Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1C53HT9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Lung Squamous Cell Carcinoma (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/C1C53HT9
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 10 molecular subtypes across 397 patients, 67 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

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

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

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

  • 9p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

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

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

  • 4p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 6p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

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

  • 14q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF'.

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

  • 21q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Xq loss cnv correlated to 'RPPA_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 67 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
10q loss 0 (0%) 306 0.00913
(1.00) 		0.000153
(0.111) 		6.19e-12
(4.82e-09) 		6.37e-05
(0.0467) 		0.266
(1.00) 		0.0118
(1.00) 		0.000233
(0.167) 		8.86e-06
(0.00658) 		0.00676
(1.00) 		0.000591
(0.417)
2p gain 0 (0%) 300 0.00698
(1.00) 		0.0105
(1.00) 		1.01e-11
(7.83e-09) 		6.91e-05
(0.0505) 		0.0657
(1.00) 		0.216
(1.00) 		0.000131
(0.0949) 		7.04e-06
(0.00524) 		0.865
(1.00) 		0.0195
(1.00)
1p loss 0 (0%) 338 0.00248
(1.00) 		0.000419
(0.299) 		6.42e-12
(5e-09) 		2.4e-06
(0.0018) 		0.251
(1.00) 		0.0392
(1.00) 		1.15e-06
(0.00087) 		1.02e-06
(0.00077) 		0.484
(1.00) 		0.0187
(1.00)
4q loss 0 (0%) 254 0.00796
(1.00) 		0.000975
(0.679) 		5.59e-11
(4.34e-08) 		1.99e-06
(0.0015) 		0.00876
(1.00) 		0.119
(1.00) 		3.85e-05
(0.0284) 		3.97e-05
(0.0292) 		0.195
(1.00) 		0.0269
(1.00)
9q loss 0 (0%) 294 0.00394
(1.00) 		0.00469
(1.00) 		5.6e-14
(4.37e-11) 		1.49e-05
(0.0111) 		1
(1.00) 		0.4
(1.00) 		3.38e-05
(0.0249) 		1.68e-05
(0.0124) 		0.0665
(1.00) 		0.00836
(1.00)
7q gain 0 (0%) 296 0.066
(1.00) 		0.0979
(1.00) 		1.72e-13
(1.34e-10) 		5.65e-07
(0.000429) 		0.825
(1.00) 		0.85
(1.00) 		0.00139
(0.958) 		1.03e-05
(0.00764) 		0.151
(1.00) 		0.00666
(1.00)
18p gain 0 (0%) 330 0.00236
(1.00) 		9.45e-06
(0.00701) 		1.66e-07
(0.000126) 		0.0226
(1.00) 		0.175
(1.00) 		0.0917
(1.00) 		0.00287
(1.00) 		0.0003
(0.215) 		0.348
(1.00) 		0.0225
(1.00)
10p loss 0 (0%) 310 0.0543
(1.00) 		0.134
(1.00) 		9.56e-10
(7.39e-07) 		4.4e-06
(0.00328) 		1
(1.00) 		0.132
(1.00) 		0.000813
(0.569) 		0.000131
(0.0949) 		0.0616
(1.00) 		0.000432
(0.307)
3p loss 0 (0%) 236 0.0501
(1.00) 		0.448
(1.00) 		4.11e-06
(0.00307) 		7.19e-05
(0.0524) 		0.493
(1.00) 		0.275
(1.00) 		0.439
(1.00) 		0.0165
(1.00) 		0.912
(1.00) 		0.538
(1.00)
4p loss 0 (0%) 233 0.171
(1.00) 		0.0319
(1.00) 		7.02e-10
(5.44e-07) 		5.36e-08
(4.1e-05) 		0.0533
