Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1G15XXX
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/C1G15XXX
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 416 patients, 77 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'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p 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'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

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

  • 18q gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_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',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 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 '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',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF'.

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

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 77 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
4q loss 0 (0%) 265 0.0199
(1.00) 		0.00568
(1.00) 		9.29e-12
(8.64e-09) 		1.31e-06
(0.00119) 		0.00826
(1.00) 		0.133
(1.00) 		5.51e-05
(0.0484) 		3.97e-05
(0.035) 		0.195
(1.00) 		0.0428
(1.00) 		1.59e-05
(0.0142) 		0.0499
(1.00)
2p gain 0 (0%) 313 0.0311
(1.00) 		0.0256
(1.00) 		6.42e-14
(6.01e-11) 		1.76e-05
(0.0156) 		0.0657
(1.00) 		0.216
(1.00) 		0.000249
(0.215) 		1.47e-05
(0.0132) 		0.913
(1.00) 		0.0285
(1.00) 		0.00719
(1.00) 		0.0258
(1.00)
18p gain 0 (0%) 348 0.000266
(0.229) 		4.79e-06
(0.00431) 		4.58e-08
(4.21e-05) 		0.0137
(1.00) 		0.136
(1.00) 		0.148
(1.00) 		0.000436
(0.372) 		4.98e-05
(0.0438) 		0.232
(1.00) 		0.0165
(1.00) 		0.0182
(1.00) 		0.234
(1.00)
1p loss 0 (0%) 356 0.00447
(1.00) 		0.00177
(1.00) 		2.2e-12
(2.05e-09) 		4.84e-06
(0.00436) 		0.363
(1.00) 		0.0369
(1.00) 		1.53e-06
(0.00138) 		1.34e-06
(0.00122) 		0.355
(1.00) 		0.0132
(1.00) 		0.000659
(0.557) 		0.29
(1.00)
9q loss 0 (0%) 308 0.00358
(1.00) 		0.00213
(1.00) 		1.56e-13
(1.46e-10) 		2.24e-05
(0.0199) 		0.978
(1.00) 		0.32
(1.00) 		9.61e-05
(0.0841) 		5.86e-05
(0.0514) 		0.14
(1.00) 		0.00836
(1.00) 		0.0695
(1.00) 		0.0951
(1.00)
10q loss 0 (0%) 320 0.00315
(1.00) 		0.000417
(0.356) 		5.05e-12
(4.71e-09) 		7.18e-06
(0.00644) 		0.266
(1.00) 		0.0118
(1.00) 		0.000233
(0.201) 		8.86e-06
(0.00794) 		0.00676
(1.00) 		0.000591
(0.501) 		0.00599
(1.00) 		0.12
(1.00)
7q gain 0 (0%) 311 0.14
(1.00) 		0.0608
(1.00) 		1.07e-12
(9.97e-10) 		1.22e-06
(0.00111) 		0.679
(1.00) 		0.768
(1.00) 		0.00261
(1.00) 		2.33e-05
(0.0207) 		0.236
(1.00) 		0.0104
(1.00) 		0.00479
(1.00) 		0.0213
(1.00)
4p loss 0 (0%) 244 0.105
(1.00) 		0.0329
(1.00) 		1.68e-10
(1.56e-07) 		7.54e-08
(6.92e-05) 		0.0537
(1.00) 		0.409
(1.00) 		0.0433
(1.00) 		0.0115
(1.00) 		0.251
(1.00) 		0.225
(1.00) 		1.94e-06
(0.00175) 		0.176
(1.00)
10p loss 0 (0%) 323 0.0192
(1.00) 		0.0643
(1.00) 		2.47e-10
(2.29e-07) 		1.44e-06
(0.00131) 		1
(1.00) 		0.132
(1.00) 		0.000813
(0.683) 		0.000131
(0.114) 		0.0616
(1.00) 		0.000432
(0.369) 		0.0155
(1.00) 		0.0737
(1.00)
14q loss 0 (0%) 344 0.0023
(1.00) 		0.0258
(1.00) 		0.00121
(1.00) 		0.0124
(1.00) 		0.0458
(1.00) 		0.0422
(1.00) 		1.01e-06
(0.000916) 		9.83e-08
(9e-05) 		0.412
(1.00) 		0.28
(1.00) 		0.000904
(0.757) 		2.48e-05
(0.022)
18q gain 0 (0%) 371 0.000249
(0.215) 		0.000317
