00177
(1.00) 		0.00797
(1.00) 		0.0118
(1.00) 		0.00677
(1.00)
6q loss 0 (0%) 381 0.803
(1.00) 		0.722
(1.00) 		0.0376
(1.00) 		7.67e-07
(0.000656) 		0.289
(1.00) 		0.117
(1.00) 		0.553
(1.00) 		0.574
(1.00) 		0.742
(1.00) 		0.313
(1.00) 		0.219
(1.00) 		0.212
(1.00)
8q loss 0 (0%) 472 0.000285
(0.228) 		0.373
(1.00) 		0.00996
(1.00) 		0.201
(1.00) 		0.0474
(1.00) 		0.00301
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.322
(1.00) 		0.393
(1.00)
11p loss 0 (0%) 457 0.335
(1.00) 		0.102
(1.00) 		0.000306
(0.244) 		0.415
(1.00) 		0.0368
(1.00) 		0.00473
(1.00) 		0.00282
(1.00) 		0.00428
(1.00) 		0.0344
(1.00) 		0.198
(1.00) 		0.00296
(1.00) 		0.00723
(1.00)
17p loss 0 (0%) 375 0.399
(1.00) 		0.631
(1.00) 		3.35e-08
(2.93e-05) 		0.00125
(0.944) 		0.0508
(1.00) 		0.00658
(1.00) 		0.134
(1.00) 		0.289
(1.00) 		0.64
(1.00) 		0.301
(1.00) 		0.501
(1.00) 		0.522
(1.00)
18p loss 0 (0%) 413 0.42
(1.00) 		0.412
(1.00) 		5.92e-09
(5.21e-06) 		0.00938
(1.00) 		0.453
(1.00) 		0.193
(1.00) 		0.0318
(1.00) 		0.198
(1.00) 		0.674
(1.00) 		0.643
(1.00) 		0.0725
(1.00) 		0.207
(1.00)
18q loss 0 (0%) 381 0.42
(1.00) 		0.412
(1.00) 		9.98e-13
(8.9e-10) 		0.00203
(1.00) 		0.182
(1.00) 		0.122
(1.00) 		0.00749
(1.00) 		0.0643
(1.00) 		0.0922
(1.00) 		0.791
(1.00) 		0.209
(1.00) 		0.167
(1.00)
19q loss 0 (0%) 421 0.71
(1.00) 		0.722
(1.00) 		0.000732
(0.569) 		8.24e-07
(0.000705) 		0.315
(1.00) 		0.355
(1.00) 		0.0239
(1.00) 		0.048
(1.00) 		0.00554
(1.00) 		0.0569
(1.00) 		0.000372
(0.295) 		0.026
(1.00)
20p loss 0 (0%) 427 0.192
(1.00) 		0.412
(1.00) 		7.02e-05
(0.0577) 		0.0098
(1.00) 		0.00271
(1.00) 		0.0026
(1.00) 		0.0859
(1.00) 		0.158
(1.00) 		0.75
(1.00) 		0.146
(1.00) 		0.471
(1.00) 		0.938
(1.00)
3p gain 0 (0%) 480 0.0167
(1.00) 		0.0346
(1.00) 		0.494
(1.00) 		0.588
(1.00) 		0.00503
(1.00) 		0.00292
(1.00) 		0.599
(1.00) 		0.842
(1.00) 		1
(1.00) 		0.486
(1.00)
3q gain 0 (0%) 463 0.00235
(1.00) 		0.0413
(1.00) 		0.0851
(1.00) 		0.429
(1.00) 		0.0187
(1.00) 		0.187
(1.00) 		0.0407
(1.00) 		0.107
(1.00) 		0.046
(1.00) 		0.187
(1.00)
4q gain 0 (0%) 483 0.0225
(1.00) 		0.823
(1.00) 		0.0451
(1.00) 		0.0689
(1.00) 		0.161
(1.00) 		0.152
(1.00) 		0.0134
(1.00) 		0.0918
(1.00) 		0.33
(1.00) 		0.0186
(1.00)
5q gain 0 (0%) 433 0.0177
(1.00) 		0.644
(1.00) 		0.0774
(1.00) 		0.558
(1.00) 		0.478
(1.00) 		0.391
(1.00) 		0.0155
(1.00) 		0.00381
(1.00) 		0.297
(1.00) 		0.0449
(1.00) 		0.04