(1.00) 		0.327
(1.00) 		0.0234
(1.00) 		0.00737
(1.00) 		0.192
(1.00) 		0.182
(1.00)
5q loss 0 (0%) 251 0.23
(1.00) 		0.213
(1.00) 		1.3e-09
(1e-06) 		6.65e-09
(5.13e-06) 		0.0543
(1.00) 		0.0892
(1.00) 		0.0637
(1.00) 		0.293
(1.00) 		0.259
(1.00) 		0.0197
(1.00)
6p loss 0 (0%) 362 0.0798
(1.00) 		0.0164
(1.00) 		0.000112
(0.0819) 		0.00847
(1.00) 		0.0753
(1.00) 		0.0297
(1.00) 		0.00261
(1.00) 		0.000195
(0.141) 		0.937
(1.00) 		0.822
(1.00)
9p loss 0 (0%) 233 0.114
(1.00) 		0.751
(1.00) 		2.79e-16
(2.18e-13) 		3.04e-08
(2.34e-05) 		0.983
(1.00) 		0.487
(1.00) 		0.293
(1.00) 		0.207
(1.00) 		0.387
(1.00) 		0.427
(1.00)
13q loss 0 (0%) 251 0.229
(1.00) 		0.609
(1.00) 		3.86e-08
(2.96e-05) 		0.000231
(0.166) 		0.149
(1.00) 		0.44
(1.00) 		0.582
(1.00) 		0.599
(1.00) 		0.853
(1.00) 		0.123
(1.00)
14q loss 0 (0%) 327 0.00058
(0.41) 		0.0217
(1.00) 		0.00225
(1.00) 		0.0148
(1.00) 		0.0458
(1.00) 		0.0422
(1.00) 		1.01e-06
(0.000762) 		9.83e-08
(7.5e-05) 		0.412
(1.00) 		0.28
(1.00)
17p loss 0 (0%) 252 0.102
(1.00) 		1
(1.00) 		7.1e-05
(0.0518) 		0.000123
(0.0892) 		0.0107
(1.00) 		0.0694
(1.00) 		0.204
(1.00) 		0.184
(1.00) 		0.215
(1.00) 		0.316
(1.00)
21q loss 0 (0%) 275 0.0247
(1.00) 		0.0161
(1.00) 		8.71e-10
(6.74e-07) 		9.29e-07
(0.000705) 		0.318
(1.00) 		0.241
(1.00) 		0.0108
(1.00) 		0.0134
(1.00) 		0.109
(1.00) 		0.214
(1.00)
1q gain 0 (0%) 314 0.133
(1.00) 		0.1
(1.00) 		4.61e-05
(0.0338) 		0.0144
(1.00) 		0.627
(1.00) 		0.472
(1.00) 		0.00726
(1.00) 		0.00801
(1.00) 		0.00719
(1.00) 		0.006
(1.00)
2q gain 0 (0%) 354 0.126
(1.00) 		0.0181
(1.00) 		5.41e-06
(0.00403) 		0.00399
(1.00) 		0.188
(1.00) 		0.306
(1.00) 		0.000593
(0.418) 		0.000763
(0.536) 		0.487
(1.00) 		0.301
(1.00)
5p gain 0 (0%) 212 0.85
(1.00) 		0.954
(1.00) 		1.87e-06
(0.0014) 		0.0113
(1.00) 		0.216
(1.00) 		0.25
(1.00) 		0.091
(1.00) 		0.228
(1.00) 		0.546
(1.00) 		0.557
(1.00)
6q gain 0 (0%) 373 0.00289
(1.00) 		0.073
(1.00) 		0.000233
(0.168) 		0.00132
(0.914) 		0.723
(1.00) 		0.594
(1.00) 		0.0836
(1.00) 		0.0196
(1.00) 		0.657
(1.00) 		0.399
(1.00)
7p gain 0 (0%) 288 0.173
(1.00) 		0.248
(1.00) 		2.78e-06
(0.00208) 		0.00121
(0.84) 		0.731
(1.00) 		0.988
(1.00) 		0.0639
(1.00) 		0.00205
(1.00) 		0.451
(1.00) 		0.0372
(1.00)
9p gain 0 (0%) 378 0.29
(1.00) 		0.139
(1.00) 		0.145
(1.00) 		0.871
(1.00) 		0.172
(1.00) 		0.000216
(0.156) 		0.0899
(1.00) 		0.011
(1.00) 		0.446
(1.00) 		0.109
(1.00)
12p gain 0 (0%) 286 0.0146
(1.00) 		0.119
(1.00) 		1.03e-06
(0.000778) 		0.0784
(1.00) 		0.197
(1.00) 		0.593
(1.00) 		0.0279
(1.00) 		0.0656
(1.00) 		0.907
(1.00) 		0.384
(1.00)
12q gain 0 (0%) 348 0.0488
(1.00) 		0.258
(1.00) 		1.15e-06
(0.000868) 		0.0339
(1.00) 		0.216
(1.00) 		0.775
(1.00) 		0.417
(1.00) 		0.0161
(1.00) 		0.565
(1.00) 		0.526
(1.00)
16q gain 0 (0%) 374 0.237
(1.00) 		0.844
(1.00) 		3.99e-05
(0.0293) 		0.429
(1.00) 		0.455
(1.00) 		0.154
(1.00) 		0.441
(1.00) 		0.953
(1.00) 		0.582
(1.00) 		0.302
(1.00)
17q gain 0 (0%) 353 0.013
(1.00) 		0.0282
(1.00) 		2.36e-07