(0.273) 		0.000131
(0.115) 		0.162
(1.00) 		0.113
(1.00) 		0.0463
(1.00) 		0.000542
(0.46) 		0.000906
(0.758) 		0.0873
(1.00) 		0.00263
(1.00) 		0.0276
(1.00) 		0.452
(1.00)
19p gain 0 (0%) 376 0.304
(1.00) 		0.671
(1.00) 		2.64e-05
(0.0234) 		0.00639
(1.00) 		0.00439
(1.00) 		0.00398
(1.00) 		0.00972
(1.00) 		0.00936
(1.00) 		0.045
(1.00) 		0.207
(1.00) 		9.51e-06
(0.00851) 		0.0112
(1.00)
3p loss 0 (0%) 251 0.0417
(1.00) 		0.475
(1.00) 		3.7e-07
(0.000339) 		1.72e-05
(0.0153) 		0.406
(1.00) 		0.275
(1.00) 		0.399
(1.00) 		0.00673
(1.00) 		0.78
(1.00) 		0.576
(1.00) 		0.183
(1.00) 		0.571
(1.00)
5q loss 0 (0%) 266 0.272
(1.00) 		0.669
(1.00) 		2.94e-10
(2.72e-07) 		2.07e-08
(1.91e-05) 		0.0939
(1.00) 		0.18
(1.00) 		0.0369
(1.00) 		0.293
(1.00) 		0.304
(1.00) 		0.0197
(1.00) 		0.00558
(1.00) 		0.16
(1.00)
6p loss 0 (0%) 379 0.0916
(1.00) 		0.0391
(1.00) 		0.000159
(0.138) 		0.00298
(1.00) 		0.0753
(1.00) 		0.0297
(1.00) 		0.00261
(1.00) 		0.000195
(0.169) 		0.937
(1.00) 		0.822
(1.00) 		0.657
(1.00) 		0.726
(1.00)
9p loss 0 (0%) 244 0.0914
(1.00) 		0.133
(1.00) 		5.57e-19
(5.22e-16) 		8.01e-08
(7.34e-05) 		0.966
(1.00) 		0.399
(1.00) 		0.347
(1.00) 		0.278
(1.00) 		0.574
(1.00) 		0.365
(1.00) 		0.0624
(1.00) 		0.19
(1.00)
13q loss 0 (0%) 260 0.129
(1.00) 		0.376
(1.00) 		1.43e-10
(1.32e-07) 		0.000188
(0.164) 		0.149
(1.00) 		0.44
(1.00) 		0.609
(1.00) 		0.567
(1.00) 		0.853
(1.00) 		0.123
(1.00) 		0.0765
(1.00) 		0.0176
(1.00)
16q loss 0 (0%) 335 0.161
(1.00) 		0.354
(1.00) 		0.000196
(0.17) 		0.00711
(1.00) 		0.172
(1.00) 		0.132
(1.00) 		0.072
(1.00) 		0.00708
(1.00) 		0.802
(1.00) 		0.00587
(1.00) 		0.0182
(1.00) 		2.98e-05
(0.0263)
21q loss 0 (0%) 289 0.019
(1.00) 		0.064
(1.00) 		1.75e-12
(1.63e-09) 		5.61e-08
(5.16e-05) 		0.318
(1.00) 		0.241
(1.00) 		0.0108
(1.00) 		0.0134
(1.00) 		0.109
(1.00) 		0.214
(1.00) 		0.0881
(1.00) 		0.438
(1.00)
1q gain 0 (0%) 330 0.242
(1.00) 		0.234
(1.00) 		3.84e-05
(0.0339) 		0.0332
(1.00) 		0.482
(1.00) 		0.444
(1.00) 		0.00274
(1.00) 		0.00285
(1.00) 		0.0201
(1.00) 		0.0158
(1.00) 		0.044
(1.00) 		0.19
(1.00)
2q gain 0 (0%) 370 0.151
(1.00) 		0.105
(1.00) 		4.89e-05
(0.0431) 		0.00914
(1.00) 		0.32
(1.00) 		0.387
(1.00) 		0.000694
(0.585) 		0.000906
(0.758) 		0.463
(1.00) 		0.227
(1.00) 		0.05
(1.00) 		0.561
(1.00)
3q gain 0 (0%) 223 0.0816
(1.00) 		0.602
(1.00) 		0.00011
(0.0959) 		0.0806
(1.00) 		0.487
(1.00) 		0.402
(1.00) 		0.0756
(1.00) 		0.307
(1.00) 		0.905
(1.00) 		0.344
(1.00) 		0.471
(1.00) 		0.349
(1.00)
5p gain 0 (0%) 221 0.923
(1.00) 		0.44
(1.00) 		5.07e-05
(0.0445) 		0.0174
(1.00) 		0.336
(1.00) 		0.496
(1.00) 		0.112
(1.00) 		0.294
(1.00) 		0.495
(1.00) 		0.603
(1.00) 		0.389
(1.00) 		0.938
(1.00)
7p gain 0 (0%) 302 0.45
(1.00) 		0.27
(1.00) 		1.63e-06
(0.00147) 		0.000974
(0.812) 		0.731
(1.00) 		0.988
(1.00) 		0.0639
(1.00) 		0.00205
(1.00) 		0.451
(1.00) 		0.0372
(1.00) 		0.025
(1.00) 		0.0255
(1.00)
9p gain 0 (0%) 396 0.534
(1.00) 		0.624
(1.00) 		0.239
(1.00) 		0.824
(1.00) 		0.172
(1.00) 		0.000216
(0.187) 		0.0899
(1.00) 		0.011
(1.00) 		0.625
(1.00) 		0.284
(1.00) 		1
(1.00) 		0.315
(1.00)
12p gain 0 (0%) 301 0.0487
(1.00) 		0.43
(1.00) 		5.64e-07
(0.000515) 		0.138
(1.00) 		0.272
(1.00) 		0.723
(1.00) 		0.0231
(1.00) 		0.118
(1.00) 		0.918
(1.00) 		0.282