(1.00) 		0.281
(1.00)
6q gain 0 (0%) 474 0.0835
(1.00) 		0.00555
(1.00) 		0.155
(1.00) 		0.0335
(1.00) 		0.309
(1.00) 		0.759
(1.00) 		0.0134
(1.00) 		0.0186
(1.00) 		0.332
(1.00) 		0.123
(1.00)
9p gain 0 (0%) 477 0.104
(1.00) 		0.0954
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.898
(1.00) 		0.275
(1.00) 		0.276
(1.00) 		0.405
(1.00) 		0.0638
(1.00) 		0.0457
(1.00)
9q gain 0 (0%) 485 0.0242
(1.00) 		0.823
(1.00) 		0.237
(1.00) 		0.475
(1.00) 		0.824
(1.00) 		0.902
(1.00) 		0.271
(1.00) 		0.13
(1.00) 		0.33
(1.00) 		0.0186
(1.00)
10q gain 0 (0%) 463 0.251
(1.00) 		0.00073
(0.568) 		0.188
(1.00) 		0.0649
(1.00) 		0.00824
(1.00) 		0.0734
(1.00) 		0.164
(1.00) 		0.813
(1.00) 		0.356
(1.00) 		0.8
(1.00)
11p gain 0 (0%) 457 0.0152
(1.00) 		0.00478
(1.00) 		0.628
(1.00) 		0.855
(1.00) 		0.288
(1.00) 		0.0971
(1.00) 		0.071
(1.00) 		0.0737
(1.00) 		0.125
(1.00) 		0.15
(1.00)
15q gain 0 (0%) 479 0.723
(1.00) 		0.191
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.0534
(1.00) 		0.219
(1.00) 		0.327
(1.00) 		0.555
(1.00) 		0.582
(1.00) 		0.326
(1.00)
16p gain 0 (0%) 422 0.358
(1.00) 		0.322
(1.00) 		0.00333
(1.00) 		0.36
(1.00) 		0.328
(1.00) 		0.201
(1.00) 		0.00332
(1.00) 		0.0644
(1.00) 		0.0467
(1.00) 		0.0298
(1.00) 		0.0271
(1.00) 		0.456
(1.00)
16q gain 0 (0%) 450 0.192
(1.00) 		0.0514
(1.00) 		0.0175
(1.00) 		0.787
(1.00) 		0.0527
(1.00) 		0.0515
(1.00) 		0.0239
(1.00) 		0.493
(1.00) 		0.0225
(1.00) 		0.152
(1.00) 		0.119
(1.00) 		0.69
(1.00)
19p gain 0 (0%) 487 1
(1.00) 		0.222
(1.00) 		0.781
(1.00) 		1
(1.00) 		1
(1.00) 		0.877
(1.00) 		1
(1.00) 		0.157
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 0 (0%) 469 0.000818
(0.632) 		0.00213
(1.00) 		0.506
(1.00) 		0.148
(1.00) 		0.118
(1.00) 		0.0273
(1.00) 		0.353
(1.00) 		0.0678
(1.00) 		0.257
(1.00) 		0.231
(1.00)
22q gain 0 (0%) 473 0.00294
(1.00) 		0.855
(1.00) 		0.281
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.768
(1.00) 		0.202
(1.00) 		0.0486
(1.00) 		0.115
(1.00) 		0.105
(1.00)
1q loss 0 (0%) 483 0.000693
(0.542) 		0.019
(1.00) 		0.547
(1.00) 		0.0561
(1.00) 		0.0108
(1.00) 		0.424
(1.00) 		0.289
(1.00) 		0.137
(1.00) 		0.236
(1.00) 		0.0893
(1.00)
2p loss 0 (0%) 487 0.867
(1.00) 		1
(1.00) 		1
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.877
(1.00) 		0.46
(1.00) 		0.697
(1.00) 		1
(1.00) 		1
(1.00)
2q loss 0 (0%) 489 0.0421
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.479