(0.00018) 		0.00229
(1.00) 		0.42
(1.00) 		0.42
(1.00) 		0.00138
(0.954) 		0.0037
(1.00) 		0.164
(1.00) 		0.0443
(1.00)
19p gain 0 (0%) 357 0.0516
(1.00) 		0.163
(1.00) 		1.86e-06
(0.0014) 		0.00415
(1.00) 		0.000468
(0.333) 		0.00166
(1.00) 		0.00876
(1.00) 		0.00278
(1.00) 		0.045
(1.00) 		0.0933
(1.00)
20p gain 0 (0%) 288 0.132
(1.00) 		0.0379
(1.00) 		5.05e-08
(3.87e-05) 		0.0159
(1.00) 		0.684
(1.00) 		0.194
(1.00) 		0.0969
(1.00) 		0.21
(1.00) 		0.273
(1.00) 		0.00779
(1.00)
20q gain 0 (0%) 302 0.672
(1.00) 		0.599
(1.00) 		1.6e-08
(1.23e-05) 		0.184
(1.00) 		0.885
(1.00) 		0.331
(1.00) 		0.0746
(1.00) 		0.0475
(1.00) 		0.882
(1.00) 		0.165
(1.00)
22q gain 0 (0%) 300 0.00362
(1.00) 		0.00858
(1.00) 		7.95e-09
(6.13e-06) 		0.00207
(1.00) 		0.227
(1.00) 		0.0167
(1.00) 		0.0103
(1.00) 		0.0112
(1.00) 		0.434
(1.00) 		0.00335
(1.00)
8p loss 0 (0%) 280 0.367
(1.00) 		0.554
(1.00) 		6.3e-08
(4.81e-05) 		0.000785
(0.551) 		0.115
(1.00) 		0.83
(1.00) 		0.474
(1.00) 		0.231
(1.00) 		0.402
(1.00) 		0.634
(1.00)
11p loss 0 (0%) 338 0.0129
(1.00) 		0.184
(1.00) 		0.000175
(0.127) 		0.00332
(1.00) 		0.0905
(1.00) 		0.0415
(1.00) 		0.0324
(1.00) 		0.155
(1.00) 		0.253
(1.00) 		0.493
(1.00)
11q loss 0 (0%) 355 0.42
(1.00) 		0.483
(1.00) 		3.81e-06
(0.00285) 		0.00879
(1.00) 		0.119
(1.00) 		0.315
(1.00) 		0.0182
(1.00) 		0.0573
(1.00) 		0.0434
(1.00) 		0.145
(1.00)
16p loss 0 (0%) 337 0.329
(1.00) 		0.388
(1.00) 		1.96e-05
(0.0145) 		0.0247
(1.00) 		0.388
(1.00) 		0.305
(1.00) 		0.0772
(1.00) 		0.143
(1.00) 		0.72
(1.00) 		0.0965
(1.00)
Xq loss 0 (0%) 382 0.634
(1.00) 		1
(1.00) 		0.431
(1.00) 		0.914
(1.00) 		0.277
(1.00) 		0.000261
(0.187) 		0.608
(1.00) 		0.347
(1.00) 		0.0878
(1.00) 		0.421
(1.00)
1p gain 0 (0%) 373 0.816
(1.00) 		0.642
(1.00) 		0.486
(1.00) 		0.607
(1.00) 		0.867
(1.00) 		0.247
(1.00) 		0.36
(1.00) 		0.179
(1.00) 		0.596
(1.00) 		0.918
(1.00)
3p gain 0 (0%) 350 0.539
(1.00) 		0.215
(1.00) 		0.0123
(1.00) 		0.000375
(0.268) 		0.741
(1.00) 		0.486
(1.00) 		0.177
(1.00) 		0.165
(1.00) 		0.868
(1.00) 		0.11
(1.00)
3q gain 0 (0%) 217 0.072
(1.00) 		0.653
(1.00) 		0.0114
(1.00) 		0.0373
(1.00) 		0.301
(1.00) 		0.402
(1.00) 		0.0389
(1.00) 		0.193
(1.00) 		0.942
(1.00) 		0.533
(1.00)
4p gain 0 (0%) 383 0.148
(1.00) 		0.15
(1.00) 		0.0062
(1.00) 		0.156
(1.00) 		0.132
(1.00) 		0.464
(1.00) 		0.00632
(1.00) 		0.0102
(1.00) 		0.5
(1.00) 		0.547
(1.00)
4q gain 0 (0%) 390 1
(1.00) 		0.715
(1.00) 		0.0634
(1.00) 		0.771
(1.00) 		0.0128
(1.00) 		0.863
(1.00) 		1
(1.00)
5q gain 0 (0%) 354 0.0754
(1.00) 		0.279
(1.00) 		0.0985
(1.00) 		0.148
(1.00) 		0.687
(1.00) 		0.656
(1.00) 		0.0774
(1.00) 		0.124
(1.00) 		0.507
(1.00) 		0.15
(1.00)
6p gain 0 (0%) 361 0.00213
(1.00) 		0.0106
(1.00) 		0.000574
(0.406) 		0.544
(1.00) 		0.643
(1.00) 		0.279
(1.00) 		0.261
(1.00) 		0.00774
(1.00) 		0.971
(1.00) 		0.916
(1.00)
8p gain 0 (0%) 349 0.129
(1.00) 		0.143
(1.00) 		0.0316
(1.00) 		0.0875
(1.00) 		0.756
(1.00) 		0.441
(1.00) 		0.0668
(1.00) 		0.00163
(1.00) 		0.217
(1.00) 		0.0926