(1.00) 		0.0168
(1.00) 		0.446
(1.00)
12q gain 0 (0%) 366 0.0515
(1.00) 		0.512
(1.00) 		6.39e-07
(0.000583) 		0.0455
(1.00) 		0.244
(1.00) 		0.793
(1.00) 		0.304
(1.00) 		0.0326
(1.00) 		0.482
(1.00) 		0.575
(1.00) 		0.0282
(1.00) 		0.19
(1.00)
15q gain 0 (0%) 376 0.362
(1.00) 		0.178
(1.00) 		1.31e-05
(0.0117) 		0.0218
(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) 		0.0276
(1.00) 		0.00416
(1.00)
16q gain 0 (0%) 393 0.162
(1.00) 		0.234
(1.00) 		7.32e-05
(0.0641) 		0.238
(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) 		0.41
(1.00) 		0.223
(1.00)
17p gain 0 (0%) 405 0.262
(1.00) 		0.241
(1.00) 		3.37e-05
(0.0298) 		0.145
(1.00) 		0.0793
(1.00) 		0.207
(1.00) 		0.105
(1.00) 		0.0476
(1.00) 		0.00271
(1.00) 		0.00475
(1.00) 		0.0125
(1.00) 		0.00223
(1.00)
17q gain 0 (0%) 367 0.00305
(1.00) 		0.000509
(0.433) 		3.06e-10
(2.83e-07) 		0.000771
(0.649) 		0.324
(1.00) 		0.394
(1.00) 		0.000324
(0.278) 		0.000963
(0.804) 		0.0673
(1.00) 		0.0113
(1.00) 		0.00117
(0.973) 		0.00533
(1.00)
20p gain 0 (0%) 299 0.15
(1.00) 		0.0698
(1.00) 		9.33e-09
(8.6e-06) 		0.00485
(1.00) 		0.684
(1.00) 		0.194
(1.00) 		0.0735
(1.00) 		0.161
(1.00) 		0.193
(1.00) 		0.00477
(1.00) 		0.401
(1.00) 		0.0496
(1.00)
20q gain 0 (0%) 312 0.402
(1.00) 		0.708
(1.00) 		2.66e-09
(2.45e-06) 		0.0758
(1.00) 		0.644
(1.00) 		0.331
(1.00) 		0.0221
(1.00) 		0.014
(1.00) 		0.86
(1.00) 		0.0828
(1.00) 		0.71
(1.00) 		0.0871
(1.00)
22q gain 0 (0%) 315 0.00739
(1.00) 		0.0045
(1.00) 		3.77e-07
(0.000345) 		0.00106
(0.885) 		0.227
(1.00) 		0.0167
(1.00) 		0.0103
(1.00) 		0.0112
(1.00) 		0.434
(1.00) 		0.00335
(1.00) 		0.00216
(1.00) 		0.559
(1.00)
8p loss 0 (0%) 291 0.514
(1.00) 		0.986
(1.00) 		3.28e-09
(3.03e-06) 		0.000461
(0.392) 		0.075
(1.00) 		0.78
(1.00) 		0.424
(1.00) 		0.185
(1.00) 		0.418
(1.00) 		0.681
(1.00) 		0.0146
(1.00) 		0.558
(1.00)
11p loss 0 (0%) 351 0.0635
(1.00) 		0.0416
(1.00) 		1.3e-06
(0.00118) 		0.000613
(0.519) 		0.0596
(1.00) 		0.0265
(1.00) 		0.0405
(1.00) 		0.106
(1.00) 		0.365
(1.00) 		0.526
(1.00) 		0.00527
(1.00) 		0.0947
(1.00)
11q loss 0 (0%) 373 0.312
(1.00) 		0.765
(1.00) 		2.08e-06
(0.00188) 		0.00322
(1.00) 		0.119
(1.00) 		0.315
(1.00) 		0.0168
(1.00) 		0.0481
(1.00) 		0.106
(1.00) 		0.272
(1.00) 		0.0174
(1.00) 		0.332
(1.00)
16p loss 0 (0%) 352 0.693
(1.00) 		0.105
(1.00) 		7.08e-06
(0.00636) 		0.0524
(1.00) 		0.388
(1.00) 		0.305
(1.00) 		0.108
(1.00) 		0.207
(1.00) 		0.683
(1.00) 		0.12
(1.00) 		0.11
(1.00) 		0.198
(1.00)
17p loss 0 (0%) 266 0.0671
(1.00) 		0.496
(1.00) 		2.18e-06
(0.00196) 		0.000699
(0.589) 		0.0107
(1.00) 		0.0948
(1.00) 		0.124
(1.00) 		0.147
(1.00) 		0.119
(1.00) 		0.214
(1.00) 		0.455
(1.00) 		0.502
(1.00)
19p loss 0 (0%) 349 0.0307
(1.00) 		0.0138
(1.00) 		0.000212
(0.184) 		0.248
(1.00) 		0.708
(1.00) 		0.867
(1.00) 		0.00376
(1.00) 		0.015
(1.00) 		0.00111
(0.92) 		0.00265
(1.00) 		0.399
(1.00) 		0.0208
(1.00)
Xq loss 0 (0%) 399 0.907
(1.00) 		0.57
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.000261
(0.225) 		0.542
(1.00) 		0.373
(1.00) 		0.0574
(1.00) 		0.448
(1.00) 		0.0386
(1.00) 		1
(1.00)
1p gain 0 (0%) 392 0.754
(1.00) 		0.81
(1.00) 		0.468
(1.00) 		0.238
(1.00) 		0.867
(1.00) 		0.247
(1.00) 		0.36
(1.00) 		0.179
(1.00) 		0.919
(1.00) 		0.879
(1.00) 		0.313