(1.00) 		0.66
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.769
(1.00)
5p loss 0 (0%) 482 0.0262
(1.00) 		0.0584
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.0134
(1.00) 		0.00112
(0.86) 		0.0239
(1.00) 		0.0918
(1.00) 		0.0267
(1.00) 		0.0244
(1.00)
6p loss 0 (0%) 450 0.335
(1.00) 		0.308
(1.00) 		0.00149
(1.00) 		0.00044
(0.347) 		0.227
(1.00) 		0.618
(1.00) 		0.316
(1.00) 		0.386
(1.00) 		0.664
(1.00) 		0.569
(1.00) 		0.472
(1.00) 		0.69
(1.00)
7p loss 0 (0%) 479 0.554
(1.00) 		0.418
(1.00) 		0.0119
(1.00) 		0.113
(1.00) 		1
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.219
(1.00) 		0.214
(1.00) 		0.924
(1.00) 		0.841
(1.00) 		1
(1.00)
7q loss 0 (0%) 476 0.53
(1.00) 		0.186
(1.00) 		0.614
(1.00) 		0.508
(1.00) 		0.881
(1.00) 		0.665
(1.00) 		0.303
(1.00) 		0.438
(1.00) 		0.947
(1.00) 		0.514
(1.00) 		0.397
(1.00) 		0.176
(1.00)
10q loss 0 (0%) 444 0.75
(1.00) 		0.591
(1.00) 		0.000447
(0.353) 		0.00121
(0.919) 		0.0564
(1.00) 		0.154
(1.00) 		0.731
(1.00) 		0.474
(1.00) 		0.171
(1.00) 		0.00487
(1.00) 		0.00334
(1.00) 		0.00059
(0.462)
11q loss 0 (0%) 462 0.474
(1.00) 		0.157
(1.00) 		0.000754
(0.585) 		0.501
(1.00) 		0.00564
(1.00) 		0.208
(1.00) 		0.394
(1.00) 		0.28
(1.00) 		0.723
(1.00) 		0.633
(1.00) 		0.507
(1.00) 		0.294
(1.00)
12p loss 0 (0%) 453 0.728
(1.00) 		0.818
(1.00) 		0.728
(1.00) 		0.024
(1.00) 		0.126
(1.00) 		0.81
(1.00) 		0.061
(1.00) 		0.622
(1.00) 		0.811
(1.00) 		0.65
(1.00) 		0.117
(1.00) 		0.594
(1.00)
12q loss 0 (0%) 469 0.0956
(1.00) 		0.0549
(1.00) 		0.737
(1.00) 		0.193
(1.00) 		0.289
(1.00) 		0.926
(1.00) 		0.959
(1.00) 		0.546
(1.00) 		0.2
(1.00) 		0.568
(1.00)
14q loss 0 (0%) 446 0.401
(1.00) 		0.418
(1.00) 		0.026
(1.00) 		0.0403
(1.00) 		0.0202
(1.00) 		0.0601
(1.00) 		0.227
(1.00) 		0.566
(1.00) 		0.0683
(1.00) 		0.154
(1.00) 		0.0007
(0.546) 		0.0934
(1.00)
17q loss 0 (0%) 474 0.103
(1.00) 		0.41
(1.00) 		0.106
(1.00) 		0.531
(1.00) 		0.103
(1.00) 		0.129
(1.00) 		0.54
(1.00) 		0.00714
(1.00) 		0.412
(1.00) 		0.74
(1.00)
20q loss 0 (0%) 468 0.0877
(1.00) 		0.0362
(1.00) 		0.517
(1.00) 		0.821
(1.00) 		0.525
(1.00) 		0.531
(1.00) 		0.228
(1.00) 		0.0607
(1.00) 		0.611
(1.00) 		0.382
(1.00)
Xq loss 0 (0%) 482 0.477
(1.00) 		0.184
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.114
(1.00) 		0.361
(1.00) 		0.648
(1.00) 		0.351
(1.00) 		0.33
(1.00) 		0.782
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00014