(1.00)
8q gain 0 (0%) 283 0.0326
(1.00) 		0.0311
(1.00) 		0.0135
(1.00) 		0.00439
(1.00) 		0.708
(1.00) 		0.618
(1.00) 		0.00246
(1.00) 		0.00207
(1.00) 		0.0136
(1.00) 		0.0994
(1.00)
9q gain 0 (0%) 365 0.186
(1.00) 		0.075
(1.00) 		0.00432
(1.00) 		0.047
(1.00) 		0.0746
(1.00) 		0.00212
(1.00) 		0.0157
(1.00) 		0.0128
(1.00) 		0.035
(1.00) 		0.121
(1.00)
10p gain 0 (0%) 375 0.208
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.372
(1.00) 		0.53
(1.00) 		0.389
(1.00) 		0.581
(1.00) 		0.734
(1.00) 		0.332
(1.00) 		0.509
(1.00)
10q gain 0 (0%) 389 0.327
(1.00) 		1
(1.00) 		0.162
(1.00) 		0.684
(1.00) 		0.275
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.634
(1.00)
11p gain 0 (0%) 374 1
(1.00) 		0.929
(1.00) 		0.136
(1.00) 		0.12
(1.00) 		0.398
(1.00) 		0.272
(1.00) 		0.392
(1.00) 		0.116
(1.00) 		0.718
(1.00) 		0.661
(1.00)
11q gain 0 (0%) 371 0.096
(1.00) 		0.491
(1.00) 		0.0171
(1.00) 		0.0342
(1.00) 		0.773
(1.00) 		0.379
(1.00) 		0.691
(1.00) 		0.108
(1.00) 		0.927
(1.00) 		0.608
(1.00)
13q gain 0 (0%) 387 0.769
(1.00) 		1
(1.00) 		0.00306
(1.00) 		0.582
(1.00) 		0.289
(1.00) 		0.349
(1.00) 		0.656
(1.00) 		0.903
(1.00) 		0.405
(1.00) 		0.912
(1.00)
14q gain 0 (0%) 356 0.103
(1.00) 		0.82
(1.00) 		0.549
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.11
(1.00) 		0.412
(1.00) 		0.0831
(1.00) 		0.0348
(1.00)
15q gain 0 (0%) 358 0.206
(1.00) 		0.0334
(1.00) 		0.00173
(1.00) 		0.0176
(1.00) 		0.193
(1.00) 		0.112
(1.00) 		0.00148
(1.00) 		0.0733
(1.00) 		0.00228
(1.00) 		0.00952
(1.00)
16p gain 0 (0%) 380 0.589
(1.00) 		1
(1.00) 		0.000993
(0.691) 		0.364
(1.00) 		0.723
(1.00) 		0.341
(1.00) 		0.652
(1.00) 		0.147
(1.00) 		0.708
(1.00) 		0.662
(1.00)
17p gain 0 (0%) 386 0.298
(1.00) 		0.0881
(1.00) 		0.000891
(0.622) 		0.123
(1.00) 		0.0669
(1.00) 		0.343
(1.00) 		0.204
(1.00) 		0.0504
(1.00) 		0.00622
(1.00) 		0.0119
(1.00)
18q gain 0 (0%) 353 0.00783
(1.00) 		0.000419
(0.299) 		0.00285
(1.00) 		0.165
(1.00) 		0.136
(1.00) 		0.0285
(1.00) 		0.00194
(1.00) 		0.00621
(1.00) 		0.0873
(1.00) 		0.000741
(0.521)
19q gain 0 (0%) 339 0.0577
(1.00) 		0.773
(1.00) 		0.000368
(0.263) 		0.381
(1.00) 		0.0595
(1.00) 		0.019
(1.00) 		0.0218
(1.00) 		0.00453
(1.00) 		0.778
(1.00) 		0.705
(1.00)
21q gain 0 (0%) 378 0.968
(1.00) 		0.425
(1.00) 		0.839
(1.00) 		0.00187
(1.00) 		0.524
(1.00) 		0.937
(1.00) 		0.687
(1.00) 		0.514
(1.00) 		0.644
(1.00) 		0.245
(1.00)
Xq gain 0 (0%) 386 0.769
(1.00) 		1
(1.00) 		0.0567
(1.00) 		0.0729
(1.00) 		0.451
(1.00) 		0.582
(1.00) 		0.858
(1.00) 		0.13
(1.00) 		0.251
(1.00) 		0.204
(1.00)
1q loss 0 (0%) 388 0.183
(1.00) 		0.25
(1.00) 		0.799
(1.00) 		0.32
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.147
(1.00)
2p loss 0 (0%) 393 0.0769
(1.00) 		1
(1.00) 		1
(1.00) 		0.777
(1.00) 		0.592
(1.00)
2q loss 0 (0%) 386 0.532
(1.00) 		1
(1.00) 		0.0131
(1.00) 		0.131
(1.00) 		0.737
(1.00) 		0.582
(1.00) 		0.259
(1.00) 		0.253
(1.00) 		0.188
(1.00) 		0.446
(1.00)
3q loss 0 (0%) 371 0.261
(1.00) 		0.701
(1.00) 		0.0411
(1.00) 		0.12