(1.00) 		0.863
(1.00)
3p gain 0 (0%) 365 0.342
(1.00) 		0.39
(1.00) 		0.0213
(1.00) 		0.000405
(0.347) 		0.65
(1.00) 		0.388
(1.00) 		0.074
(1.00) 		0.0696
(1.00) 		0.978
(1.00) 		0.111
(1.00) 		0.328
(1.00) 		0.75
(1.00)
4p gain 0 (0%) 402 0.101
(1.00) 		0.339
(1.00) 		0.0429
(1.00) 		0.216
(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) 		0.744
(1.00) 		0.657
(1.00)
4q gain 0 (0%) 408 1
(1.00) 		0.683
(1.00) 		0.0635
(1.00) 		0.0576
(1.00) 		0.568
(1.00) 		0.107
(1.00) 		0.545
(1.00) 		0.881
(1.00)
5q gain 0 (0%) 372 0.0906
(1.00) 		0.165
(1.00) 		0.106
(1.00) 		0.108
(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) 		0.855
(1.00) 		0.857
(1.00)
6p gain 0 (0%) 379 0.000449
(0.382) 		0.0504
(1.00) 		0.00222
(1.00) 		0.569
(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) 		0.544
(1.00) 		0.861
(1.00)
6q gain 0 (0%) 391 0.0125
(1.00) 		0.146
(1.00) 		0.000532
(0.452) 		0.00148
(1.00) 		0.723
(1.00) 		0.594
(1.00) 		0.0836
(1.00) 		0.0196
(1.00) 		0.657
(1.00) 		0.399
(1.00) 		0.00686
(1.00) 		0.032
(1.00)
8p gain 0 (0%) 363 0.0424
(1.00) 		0.0715
(1.00) 		0.185
(1.00) 		0.403
(1.00) 		0.738
(1.00) 		0.431
(1.00) 		0.0868
(1.00) 		0.00362
(1.00) 		0.355
(1.00) 		0.19
(1.00) 		0.275
(1.00) 		0.93
(1.00)
8q gain 0 (0%) 295 0.0165
(1.00) 		0.0502
(1.00) 		0.00879
(1.00) 		0.0103
(1.00) 		0.819
(1.00) 		0.883
(1.00) 		0.00697
(1.00) 		0.00758
(1.00) 		0.0411
(1.00) 		0.174
(1.00) 		0.174
(1.00) 		0.869
(1.00)
9q gain 0 (0%) 383 0.113
(1.00) 		0.082
(1.00) 		0.00242
(1.00) 		0.0185
(1.00) 		0.0746
(1.00) 		0.00212
(1.00) 		0.015
(1.00) 		0.00605
(1.00) 		0.1
(1.00) 		0.121
(1.00) 		0.159
(1.00) 		0.599
(1.00)
10p gain 0 (0%) 392 0.636
(1.00) 		1
(1.00) 		0.0675
(1.00) 		0.374
(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) 		0.0365
(1.00) 		0.212
(1.00)
10q gain 0 (0%) 408 0.401
(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) 		0.262
(1.00) 		0.127
(1.00)
11p gain 0 (0%) 392 0.917
(1.00) 		0.571
(1.00) 		0.0767
(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) 		1
(1.00) 		0.472
(1.00)
11q gain 0 (0%) 389 0.0583
(1.00) 		0.581
(1.00) 		0.0431
(1.00) 		0.0488
(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) 		0.0109
(1.00) 		0.376
(1.00)
13q gain 0 (0%) 405 0.701
(1.00) 		0.664
(1.00) 		0.0488
(1.00) 		0.517
(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) 		1
(1.00) 		0.859
(1.00)
14q gain 0 (0%) 371 0.166
(1.00) 		0.695
(1.00) 		0.574
(1.00) 		0.376
(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) 		0.948
(1.00) 		0.0547
(1.00)
16p gain 0 (0%) 400 0.503
(1.00) 		1
(1.00) 		0.000701
(0.59) 		0.581
(1.00) 		0.723
(1.00) 		0.341
(1.00) 		0.583
(1.00) 		0.178
(1.00) 		0.832
(1.00) 		0.831
(1.00) 		0.316
(1.00) 		0.355
(1.00)
19q gain 0 (0%) 356 0.229
(1.00) 		1
(1.00) 		0.0105
(1.00) 		0.49
(1.00) 		0.165
(1.00) 		0.0204
(1.00) 		0.0129
(1.00) 		0.00635
(1.00) 		0.778
(1.00) 		0.89
(1.00) 		0.156
(1.00) 		0.681
(1.00)
21q gain 0 (0%) 397 0.969
(1.00) 		0.306
(1.00) 		0.558
(1.00) 		0.00314
(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) 		0.26
(1.00) 		0.637
(1.00)
Xq gain 0 (0%) 404 0.701
(1.00) 		0.589
(1.00) 		0.0712
(1.00) 		0.0995
(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) 		0.0362
(1.00) 		0.413
(1.00)
1q loss 0 (0%) 405 0.131
(1.00) 		0.279