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
1P GAIN CNV 41 9 8
1P GAIN WILD-TYPE 146 205 84

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 3.24e-08 (Fisher's exact test), Q value = 2.8e-05

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
1Q GAIN CNV 73 63 31
1Q GAIN WILD-TYPE 68 77 119

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 2.28e-08 (Fisher's exact test), Q value = 2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
2P GAIN CNV 28 4 18
2P GAIN WILD-TYPE 159 210 74

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 1e-04

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
2P GAIN CNV 28 10 2
2P GAIN WILD-TYPE 113 130 148

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.0018

Table S5.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
2Q GAIN CNV 20 6 19
2Q GAIN WILD-TYPE 167 208 73

Figure S5.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 9.64e-08 (Fisher's exact test), Q value = 8.4e-05

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
2Q GAIN CNV 26 11 1
2Q GAIN WILD-TYPE 115 129 149

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.24

Table S7.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
2Q GAIN CNV 9 9 27
2Q GAIN WILD-TYPE 146 152 123

Figure S7.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.093

Table S8.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
4P GAIN CNV 22 4 4
4P GAIN WILD-TYPE 165 210 88

Figure S8.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 5.03e-12 (Fisher's exact test), Q value = 4.5e-09

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
5P GAIN CNV 105 46 33
5P GAIN WILD-TYPE 82 168 59

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 3.02e-06 (Fisher's exact test), Q value = 0.0026

Table S10.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
6P GAIN CNV 35 19 7
6P GAIN WILD-TYPE 106 121 143

Figure S10.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3.51e-21 (Fisher's exact test), Q value = 3.1e-18

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
7P GAIN CNV 108 29 22
7P GAIN WILD-TYPE 79 185 70

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 2.48e-06 (Fisher's exact test), Q value = 0.0021

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
7P GAIN CNV 40 78 36
7P GAIN WILD-TYPE 115 83 114

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-09 (Fisher's exact test), Q value = 5.5e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
7P GAIN CNV 66 47 41
7P GAIN WILD-TYPE 52 161 99

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

'7p gain' versus 'MIRSEQ_CNMF'

P value = 2.92e-05 (Fisher's exact test), Q value = 0.024

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
7P GAIN CNV 38 82 38
7P GAIN WILD-TYPE 141 149 40

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 3.13e-10 (Fisher's exact test), Q value = 2.8e-07

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
7Q GAIN CNV 72 24 16
7Q GAIN WILD-TYPE 115 190 76

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.045

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
7Q GAIN CNV 29 57 23
7Q GAIN WILD-TYPE 126 104 127

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-06 (Fisher's exact test), Q value = 0.00087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
7Q GAIN CNV 49 33 27
7Q GAIN WILD-TYPE 69 175 113

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

'8p gain' versus 'CN_CNMF'

P value = 7.74e-11 (Fisher's exact test), Q value = 6.9e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
8P GAIN CNV 14 14 33
8P GAIN WILD-TYPE 173 200 59

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

'8q gain' versus 'CN_CNMF'

P value = 1.84e-23 (Fisher's exact test), Q value = 1.6e-20

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
8Q GAIN CNV 65 22 62
8Q GAIN WILD-TYPE 122 192 30

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

'8q gain' versus 'METHLYATION_CNMF'

P value = 7.33e-09 (Fisher's exact test), Q value = 6.4e-06

Table S20.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
8Q GAIN CNV 58 54 19
8Q GAIN WILD-TYPE 83 86 131

Figure S20.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.024

Table S21.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
8Q GAIN CNV 38 42 60
8Q GAIN WILD-TYPE 80 166 80

Figure S21.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 8.13e-08 (Fisher's exact test), Q value = 7.1e-05

Table S22.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
8Q GAIN CNV 28 95 24
8Q GAIN WILD-TYPE 151 136 54

Figure S22.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.45e-07 (Fisher's exact test), Q value = 0.00013

Table S23.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
8Q GAIN CNV 11 103 33
8Q GAIN WILD-TYPE 40 146 155

Figure S23.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.12

Table S24.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
10P GAIN CNV 20 21 4
10P GAIN WILD-TYPE 121 119 146

Figure S24.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.15

Table S25.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
11Q GAIN CNV 29 9 13
11Q GAIN WILD-TYPE 158 205 79

Figure S25.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.11

Table S26.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
11Q GAIN CNV 18 9 23
11Q GAIN WILD-TYPE 100 199 117

Figure S26.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 4.74e-08 (Fisher's exact test), Q value = 4.1e-05

Table S27.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
12P GAIN CNV 30 7 22
12P GAIN WILD-TYPE 157 207 70

Figure S27.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.1

Table S28.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
12P GAIN CNV 7 19 30
12P GAIN WILD-TYPE 148 142 120

Figure S28.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.98e-06 (Fisher's exact test), Q value = 0.0042

Table S29.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
12P GAIN CNV 15 10 31
12P GAIN WILD-TYPE 103 198 109

Figure S29.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000229 (Fisher's exact test), Q value = 0.18