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.128
(1.00) 		0.547
(1.00) 		1
(1.00)
5p loss 0 (0%) 373 0.122
(1.00) 		0.252
(1.00) 		0.0331
(1.00) 		0.14
(1.00) 		0.255
(1.00) 		0.207
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.772
(1.00) 		0.918
(1.00)
6q loss 0 (0%) 357 0.166
(1.00) 		0.0264
(1.00) 		0.0141
(1.00) 		0.0667
(1.00) 		0.0883
(1.00) 		0.159
(1.00) 		0.112
(1.00) 		0.0464
(1.00) 		1
(1.00) 		0.532
(1.00)
7p loss 0 (0%) 374 0.408
(1.00) 		0.834
(1.00) 		0.00207
(1.00) 		0.0131
(1.00) 		0.504
(1.00) 		0.114
(1.00) 		0.689
(1.00) 		0.71
(1.00) 		0.234
(1.00) 		0.65
(1.00)
7q loss 0 (0%) 384 0.472
(1.00) 		0.848
(1.00) 		0.078
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.0592
(1.00) 		0.0234
(1.00) 		0.199
(1.00) 		0.121
(1.00)
8q loss 0 (0%) 385 0.254
(1.00) 		0.0397
(1.00) 		0.0303
(1.00) 		0.0254
(1.00) 		0.0801
(1.00) 		0.288
(1.00) 		0.392
(1.00) 		0.0041
(1.00) 		0.642
(1.00) 		0.589
(1.00)
12p loss 0 (0%) 390 0.131
(1.00) 		0.684
(1.00) 		0.319
(1.00) 		0.33
(1.00) 		0.347
(1.00) 		0.712
(1.00)
12q loss 0 (0%) 388 0.34
(1.00) 		0.383
(1.00) 		0.292
(1.00) 		0.381
(1.00) 		0.933
(1.00) 		0.0385
(1.00) 		0.224
(1.00) 		0.514
(1.00)
15q loss 0 (0%) 353 0.764
(1.00) 		0.115
(1.00) 		0.152
(1.00) 		0.00246
(1.00) 		0.00801
(1.00) 		0.00172
(1.00) 		0.43
(1.00) 		0.013
(1.00) 		0.197
(1.00) 		0.419
(1.00)
16q loss 0 (0%) 317 0.0651
(1.00) 		0.237
(1.00) 		0.000639
(0.45) 		0.00453
(1.00) 		0.172
(1.00) 		0.132
(1.00) 		0.072
(1.00) 		0.00708
(1.00) 		0.925
(1.00) 		0.00602
(1.00)
17q loss 0 (0%) 372 0.275
(1.00) 		0.282
(1.00) 		0.0524
(1.00) 		0.00497
(1.00) 		0.304
(1.00) 		0.943
(1.00) 		0.0315
(1.00) 		0.055
(1.00) 		0.738
(1.00) 		0.706
(1.00)
18p loss 0 (0%) 354 0.49
(1.00) 		0.653
(1.00) 		0.00527
(1.00) 		0.0637
(1.00) 		0.213
(1.00) 		0.86
(1.00) 		0.256
(1.00) 		0.222
(1.00) 		0.603
(1.00) 		0.456
(1.00)
18q loss 0 (0%) 321 0.363
(1.00) 		0.932
(1.00) 		0.00107
(0.744) 		0.341
(1.00) 		0.253
(1.00) 		0.79
(1.00) 		0.277
(1.00) 		0.0139
(1.00) 		0.329
(1.00) 		0.318
(1.00)
19p loss 0 (0%) 332 0.0166
(1.00) 		0.0152
(1.00) 		0.000572
(0.405) 		0.0984
(1.00) 		0.708
(1.00) 		0.867
(1.00) 		0.00252
(1.00) 		0.016
(1.00) 		0.000917
(0.64) 		0.00275
(1.00)
19q loss 0 (0%) 354 0.541
(1.00) 		0.243
(1.00) 		0.307
(1.00) 		0.0513
(1.00) 		0.0346
(1.00) 		0.103
(1.00) 		1
(1.00) 		0.974
(1.00) 		0.101
(1.00) 		0.503
(1.00)
20p loss 0 (0%) 380 0.268
(1.00) 		0.0237
(1.00) 		0.0868
(1.00) 		0.212
(1.00) 		0.0412
(1.00) 		0.555
(1.00) 		0.588
(1.00) 		0.514
(1.00) 		0.311
(1.00) 		0.435
(1.00)
20q loss 0 (0%) 375 0.0376
(1.00) 		0.0203
(1.00) 		0.0349
(1.00) 		0.084
(1.00) 		0.0774
(1.00) 		0.429
(1.00) 		0.00187
(1.00) 		0.0015
(1.00) 		0.545
(1.00) 		0.593
(1.00)
22q loss 0 (0%) 359 0.057
(1.00) 		0.157
(1.00) 		0.466
(1.00) 		0.479
(1.00) 		0.485
(1.00) 		0.202
(1.00) 		0.652
(1.00) 		0.115
(1.00) 		0.0478
(1.00) 		0.0905
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 4.61e-05 (Fisher's exact test), Q value = 0.034