(1.00) 		0.799
(1.00) 		0.32
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.92
(1.00) 		0.117
(1.00) 		0.00875
(1.00) 		0.146
(1.00)
2p loss 0 (0%) 413 0.202
(1.00) 		1
(1.00) 		0.779
(1.00)
2q loss 0 (0%) 405 0.813
(1.00) 		0.192
(1.00) 		0.0169
(1.00) 		0.162
(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) 		0.321
(1.00) 		1
(1.00)
3q loss 0 (0%) 390 0.302
(1.00) 		0.6
(1.00) 		0.0433
(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) 		0.0221
(1.00) 		0.624
(1.00)
5p loss 0 (0%) 391 0.141
(1.00) 		0.727
(1.00) 		0.00446
(1.00) 		0.172
(1.00) 		0.17
(1.00) 		0.355
(1.00) 		1
(1.00) 		1
(1.00) 		0.807
(1.00) 		0.918
(1.00) 		0.407
(1.00) 		0.646
(1.00)
6q loss 0 (0%) 373 0.189
(1.00) 		0.0774
(1.00) 		0.00385
(1.00) 		0.0276
(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) 		0.548
(1.00) 		0.341
(1.00)
7p loss 0 (0%) 392 0.312
(1.00) 		0.208
(1.00) 		0.000326
(0.28) 		0.0179
(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) 		0.746
(1.00) 		0.646
(1.00)
7q loss 0 (0%) 404 0.356
(1.00) 		0.302
(1.00) 		0.0545
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.0733
(1.00) 		0.0331
(1.00) 		0.169
(1.00) 		0.184
(1.00) 		0.124
(1.00) 		1
(1.00)
8q loss 0 (0%) 403 0.136
(1.00) 		0.066
(1.00) 		0.0024
(1.00) 		0.0318
(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) 		0.216
(1.00) 		0.222
(1.00)
12p loss 0 (0%) 410 0.194
(1.00) 		0.0692
(1.00) 		0.604
(1.00) 		0.0754
(1.00) 		0.347
(1.00) 		0.712
(1.00) 		0.303
(1.00) 		0.664
(1.00)
12q loss 0 (0%) 406 0.618
(1.00) 		0.0465
(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) 		0.529
(1.00) 		0.353
(1.00)
15q loss 0 (0%) 370 0.805
(1.00) 		0.00984
(1.00) 		0.126
(1.00) 		0.00836
(1.00) 		0.00801
(1.00) 		0.00172
(1.00) 		0.39
(1.00) 		0.0408
(1.00) 		0.327
(1.00) 		0.608
(1.00) 		0.401
(1.00) 		0.177
(1.00)
17q loss 0 (0%) 389 0.299
(1.00) 		0.135
(1.00) 		0.00491
(1.00) 		0.00756
(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) 		0.263
(1.00) 		0.0531
(1.00)
18p loss 0 (0%) 369 0.33
(1.00) 		1
(1.00) 		0.000401
(0.344) 		0.0924
(1.00) 		0.239
(1.00) 		0.769
(1.00) 		0.286
(1.00) 		0.2
(1.00) 		0.73
(1.00) 		0.359
(1.00) 		0.915
(1.00) 		0.84
(1.00)
18q loss 0 (0%) 336 0.475
(1.00) 		0.689
(1.00) 		0.000879
(0.737) 		0.447
(1.00) 		0.335
(1.00) 		0.829
(1.00) 		0.226
(1.00) 		0.00902
(1.00) 		0.194
(1.00) 		0.2
(1.00) 		0.27
(1.00) 		0.484
(1.00)
19q loss 0 (0%) 371 0.316
(1.00) 		0.528
(1.00) 		0.0353
(1.00) 		0.0613
(1.00) 		0.0191
(1.00) 		0.0928
(1.00) 		0.995
(1.00) 		0.902
(1.00) 		0.104
(1.00) 		0.726
(1.00) 		0.0282
(1.00) 		0.509
(1.00)
20p loss 0 (0%) 397 0.208
(1.00) 		0.11
(1.00) 		0.324
(1.00) 		0.24
(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) 		0.529
(1.00) 		0.537
(1.00)
20q loss 0 (0%) 393 0.0473
(1.00) 		0.0261
(1.00) 		0.00578
(1.00) 		0.0925
(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) 		0.0419
(1.00) 		0.598
(1.00)
22q loss 0 (0%) 378 0.0729
(1.00) 		0.0687
(1.00) 		0.7
(1.00) 		0.346
(1.00) 		0.445
(1.00) 		0.0904
(1.00) 		0.501
(1.00) 		0.0867
(1.00) 		0.059
(1.00) 		0.118
(1.00) 		0.00943
(1.00) 		0.0304
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 3.84e-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 150 124 142
1Q GAIN CNV 20 43 23
1Q GAIN WILD-TYPE 130 81 119