Table S30.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
12P GAIN CNV 6 33 8
12P GAIN WILD-TYPE 149 159 70

Figure S30.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 8.62e-06 (Fisher's exact test), Q value = 0.0072

Table S31.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
12Q GAIN CNV 20 8 20
12Q GAIN WILD-TYPE 167 206 72

Figure S31.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.13

Table S32.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
12Q GAIN CNV 11 9 25
12Q GAIN WILD-TYPE 107 199 115

Figure S32.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'METHLYATION_CNMF'

P value = 4.53e-05 (Fisher's exact test), Q value = 0.037

Table S33.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
13Q GAIN CNV 11 1 0
13Q GAIN WILD-TYPE 130 139 150

Figure S33.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.1e-07 (Fisher's exact test), Q value = 0.00044

Table S34.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
14Q GAIN CNV 27 9 23
14Q GAIN WILD-TYPE 160 205 69

Figure S34.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.17

Table S35.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
14Q GAIN CNV 30 17 8
14Q GAIN WILD-TYPE 111 123 142

Figure S35.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 4.76e-06 (Fisher's exact test), Q value = 0.004

Table S36.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
17P GAIN CNV 9 4 16
17P GAIN WILD-TYPE 178 210 76

Figure S36.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.11

Table S37.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
17P GAIN CNV 17 4 2
17P GAIN WILD-TYPE 124 136 148

Figure S37.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 4.62e-10 (Fisher's exact test), Q value = 4.1e-07

Table S38.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
17Q GAIN CNV 44 10 26
17Q GAIN WILD-TYPE 143 204 66

Figure S38.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 4.36e-07 (Fisher's exact test), Q value = 0.00037

Table S39.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
17Q GAIN CNV 33 30 6
17Q GAIN WILD-TYPE 108 110 144

Figure S39.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 3.57e-07 (Fisher's exact test), Q value = 0.00031

Table S40.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
18P GAIN CNV 23 4 17
18P GAIN WILD-TYPE 164 210 75

Figure S40.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000241 (Fisher's exact test), Q value = 0.19

Table S41.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
18P GAIN CNV 2 30 8
18P GAIN WILD-TYPE 47 158 180

Figure S41.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 2.24e-06 (Fisher's exact test), Q value = 0.0019

Table S42.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
18Q GAIN CNV 14 1 12
18Q GAIN WILD-TYPE 173 213 80

Figure S42.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.88e-06 (Fisher's exact test), Q value = 0.0016

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
20P GAIN CNV 24 13 26
20P GAIN WILD-TYPE 163 201 66

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 4.43e-05 (Fisher's exact test), Q value = 0.037

Table S44.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
20P GAIN CNV 32 15 8
20P GAIN WILD-TYPE 109 125 142

Figure S44.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.06e-05 (Fisher's exact test), Q value = 0.034

Table S45.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
20P GAIN CNV 10 17 34
20P GAIN WILD-TYPE 108 191 106

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 0.00027

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
20Q GAIN CNV 37 14 27
20Q GAIN WILD-TYPE 150 200 65

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 7.35e-08 (Fisher's exact test), Q value = 6.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
20Q GAIN CNV 42 16 9
20Q GAIN WILD-TYPE 99 124 141

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

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
20Q GAIN CNV 15 22 38
20Q GAIN WILD-TYPE 103 186 102

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

'21q gain' versus 'CN_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.18

Table S49.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
21Q GAIN CNV 29 9 5
21Q GAIN WILD-TYPE 158 205 87

Figure S49.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'Xq gain' versus 'CN_CNMF'

P value = 8.37e-05 (Fisher's exact test), Q value = 0.069

Table S50.  Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
XQ GAIN CNV 13 0 4
XQ GAIN WILD-TYPE 174 214 88

Figure S50.  Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.018

Table S51.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
1P LOSS CNV 6 7 16
1P LOSS WILD-TYPE 181 207 76

Figure S51.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0053

Table S52.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
1P LOSS CNV 20 4 2
1P LOSS WILD-TYPE 121 136 148

Figure S52.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.86e-06 (Fisher's exact test), Q value = 0.0016

Table S53.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
3P LOSS CNV 45 21 30
3P LOSS WILD-TYPE 142 193 62

Figure S53.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.05e-09 (Fisher's exact test), Q value = 9.3e-07