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
1Q GAIN CNV 18 44 21
1Q GAIN WILD-TYPE 125 85 104

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1.01e-11 (Fisher's exact test), Q value = 7.8e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
2P GAIN CNV 12 58 27
2P GAIN WILD-TYPE 131 71 98

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 6.91e-05 (Fisher's exact test), Q value = 0.051

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
2P GAIN CNV 14 35 14
2P GAIN WILD-TYPE 84 48 55

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.095

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
2P GAIN CNV 8 36 25 6
2P GAIN WILD-TYPE 69 66 86 49

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.04e-06 (Fisher's exact test), Q value = 0.0052

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
2P GAIN CNV 38 18 19
2P GAIN WILD-TYPE 69 52 149

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 5.41e-06 (Fisher's exact test), Q value = 0.004

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
2Q GAIN CNV 4 27 12
2Q GAIN WILD-TYPE 139 102 113

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0014

Table S7.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
5P GAIN CNV 47 58 80
5P GAIN WILD-TYPE 96 71 45

Figure S7.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.17

Table S8.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
6Q GAIN CNV 3 4 17
6Q GAIN WILD-TYPE 140 125 108

Figure S8.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 2.78e-06 (Fisher's exact test), Q value = 0.0021

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
7P GAIN CNV 22 55 32
7P GAIN WILD-TYPE 121 74 93

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

'7q gain' versus 'CN_CNMF'

P value = 1.72e-13 (Fisher's exact test), Q value = 1.3e-10

Table S10.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
7Q GAIN CNV 13 63 25
7Q GAIN WILD-TYPE 130 66 100

Figure S10.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 5.65e-07 (Fisher's exact test), Q value = 0.00043

Table S11.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
7Q GAIN CNV 9 35 12
7Q GAIN WILD-TYPE 89 48 57

Figure S11.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0076

Table S12.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
7Q GAIN CNV 44 15 26
7Q GAIN WILD-TYPE 63 55 142

Figure S12.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000216 (Fisher's exact test), Q value = 0.16

Table S13.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
9P GAIN CNV 9 0 0 1
9P GAIN WILD-TYPE 49 47 49 39

Figure S13.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00078

Table S14.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
12P GAIN CNV 19 52 40
12P GAIN WILD-TYPE 124 77 85

Figure S14.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00087

Table S15.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
12Q GAIN CNV 5 31 13
12Q GAIN WILD-TYPE 138 98 112