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

'2p gain' versus 'CN_CNMF'

P value = 6.42e-14 (Fisher's exact test), Q value = 6e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
2P GAIN CNV 12 60 31
2P GAIN WILD-TYPE 138 64 111

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
2P GAIN CNV 14 36 13
2P GAIN WILD-TYPE 82 46 59

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.22

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 7
2P GAIN WILD-TYPE 69 66 86 48

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.013

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 20
2P GAIN WILD-TYPE 69 52 148

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

'2q gain' versus 'CN_CNMF'

P value = 4.89e-05 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
2Q GAIN CNV 6 26 14
2Q GAIN WILD-TYPE 144 98 128

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

'3q gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
3Q GAIN CNV 50 61 82
3Q GAIN WILD-TYPE 100 63 60

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

'5p gain' versus 'CN_CNMF'

P value = 5.07e-05 (Fisher's exact test), Q value = 0.045

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
5P GAIN CNV 51 59 85
5P GAIN WILD-TYPE 99 65 57

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
7P GAIN CNV 25 55 34
7P GAIN WILD-TYPE 125 69 108

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

'7q gain' versus 'CN_CNMF'

P value = 1.07e-12 (Fisher's exact test), Q value = 1e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
7Q GAIN CNV 16 61 28
7Q GAIN WILD-TYPE 134 63 114

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

'7q gain' versus 'METHLYATION_CNMF'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
7Q GAIN CNV 9 34 12
7Q GAIN WILD-TYPE 87 48 60

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.33e-05 (Fisher's exact test), Q value = 0.021

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 43 15 26
7Q GAIN WILD-TYPE 64 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 = 0.19

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 = 5.64e-07 (Fisher's exact test), Q value = 0.00051

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
12P GAIN CNV 21 53 41
12P GAIN WILD-TYPE 129 71 101

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

'12q gain' versus 'CN_CNMF'

P value = 6.39e-07 (Fisher's exact test), Q value = 0.00058

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
12Q GAIN CNV 6 31 13
12Q GAIN WILD-TYPE 144 93 129

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

'15q gain' versus 'CN_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.012

Table S16.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
15Q GAIN CNV 5 25 10
15Q GAIN WILD-TYPE 145 99 132

Figure S16.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 7.32e-05 (Fisher's exact test), Q value = 0.064

Table S17.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
16Q GAIN CNV 0 11 12
16Q GAIN WILD-TYPE 150 113 130

Figure S17.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.03

Table S18.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
17P GAIN CNV 0 10 1
17P GAIN WILD-TYPE 150 114 141

Figure S18.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 3.06e-10 (Fisher's exact test), Q value = 2.8e-07