Table S54.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
3P LOSS CNV 51 24 10
3P LOSS WILD-TYPE 90 116 140

Figure S54.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 2.02e-09 (Fisher's exact test), Q value = 1.8e-06

Table S55.  Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
3Q LOSS CNV 34 16 2
3Q LOSS WILD-TYPE 107 124 148

Figure S55.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.01

Table S56.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
4P LOSS CNV 19 5 16
4P LOSS WILD-TYPE 168 209 76

Figure S56.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1.23e-10 (Fisher's exact test), Q value = 1.1e-07

Table S57.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
4Q LOSS CNV 24 2 21
4Q LOSS WILD-TYPE 163 212 71

Figure S57.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0013

Table S58.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
4Q LOSS CNV 27 7 4
4Q LOSS WILD-TYPE 114 133 146

Figure S58.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 4.25e-05 (Fisher's exact test), Q value = 0.035

Table S59.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
4Q LOSS CNV 6 11 28
4Q LOSS WILD-TYPE 149 150 122

Figure S59.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.19e-06 (Fisher's exact test), Q value = 0.0027

Table S60.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
4Q LOSS CNV 6 10 29
4Q LOSS WILD-TYPE 112 198 111

Figure S60.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0016

Table S61.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
5Q LOSS CNV 31 9 20
5Q LOSS WILD-TYPE 156 205 72

Figure S61.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 4.4e-07 (Fisher's exact test), Q value = 0.00038

Table S62.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
5Q LOSS CNV 29 20 3
5Q LOSS WILD-TYPE 112 120 147

Figure S62.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.096

Table S63.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
5Q LOSS CNV 6 21 28
5Q LOSS WILD-TYPE 149 140 122

Figure S63.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 7.67e-07 (Fisher's exact test), Q value = 0.00066

Table S64.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
6Q LOSS CNV 44 43 14
6Q LOSS WILD-TYPE 97 97 136

Figure S64.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.72e-20 (Fisher's exact test), Q value = 1.5e-17

Table S65.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
8P LOSS CNV 89 16 17
8P LOSS WILD-TYPE 98 198 75

Figure S65.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.11

Table S66.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
8P LOSS CNV 41 44 19
8P LOSS WILD-TYPE 100 96 131

Figure S66.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.000285 (Fisher's exact test), Q value = 0.23

Table S67.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
8Q LOSS CNV 17 3 1
8Q LOSS WILD-TYPE 170 211 91

Figure S67.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 5.55e-05 (Fisher's exact test), Q value = 0.046

Table S68.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
9P LOSS CNV 73 41 28
9P LOSS WILD-TYPE 114 173 64

Figure S68.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 7.61e-07 (Fisher's exact test), Q value = 0.00065

Table S69.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
9P LOSS CNV 61 39 23
9P LOSS WILD-TYPE 80 101 127

Figure S69.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00089

Table S70.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
9Q LOSS CNV 60 28 32
9Q LOSS WILD-TYPE 127 186 60

Figure S70.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 5.15e-08 (Fisher's exact test), Q value = 4.5e-05

Table S71.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
9Q LOSS CNV 56 28 17
9Q LOSS WILD-TYPE 85 112 133

Figure S71.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.017

Table S72.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
10P LOSS CNV 24 4 10
10P LOSS WILD-TYPE 163 210 82

Figure S72.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000132 (Fisher's exact test), Q value = 0.11

Table S73.  Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
10P LOSS CNV 11 17 6
10P LOSS WILD-TYPE 38 171 182

Figure S73.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.000306 (Fisher's exact test), Q value = 0.24

Table S74.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
11P LOSS CNV 22 5 9
11P LOSS WILD-TYPE 165 209 83

Figure S74.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 6.37e-27 (Fisher's exact test), Q value = 5.7e-24

Table S75.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
13Q LOSS CNV 76 4 35
13Q LOSS WILD-TYPE 111 210 57

Figure S75.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 7.41e-06 (Fisher's exact test), Q value = 0.0062

Table S76.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
13Q LOSS CNV 43 37 14
13Q LOSS WILD-TYPE 98 103 136

Figure S76.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 7.75e-14 (Fisher's exact test), Q value = 6.9e-11

Table S77.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
15Q LOSS CNV 54 11 33
15Q LOSS WILD-TYPE 133 203 59