Figure S15.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 3.99e-05 (Fisher's exact test), Q value = 0.029

Table S16.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
16Q GAIN CNV 0 10 13
16Q GAIN WILD-TYPE 143 119 112

Figure S16.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 2.36e-07 (Fisher's exact test), Q value = 0.00018

Table S17.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
17Q GAIN CNV 3 29 12
17Q GAIN WILD-TYPE 140 100 113

Figure S17.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.45e-06 (Fisher's exact test), Q value = 0.007

Table S18.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
18P GAIN CNV 2 21 5
18P GAIN WILD-TYPE 26 33 67

Figure S18.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00013

Table S19.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
18P GAIN CNV 14 42 11
18P GAIN WILD-TYPE 129 87 114

Figure S19.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.22

Table S20.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
18P GAIN CNV 29 5 19
18P GAIN WILD-TYPE 78 65 149

Figure S20.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.86e-06 (Fisher's exact test), Q value = 0.0014

Table S21.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
19P GAIN CNV 6 28 6
19P GAIN WILD-TYPE 137 101 119

Figure S21.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 5.05e-08 (Fisher's exact test), Q value = 3.9e-05

Table S22.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
20P GAIN CNV 16 51 42
20P GAIN WILD-TYPE 127 78 83

Figure S22.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.2e-05

Table S23.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
20Q GAIN CNV 12 36 47
20Q GAIN WILD-TYPE 131 93 78

Figure S23.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 7.95e-09 (Fisher's exact test), Q value = 6.1e-06

Table S24.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
22Q GAIN CNV 12 49 36
22Q GAIN WILD-TYPE 131 80 89

Figure S24.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 6.42e-12 (Fisher's exact test), Q value = 5e-09

Table S25.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
1P LOSS CNV 5 43 11
1P LOSS WILD-TYPE 138 86 114

Figure S25.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0018

Table S26.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
1P LOSS CNV 3 24 9
1P LOSS WILD-TYPE 95 59 60

Figure S26.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00087

Table S27.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
1P LOSS CNV 6 32 9 3
1P LOSS WILD-TYPE 71 70 102 52

Figure S27.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-06 (Fisher's exact test), Q value = 0.00077

Table S28.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
1P LOSS CNV 32 6 12
1P LOSS WILD-TYPE 75 64 156

Figure S28.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 4.11e-06 (Fisher's exact test), Q value = 0.0031

Table S29.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
3P LOSS CNV 35 63 63
3P LOSS WILD-TYPE 108 66 62

Figure S29.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.052

Table S30.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
3P LOSS CNV 23 41 36
3P LOSS WILD-TYPE 75 42 33

Figure S30.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 7.02e-10 (Fisher's exact test), Q value = 5.4e-07

Table S31.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
4P LOSS CNV 35 81 48
4P LOSS WILD-TYPE 108 48 77

Figure S31.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 5.36e-08 (Fisher's exact test), Q value = 4.1e-05

Table S32.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
4P LOSS CNV 17 46 34
4P LOSS WILD-TYPE 81 37 35

Figure S32.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 5.59e-11 (Fisher's exact test), Q value = 4.3e-08

Table S33.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
4Q LOSS CNV 28 76 39
4Q LOSS WILD-TYPE 115 53 86

Figure S33.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1.99e-06 (Fisher's exact test), Q value = 0.0015

Table S34.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
4Q LOSS CNV 15 40 29
4Q LOSS WILD-TYPE 83 43 40

Figure S34.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.028

Table S35.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
4Q LOSS CNV 17 55 39 14
4Q LOSS WILD-TYPE 60 47 72 41

Figure S35.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.97e-05 (Fisher's exact test), Q value = 0.029

Table S36.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
4Q LOSS CNV 55 28 42
4Q LOSS WILD-TYPE 52 42 126

Figure S36.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1.3e-09 (Fisher's exact test), Q value = 1e-06

Table S37.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
5Q LOSS CNV 24 62 60
5Q LOSS WILD-TYPE 119 67 65

Figure S37.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 6.65e-09 (Fisher's exact test), Q value = 5.1e-06

Table S38.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
5Q LOSS CNV 15 35 41
5Q LOSS WILD-TYPE 83 48 28

Figure S38.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.082

Table S39.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
6P LOSS CNV 5 23 7
6P LOSS WILD-TYPE 138 106 118

Figure S39.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000195 (Fisher's exact test), Q value = 0.14

Table S40.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
6P LOSS CNV 21 6 7
6P LOSS WILD-TYPE 86 64 161

Figure S40.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 6.3e-08 (Fisher's exact test), Q value = 4.8e-05