Table S19.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
17Q GAIN CNV 3 34 12
17Q GAIN WILD-TYPE 147 90 130

Figure S19.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
18P GAIN CNV 3 20 4 2
18P GAIN WILD-TYPE 39 32 28 26

Figure S20.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0043

Table S21.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
18P GAIN CNV 1 23 1 4
18P GAIN WILD-TYPE 21 33 22 49

Figure S21.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 4.58e-08 (Fisher's exact test), Q value = 4.2e-05

Table S22.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
18P GAIN CNV 16 41 11
18P GAIN WILD-TYPE 134 83 131

Figure S22.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.98e-05 (Fisher's exact test), Q value = 0.044

Table S23.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
18P GAIN CNV 31 5 18
18P GAIN WILD-TYPE 76 65 150

Figure S23.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.22

Table S24.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
18Q GAIN CNV 2 17 1 4
18Q GAIN WILD-TYPE 40 35 31 24

Figure S24.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.11

Table S25.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
18Q GAIN CNV 8 26 11
18Q GAIN WILD-TYPE 142 98 131

Figure S25.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.023

Table S26.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
19P GAIN CNV 6 25 9
19P GAIN WILD-TYPE 144 99 133

Figure S26.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.51e-06 (Fisher's exact test), Q value = 0.0085

Table S27.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 41
19P GAIN CNV 12 0 11
19P GAIN WILD-TYPE 106 72 30

Figure S27.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 9.33e-09 (Fisher's exact test), Q value = 8.6e-06

Table S28.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
20P GAIN CNV 17 51 49
20P GAIN WILD-TYPE 133 73 93

Figure S28.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 2.66e-09 (Fisher's exact test), Q value = 2.5e-06

Table S29.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
20Q GAIN CNV 13 37 54
20Q GAIN WILD-TYPE 137 87 88

Figure S29.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 3.77e-07 (Fisher's exact test), Q value = 0.00034

Table S30.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
22Q GAIN CNV 16 47 38
22Q GAIN WILD-TYPE 134 77 104

Figure S30.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 2.2e-12 (Fisher's exact test), Q value = 2e-09

Table S31.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
1P LOSS CNV 5 42 13
1P LOSS WILD-TYPE 145 82 129

Figure S31.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 4.84e-06 (Fisher's exact test), Q value = 0.0044

Table S32.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
1P LOSS CNV 3 23 8
1P LOSS WILD-TYPE 93 59 64

Figure S32.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

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

Table S33.  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 31 8 3
1P LOSS WILD-TYPE 71 71 103 52

Figure S33.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.0012

Table S34.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
1P LOSS CNV 31 5 12
1P LOSS WILD-TYPE 76 65 156

Figure S34.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 3.7e-07 (Fisher's exact test), Q value = 0.00034

Table S35.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
3P LOSS CNV 34 59 72
3P LOSS WILD-TYPE 116 65 70

Figure S35.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.72e-05 (Fisher's exact test), Q value = 0.015

Table S36.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
3P LOSS CNV 20 40 37
3P LOSS WILD-TYPE 76 42 35

Figure S36.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.68e-10 (Fisher's exact test), Q value = 1.6e-07

Table S37.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
4P LOSS CNV 36 79 57
4P LOSS WILD-TYPE 114 45 85

Figure S37.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 7.54e-08 (Fisher's exact test), Q value = 6.9e-05

Table S38.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
4P LOSS CNV 16 45 34
4P LOSS WILD-TYPE 80 37 38

Figure S38.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.0018

Table S39.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 41
4P LOSS CNV 54 11 23
4P LOSS WILD-TYPE 64 61 18

Figure S39.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 9.29e-12 (Fisher's exact test), Q value = 8.6e-09

Table S40.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
4Q LOSS CNV 29 75 47
4Q LOSS WILD-TYPE 121 49 95

Figure S40.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.0012

Table S41.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
4Q LOSS CNV 14 40 29
4Q LOSS WILD-TYPE 82 42 43

Figure S41.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 5.51e-05 (Fisher's exact test), Q value = 0.048

Table S42.  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 38 15
4Q LOSS WILD-TYPE 60 47 73 40

Figure S42.  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 = 0.035

Table S43.  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 S43.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.014

Table S44.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 41
4Q LOSS CNV 43 9 21
4Q LOSS WILD-TYPE 75 63 20

Figure S44.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 2.94e-10 (Fisher's exact test), Q value = 2.7e-07

Table S45.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
5Q LOSS CNV 24 60 66
5Q LOSS WILD-TYPE 126 64 76

Figure S45.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 2.07e-08 (Fisher's exact test), Q value = 1.9e-05

Table S46.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
5Q LOSS CNV 14 36 40
5Q LOSS WILD-TYPE 82 46 32