Figure S77.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1.1e-07 (Fisher's exact test), Q value = 9.6e-05

Table S78.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
15Q LOSS CNV 42 33 9
15Q LOSS WILD-TYPE 99 107 141

Figure S78.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.14

Table S79.  Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
15Q LOSS CNV 11 52 21
15Q LOSS WILD-TYPE 38 136 167

Figure S79.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 7.15e-05 (Fisher's exact test), Q value = 0.059

Table S80.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
16P LOSS CNV 21 5 13
16P LOSS WILD-TYPE 166 209 79

Figure S80.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.015

Table S81.  Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
16P LOSS CNV 22 11 2
16P LOSS WILD-TYPE 119 129 148

Figure S81.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 6.8e-09 (Fisher's exact test), Q value = 6e-06

Table S82.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
16Q LOSS CNV 36 5 16
16Q LOSS WILD-TYPE 151 209 76

Figure S82.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 8.24e-05 (Fisher's exact test), Q value = 0.068

Table S83.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
16Q LOSS CNV 26 17 5
16Q LOSS WILD-TYPE 115 123 145

Figure S83.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 3.35e-08 (Fisher's exact test), Q value = 2.9e-05

Table S84.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
17P LOSS CNV 69 26 23
17P LOSS WILD-TYPE 118 188 69

Figure S84.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 5.92e-09 (Fisher's exact test), Q value = 5.2e-06

Table S85.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
18P LOSS CNV 53 13 14
18P LOSS WILD-TYPE 134 201 78

Figure S85.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 9.98e-13 (Fisher's exact test), Q value = 8.9e-10

Table S86.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
18Q LOSS CNV 76 22 14
18Q LOSS WILD-TYPE 111 192 78

Figure S86.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 5.57e-05 (Fisher's exact test), Q value = 0.046

Table S87.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
19P LOSS CNV 51 33 35
19P LOSS WILD-TYPE 136 181 57

Figure S87.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1.68e-13 (Fisher's exact test), Q value = 1.5e-10

Table S88.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
19P LOSS CNV 60 22 10
19P LOSS WILD-TYPE 81 118 140

Figure S88.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.02

Table S89.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
19P LOSS CNV 26 29 56
19P LOSS WILD-TYPE 129 132 94

Figure S89.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 8.24e-07 (Fisher's exact test), Q value = 7e-04

Table S90.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
19Q LOSS CNV 33 17 5
19Q LOSS WILD-TYPE 108 123 145

Figure S90.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.058

Table S91.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
20P LOSS CNV 37 13 16
20P LOSS WILD-TYPE 150 201 76

Figure S91.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1.36e-09 (Fisher's exact test), Q value = 1.2e-06

Table S92.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
21Q LOSS CNV 26 11 31
21Q LOSS WILD-TYPE 161 203 61

Figure S92.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 2.9e-07 (Fisher's exact test), Q value = 0.00025

Table S93.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
21Q LOSS CNV 36 16 6
21Q LOSS WILD-TYPE 105 124 144

Figure S93.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 9.06e-10 (Fisher's exact test), Q value = 8e-07

Table S94.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 161 150
21Q LOSS CNV 7 13 43
21Q LOSS WILD-TYPE 148 148 107

Figure S94.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.16e-08 (Fisher's exact test), Q value = 1.9e-05

Table S95.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 208 140
21Q LOSS CNV 8 15 40
21Q LOSS WILD-TYPE 110 193 100

Figure S95.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.014

Table S96.  Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
21Q LOSS CNV 12 49 5
21Q LOSS WILD-TYPE 167 182 73

Figure S96.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.53e-07 (Fisher's exact test), Q value = 0.00013

Table S97.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
21Q LOSS CNV 1 54 11
21Q LOSS WILD-TYPE 50 195 177

Figure S97.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 4.23e-11 (Fisher's exact test), Q value = 3.8e-08

Table S98.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 187 214 92
22Q LOSS CNV 51 14 32
22Q LOSS WILD-TYPE 136 200 60

Figure S98.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 7.29e-06 (Fisher's exact test), Q value = 0.0061

Table S99.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
22Q LOSS CNV 42 28 12
22Q LOSS WILD-TYPE 99 112 138

Figure S99.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.091

Table S100.  Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
22Q LOSS CNV 7 53 21
22Q LOSS WILD-TYPE 42 135 167

Figure S100.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 493

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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