Table S41.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
8P LOSS CNV 23 34 60
8P LOSS WILD-TYPE 120 95 65

Figure S41.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.79e-16 (Fisher's exact test), Q value = 2.2e-13

Table S42.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
9P LOSS CNV 28 49 87
9P LOSS WILD-TYPE 115 80 38

Figure S42.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.3e-05

Table S43.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
9P LOSS CNV 20 34 45
9P LOSS WILD-TYPE 78 49 24

Figure S43.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 5.6e-14 (Fisher's exact test), Q value = 4.4e-11

Table S44.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
9Q LOSS CNV 20 18 65
9Q LOSS WILD-TYPE 123 111 60

Figure S44.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.011

Table S45.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
9Q LOSS CNV 17 13 32
9Q LOSS WILD-TYPE 81 70 37

Figure S45.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 3.38e-05 (Fisher's exact test), Q value = 0.025

Table S46.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
9Q LOSS CNV 22 10 41 15
9Q LOSS WILD-TYPE 55 92 70 40

Figure S46.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.012

Table S47.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
9Q LOSS CNV 11 26 51
9Q LOSS WILD-TYPE 96 44 117

Figure S47.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 9.56e-10 (Fisher's exact test), Q value = 7.4e-07

Table S48.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
10P LOSS CNV 8 44 35
10P LOSS WILD-TYPE 135 85 90

Figure S48.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0033

Table S49.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
10P LOSS CNV 8 32 15
10P LOSS WILD-TYPE 90 51 54

Figure S49.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.095

Table S50.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
10P LOSS CNV 38 16 23
10P LOSS WILD-TYPE 69 54 145

Figure S50.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
10Q LOSS CNV 5 21 6
10Q LOSS WILD-TYPE 23 33 66

Figure S51.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 6.19e-12 (Fisher's exact test), Q value = 4.8e-09

Table S52.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
10Q LOSS CNV 7 49 35
10Q LOSS WILD-TYPE 136 80 90

Figure S52.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 6.37e-05 (Fisher's exact test), Q value = 0.047

Table S53.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
10Q LOSS CNV 10 31 17
10Q LOSS WILD-TYPE 88 52 52

Figure S53.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.17

Table S54.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
10Q LOSS CNV 11 38 23 6
10Q LOSS WILD-TYPE 66 64 88 49

Figure S54.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.86e-06 (Fisher's exact test), Q value = 0.0066

Table S55.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
10Q LOSS CNV 40 17 21
10Q LOSS WILD-TYPE 67 53 147

Figure S55.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.13

Table S56.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
11P LOSS CNV 9 20 30
11P LOSS WILD-TYPE 134 109 95

Figure S56.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.81e-06 (Fisher's exact test), Q value = 0.0029

Table S57.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
11Q LOSS CNV 2 20 20
11Q LOSS WILD-TYPE 141 109 105

Figure S57.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3.86e-08 (Fisher's exact test), Q value = 3e-05

Table S58.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
13Q LOSS CNV 31 45 70
13Q LOSS WILD-TYPE 112 84 55

Figure S58.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.17

Table S59.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
13Q LOSS CNV 21 34 35
13Q LOSS WILD-TYPE 77 49 34

Figure S59.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00076

Table S60.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 102 111 55
14Q LOSS CNV 3 22 33 3
14Q LOSS WILD-TYPE 74 80 78 52

Figure S60.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.83e-08 (Fisher's exact test), Q value = 7.5e-05

Table S61.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
14Q LOSS CNV 23 26 12
14Q LOSS WILD-TYPE 84 44 156

Figure S61.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.014

Table S62.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
16P LOSS CNV 7 24 29
16P LOSS WILD-TYPE 136 105 96

Figure S62.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.052

Table S63.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
17P LOSS CNV 39 41 65
17P LOSS WILD-TYPE 104 88 60

Figure S63.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.089

Table S64.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
17P LOSS CNV 23 26 38
17P LOSS WILD-TYPE 75 57 31

Figure S64.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 8.71e-10 (Fisher's exact test), Q value = 6.7e-07

Table S65.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
21Q LOSS CNV 17 57 48
21Q LOSS WILD-TYPE 126 72 77

Figure S65.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 9.29e-07 (Fisher's exact test), Q value = 7e-04

Table S66.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
21Q LOSS CNV 10 32 28
21Q LOSS WILD-TYPE 88 51 41

Figure S66.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000261 (Fisher's exact test), Q value = 0.19

Table S67.  Gene #80: 'Xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
XQ LOSS CNV 0 7 1 0
XQ LOSS WILD-TYPE 58 40 48 40

Figure S67.  Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 397

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

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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