Figure S46.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.14

Table S47.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
6P LOSS CNV 5 22 10
6P LOSS WILD-TYPE 145 102 132

Figure S47.  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 = 0.17

Table S48.  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 S48.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 3.28e-09 (Fisher's exact test), Q value = 3e-06

Table S49.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
8P LOSS CNV 22 35 68
8P LOSS WILD-TYPE 128 89 74

Figure S49.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 5.57e-19 (Fisher's exact test), Q value = 5.2e-16

Table S50.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
9P LOSS CNV 26 48 98
9P LOSS WILD-TYPE 124 76 44

Figure S50.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 8.01e-08 (Fisher's exact test), Q value = 7.3e-05

Table S51.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
9P LOSS CNV 18 34 44
9P LOSS WILD-TYPE 78 48 28

Figure S51.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.56e-13 (Fisher's exact test), Q value = 1.5e-10

Table S52.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
9Q LOSS CNV 19 19 70
9Q LOSS WILD-TYPE 131 105 72

Figure S52.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.02

Table S53.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
9Q LOSS CNV 15 13 32
9Q LOSS WILD-TYPE 81 69 40

Figure S53.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 9.61e-05 (Fisher's exact test), Q value = 0.084

Table S54.  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 11 41 15
9Q LOSS WILD-TYPE 55 91 70 40

Figure S54.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.86e-05 (Fisher's exact test), Q value = 0.051

Table S55.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 70 168
9Q LOSS CNV 12 25 52
9Q LOSS WILD-TYPE 95 45 116

Figure S55.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 2.47e-10 (Fisher's exact test), Q value = 2.3e-07

Table S56.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
10P LOSS CNV 9 45 39
10P LOSS WILD-TYPE 141 79 103

Figure S56.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.0013

Table S57.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
10P LOSS CNV 7 32 16
10P LOSS WILD-TYPE 89 50 56

Figure S57.  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 = 0.11

Table S58.  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 S58.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 5.05e-12 (Fisher's exact test), Q value = 4.7e-09

Table S59.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
10Q LOSS CNV 8 48 40
10Q LOSS WILD-TYPE 142 76 102

Figure S59.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 7.18e-06 (Fisher's exact test), Q value = 0.0064

Table S60.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
10Q LOSS CNV 8 31 19
10Q LOSS WILD-TYPE 88 51 53

Figure S60.  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 = 0.2

Table S61.  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 S61.  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 = 0.0079

Table S62.  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 S62.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1.3e-06 (Fisher's exact test), Q value = 0.0012

Table S63.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
11P LOSS CNV 7 22 36
11P LOSS WILD-TYPE 143 102 106

Figure S63.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0019

Table S64.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
11Q LOSS CNV 2 18 23
11Q LOSS WILD-TYPE 148 106 119

Figure S64.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1.43e-10 (Fisher's exact test), Q value = 1.3e-07

Table S65.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
13Q LOSS CNV 29 46 81
13Q LOSS WILD-TYPE 121 78 61

Figure S65.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.000188 (Fisher's exact test), Q value = 0.16

Table S66.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
13Q LOSS CNV 20 34 36
13Q LOSS WILD-TYPE 76 48 36

Figure S66.  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 = 0.00092

Table S67.  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 S67.  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 = 9e-05

Table S68.  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 S68.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.022

Table S69.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 40 108
14Q LOSS CNV 3 12 25
14Q LOSS WILD-TYPE 80 28 83

Figure S69.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 7.08e-06 (Fisher's exact test), Q value = 0.0064

Table S70.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
16P LOSS CNV 7 27 30
16P LOSS WILD-TYPE 143 97 112

Figure S70.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.17

Table S71.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
16Q LOSS CNV 14 29 38
16Q LOSS WILD-TYPE 136 95 104

Figure S71.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.026

Table S72.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 40 108
16Q LOSS CNV 5 7 34
16Q LOSS WILD-TYPE 78 33 74

Figure S72.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 2.18e-06 (Fisher's exact test), Q value = 0.002

Table S73.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
17P LOSS CNV 39 36 75
17P LOSS WILD-TYPE 111 88 67

Figure S73.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.18

Table S74.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
19P LOSS CNV 16 13 38
19P LOSS WILD-TYPE 134 111 104

Figure S74.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1.75e-12 (Fisher's exact test), Q value = 1.6e-09

Table S75.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 124 142
21Q LOSS CNV 15 58 54
21Q LOSS WILD-TYPE 135 66 88

Figure S75.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 5.61e-08 (Fisher's exact test), Q value = 5.2e-05

Table S76.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 82 72
21Q LOSS CNV 8 33 29
21Q LOSS WILD-TYPE 88 49 43

Figure S76.  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 = 0.23

Table S77.  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 S77.  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 = 416

  • 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

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle