Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C10Z717X
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 Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10Z717X
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 472 patients, 104 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF'.

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

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

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

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

  • 10p gain cnv correlated to 'METHLYATION_CNMF'.

  • 10q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • 16p gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

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

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • Xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'METHLYATION_CNMF'.

  • 3p loss cnv correlated to 'METHLYATION_CNMF'.

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

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

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

  • 6q loss cnv correlated to 'METHLYATION_CNMF'.

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

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

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

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

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

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

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

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, 104 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 Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
21q loss 0 (0%) 406 3.03e-12
(2.2e-09) 		1e-07
(7.09e-05) 		0.103
(1.00) 		0.0176
(1.00) 		1.42e-06
(0.000992) 		4.44e-07
(0.000312) 		3.11e-05
(0.0208) 		8.05e-07
(0.000563)
7p gain 0 (0%) 318 0.754
(1.00) 		0.523
(1.00) 		3.08e-18
(2.25e-15) 		1.97e-06
(0.00137) 		8.93e-05
(0.0586) 		0.00948
(1.00) 		3.89e-06
(0.00268) 		7.47e-07
(0.000524) 		0.000553
(0.344) 		0.00525
(1.00)
4q loss 0 (0%) 427 0.00605
(1.00) 		0.00706
(1.00) 		2.2e-10
(1.6e-07) 		4.24e-07
(0.000299) 		0.469
(1.00) 		0.578
(1.00) 		9.1e-05
(0.0597) 		9.39e-08
(6.66e-05) 		0.000386
(0.243) 		0.000579
(0.359)
15q loss 0 (0%) 377 0.405
(1.00) 		0.219
(1.00) 		5.26e-12
(3.82e-09) 		1.41e-09
(1.02e-06) 		0.481
(1.00) 		0.0188
(1.00) 		6.09e-05
(0.0403) 		0.000418
(0.263) 		0.000269
(0.171) 		0.000239
(0.153)
2p gain 0 (0%) 422 0.0312
(1.00) 		0.0151
(1.00) 		7e-08
(4.99e-05) 		3.89e-06
(0.00268) 		0.0781
(1.00) 		0.0301
(1.00) 		0.000256
(0.163) 		0.00124
(0.746) 		0.00021
(0.135) 		0.00512
(1.00)
2q gain 0 (0%) 427 0.0302
(1.00) 		0.0253
(1.00) 		1.69e-06
(0.00118) 		7.92e-07
(0.000555) 		0.252
(1.00) 		0.276
(1.00) 		0.000184
(0.119) 		0.0183
(1.00) 		0.000162
(0.105) 		0.0021
(1.00)
8q gain 0 (0%) 328 0.0641
(1.00) 		0.191
(1.00) 		1.9e-21
(1.4e-18) 		3.32e-07
(0.000235) 		0.0357
(1.00) 		0.00424
(1.00) 		0.000925
(0.564) 		0.00117
(0.707) 		3.06e-07
(0.000216) 		3.97e-07
(0.000281)
12p gain 0 (0%) 415 0.565
(1.00) 		0.132
(1.00) 		3.02e-14
(2.2e-11) 		8.57e-05
(0.0564) 		0.18
(1.00) 		0.115
(1.00) 		0.000964
(0.586) 		0.000375
(0.237) 		0.000257
(0.164) 		0.00357
(1.00)
20p gain 0 (0%) 411 0.0235
(1.00) 		0.0127
(1.00) 		3.06e-06
(0.00211) 		2.78e-05
(0.0186) 		0.0249
(1.00) 		0.687
(1.00) 		5.74e-05
(0.0381) 		0.000135
(0.0881) 		0.0189
(1.00) 		0.00772
(1.00)
20q gain 0 (0%) 396 0.00237
(1.00) 		0.00219
(1.00) 		4.8e-07
(0.000337) 		5.01e-09
(3.6e-06) 		0.00132
(0.789) 		0.0914
(1.00) 		5.59e-06
(0.00382) 		6.15e-05
(0.0407) 		0.00212
(1.00) 		0.0023
(1.00)
4p loss 0 (0%) 434 1.26e-05
(0.00852) 		6.44e-05
(0.0425) 		0.192
(1.00) 		0.248
(1.00) 		0.000668
(0.412) 		4.13e-05
(0.0276) 		0.000102
(0.0667) 		0.0081
(1.00)
7q gain 0 (0%) 361 0.388
(1.00) 		0.702
(1.00) 		5.86e-09
(4.21e-06) 		0.000472
(0.295) 		0.0789
(1.00) 		0.298
(1.00) 		1.68e-05
(0.0113) 		1.22e-05
(0.00827) 		0.142
(1.00) 		0.238
(1.00)
12q gain 0 (0%) 426 0.565
(1.00) 		0.132
(1.00) 		2.9e-12
(2.11e-09) 		0.000184
(0.119) 		0.158
(1.00) 		0.0893
(1.00) 		0.000189
(0.122) 		0.00123
(0.744) 		0.00744
(1.00) 		0.0757
(1.00)
14q gain 0 (0%) 416 4.9e-06
(0.00336) 		2.98e-06
(0.00206) 		0.127
(1.00) 		0.518
(1.00) 		0.000566
(0.351) 		0.0184
(1.00) 		0.0072
(1.00) 		0.000355
(0.225)
5q loss 0 (0%) 414 0.0235
(1.00) 		0.0127
(1.00) 		3.4e-05
(0.0228) 		1.01e-05
(0.00685) 		0.0388
(1.00) 		0.0986
(1.00) 		0.000124
(0.0811) 		0.043
(1.00) 		0.00944
(1.00) 		0.00553
(1.00)
18q loss 0 (0%) 364 0.42
(1.00) 		0.412
(1.00) 		1.68e-09
(1.21e-06) 		0.00016
(0.104) 		0.301
(1.00) 		0.129
(1.00) 		0.000254
(0.163) 		0.0242
(1.00) 		0.135
(1.00) 		0.95
(1.00)
19p loss 0 (0%) 360 0.649
(1.00) 		0.688
(1.00) 		1.56e-09
(1.12e-06) 		7.15e-08
(5.09e-05) 		0.867
(1.00) 		0.69
(1.00) 		7.53e-05
(0.0496) 		0.116
(1.00) 		0.00603
(1.00) 		0.0143
(1.00)
8p gain 0 (0%) 413 3.74e-10
(2.7e-07) 		0.00323
(1.00) 		0.598
(1.00) 		0.842
(1.00) 		4.32e-05
(0.0288) 		0.00568
(1.00) 		0.424
(1.00) 		0.176
(1.00)
16p gain 0 (0%) 405 0.358
(1.00) 		0.322
(1.00) 		0.328
(1.00) 		0.000349
(0.221) 		0.0878
(1.00) 		0.448
(1.00) 		0.000179
(0.116) 		0.015
(1.00) 		0.155
(1.00) 		0.0984
(1.00)
17q gain 0 (0%) 394 0.0447
(1.00) 		0.702
(1.00) 		4.69e-08
(3.35e-05) 		1.39e-06
(0.00097) 		0.423
(1.00) 		0.199
(1.00) 		0.00575
(1.00) 		0.0595
(1.00) 		0.0218
(1.00) 		0.0298
(1.00)
21q gain 0 (0%) 431 0.192
(1.00) 		0.157
(1.00) 		5e-05
(0.0332) 		3.42e-05
(0.0229) 		0.0914
(1.00) 		0.0523
(1.00) 		0.23
(1.00) 		0.17
(1.00) 		0.0596
(1.00) 		0.38
(1.00)
8p loss 0 (0%) 354 0.104
(1.00) 		0.173
(1.00) 		4.75e-14
(3.46e-11) 		2e-06
(0.00139) 		0.173
(1.00) 		0.0281
(1.00) 		0.0403
(1.00) 		0.00246
(1.00) 		0.0271
(1.00) 		0.00979
(1.00)
9p loss 0 (0%) 333 0.155
(1.00) 		0.206
(1.00) 		2.7e-08
(1.93e-05) 		2.59e-05
(0.0174) 		0.345
(1.00) 		0.049
(1.00) 		0.00893
(1.00) 		0.0275
(1.00) 		0.797
(1.00) 		0.701
(1.00)
9q loss 0 (0%) 355 0.462
(1.00) 		0.475
(1.00) 		8.17e-08
(5.81e-05) 		1.07e-08
(7.67e-06) 		0.323
(1.00) 		0.144
(1.00) 		0.0193
(1.00) 		0.0131
(1.00) 		0.101
(1.00) 		0.21
(1.00)
13q loss 0 (0%) 363 0.0846
(1.00) 		0.0411
(1.00) 		3.55e-21
(2.61e-18) 		6.46e-07
(0.000454) 		0.285
(1.00) 		0.00936
(1.00) 		0.000966
(0.586) 		0.0668
(1.00) 		0.00306
(1.00) 		0.0328
(1.00)
22q loss 0 (0%) 382 0.308
(1.00) 		0.321
(1.00) 		5.75e-10
(4.15e-07) 		4.56e-05
(0.0303) 		0.00909
(1.00) 		0.011
(1.00) 		0.0202
(1.00) 		0.00747
(1.00) 		0.000398
(0.251) 		0.00182
(1.00)
1p gain 0 (0%) 414 1
(1.00) 		1
(1.00) 		3.6e-08
(2.57e-05) 		0.000565
(0.351) 		0.0815
(1.00) 		0.0241
(1.00) 		0.0243
(1.00) 		0.31
(1.00) 		0.635
(1.00) 		0.763
(1.00)
1q gain 0 (0%) 295 0.465
(1.00) 		0.885
(1.00) 		0.0352
(1.00) 		1.88e-05
(0.0127) 		0.131
(1.00) 		0.146
(1.00) 		0.000659
(0.407) 		0.703
(1.00) 		0.534
(1.00) 		0.598
(1.00)
5p gain 0 (0%) 294 0.487
(1.00) 		0.419
(1.00) 		9.1e-15
(6.65e-12) 		0.156
(1.00) 		0.233
(1.00) 		0.636
(1.00) 		0.0188
(1.00) 		0.0313
(1.00) 		0.19
(1.00) 		0.0971
(1.00)
6p gain 0 (0%) 401 0.292
(1.00) 		0.0507
(1.00) 		0.0199
(1.00) 		3.77e-06
(0.0026) 		0.00936
(1.00) 		0.261
(1.00) 		0.00282
(1.00) 		0.261
(1.00) 		0.0703
(1.00) 		0.342
(1.00)
10p gain 0 (0%) 423 0.0417
(1.00) 		0.00011
(0.0721) 		0.169
(1.00) 		0.16
(1.00) 		0.00385
(1.00) 		0.107
(1.00) 		0.0955
(1.00) 		0.277
(1.00)
10q gain 0 (0%) 444 0.107
(1.00) 		0.0237
(1.00) 		0.555
(1.00) 		0.188
(1.00) 		1.67e-05
(0.0113) 		0.253
(1.00) 		0.609
(1.00) 		0.292
(1.00)
17p gain 0 (0%) 444 8.73e-06
(0.00595) 		0.000427
(0.268) 		0.665
(1.00) 		0.533
(1.00) 		0.609
(1.00) 		0.334
(1.00) 		0.0634
(1.00) 		0.146
(1.00)
18p gain 0 (0%) 430 2.13e-06
(0.00148) 		0.00112
(0.678) 		0.0711
(1.00) 		0.209
(1.00) 		0.256
(1.00) 		0.054
(1.00) 		0.0163
(1.00) 		0.0164
(1.00)
18q gain 0 (0%) 446 2.2e-05
(0.0148) 		0.000608
(0.377) 		0.09
(1.00) 		0.0373
(1.00) 		0.0343
(1.00) 		0.00139
(0.834) 		0.102
(1.00) 		0.0336
(1.00)
Xq gain 0 (0%) 453 0.75
(1.00) 		0.591
(1.00) 		0.000237
(0.152) 		0.0425
(1.00) 		0.433
(1.00) 		0.598
(1.00) 		0.299
(1.00) 		0.378
(1.00) 		0.625
(1.00) 		0.641
(1.00)
1p loss 0 (0%) 444 0.00445
(1.00) 		0.000214
(0.137) 		0.111
(1.00) 		0.199
(1.00) 		0.113
(1.00) 		0.189
(1.00) 		0.789
(1.00) 		0.146
(1.00)
3p loss 0 (0%) 379 0.208
(1.00) 		0.176
(1.00) 		0.000456
(0.286) 		1.53e-05
(0.0104) 		0.156
(1.00) 		0.402
(1.00) 		0.539
(1.00) 		0.036
(1.00) 		0.0313
(1.00) 		0.0211
(1.00)
6q loss 0 (0%) 367 0.803
(1.00) 		0.722
(1.00) 		0.0704
(1.00) 		4.4e-06
(0.00302) 		0.104
(1.00) 		0.0335
(1.00) 		0.0157
(1.00) 		0.154
(1.00) 		0.397
(1.00) 		0.868
(1.00)
16p loss 0 (0%) 435 0.000307
(0.195) 		0.00182
(1.00) 		0.0447
(1.00) 		0.281
(1.00) 		0.135
(1.00) 		0.114
(1.00) 		0.0969
(1.00) 		0.0808
(1.00)
16q loss 0 (0%) 416 0.0159
(1.00) 		1
(1.00) 		4.64e-06
(0.00319) 		0.00148
(0.887) 		0.00595
(1.00) 		0.00855
(1.00) 		0.00803
(1.00) 		0.228
(1.00) 		0.0149
(1.00) 		0.218
(1.00)
17p loss 0 (0%) 363 0.13
(1.00) 		0.301
(1.00) 		5.86e-06
(0.004) 		0.00353
(1.00) 		0.0572
(1.00) 		0.21
(1.00) 		0.45
(1.00) 		0.444
(1.00) 		0.592
(1.00) 		0.6
(1.00)
18p loss 0 (0%) 397 0.42
(1.00) 		0.412
(1.00) 		1.14e-05
(0.00777) 		0.0198
(1.00) 		0.88
(1.00) 		0.223
(1.00) 		0.0335
(1.00) 		0.289
(1.00) 		0.688
(1.00) 		0.858
(1.00)
19q loss 0 (0%) 405 0.71
(1.00) 		0.722
(1.00) 		0.00019
(0.123) 		0.0288
(1.00) 		0.778
(1.00) 		0.433
(1.00) 		0.00814
(1.00) 		0.438
(1.00) 		0.0181
(1.00) 		0.0705
(1.00)
20p loss 0 (0%) 411 0.192
(1.00) 		0.412
(1.00) 		0.000194
(0.125) 		0.0535
(1.00) 		0.00631
(1.00) 		0.0252
(1.00) 		0.114
(1.00) 		0.182
(1.00) 		0.725
(1.00) 		0.108
(1.00)
3p gain 0 (0%) 459 0.0322
(1.00) 		0.0462
(1.00) 		0.137
(1.00) 		0.271
(1.00) 		0.00703
(1.00) 		0.0018
(1.00) 		0.876
(1.00) 		0.664
(1.00)
3q gain 0 (0%) 443 0.0025
(1.00) 		0.00235
(1.00) 		0.0783
(1.00) 		0.0222
(1.00) 		0.00456
(1.00) 		0.107
(1.00) 		0.043
(1.00) 		0.358
(1.00)
4p gain 0 (0%) 442 0.554
(1.00) 		0.418
(1.00) 		0.00352
(1.00) 		0.0102
(1.00) 		0.0727
(1.00) 		0.035
(1.00) 		0.76
(1.00) 		0.311
(1.00) 		0.491
(1.00) 		0.368
(1.00)
4q gain 0 (0%) 461 0.0379
(1.00) 		0.838
(1.00) 		0.222
(1.00) 		0.271
(1.00) 		0.775
(1.00) 		0.232
(1.00) 		0.104
(1.00) 		0.126
(1.00)
5q gain 0 (0%) 416 0.0177
(1.00) 		0.644
(1.00) 		0.0451
(1.00) 		0.000742
(0.456) 		0.541
(1.00) 		0.187
(1.00) 		0.0166
(1.00) 		0.0411
(1.00) 		0.356
(1.00) 		0.104
(1.00)
6q gain 0 (0%) 452 0.41
(1.00) 		0.00965
(1.00) 		0.108
(1.00) 		0.0645
(1.00) 		0.0518
(1.00) 		0.463
(1.00) 		0.0606
(1.00) 		0.0232
(1.00)
9p gain 0 (0%) 458 0.0173
(1.00) 		0.0112
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.347
(1.00) 		0.237
(1.00) 		0.471
(1.00) 		0.227
(1.00)
9q gain 0 (0%) 465 0.274
(1.00) 		0.59
(1.00) 		0.392
(1.00) 		0.269
(1.00) 		0.47
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.239
(1.00)
11p gain 0 (0%) 437 0.0527
(1.00) 		0.0419
(1.00) 		0.101
(1.00) 		0.476
(1.00) 		0.053
(1.00) 		0.274
(1.00) 		0.0313
(1.00) 		0.129
(1.00)
11q gain 0 (0%) 421 0.12
(1.00) 		0.157
(1.00) 		0.000915
(0.559) 		0.0131
(1.00) 		0.000824
(0.505) 		0.0196
(1.00) 		0.0049
(1.00) 		0.00207
(1.00) 		0.00333
(1.00) 		0.0193
(1.00)
13q gain 0 (0%) 457 0.226
(1.00) 		0.0272
(1.00) 		0.433
(1.00) 		0.294
(1.00) 		0.106
(1.00) 		0.163
(1.00) 		0.833
(1.00) 		0.269
(1.00)
15q gain 0 (0%) 458 0.263
(1.00) 		0.542
(1.00) 		0.819
(1.00) 		0.578
(1.00) 		0.2
(1.00) 		0.212
(1.00) 		0.548
(1.00) 		0.415
(1.00)
16q gain 0 (0%) 430 0.192
(1.00) 		0.0514
(1.00) 		0.428
(1.00) 		0.00977
(1.00) 		0.0253
(1.00) 		0.0252
(1.00) 		0.0103
(1.00) 		0.222
(1.00) 		0.163
(1.00) 		0.0605
(1.00)
19p gain 0 (0%) 466 0.773
(1.00) 		0.372
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.482
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.862
(1.00)
19q gain 0 (0%) 450 0.000461
(0.288) 		0.176
(1.00) 		0.402
(1.00) 		0.0144
(1.00) 		0.00341
(1.00) 		0.0431
(1.00) 		0.0966
(1.00) 		0.0683
(1.00)
22q gain 0 (0%) 452 0.061
(1.00) 		0.13
(1.00) 		0.782
(1.00) 		0.172
(1.00) 		0.175
(1.00) 		0.398
(1.00) 		0.0929
(1.00) 		0.0564
(1.00)
1q loss 0 (0%) 461 0.0619
(1.00) 		0.0811
(1.00) 		0.222
(1.00) 		0.0151
(1.00) 		0.544
(1.00) 		0.343
(1.00) 		0.418
(1.00) 		0.0968
(1.00)
2p loss 0 (0%) 466 0.931
(1.00) 		0.466
(1.00) 		1
(1.00) 		0.617
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.862
(1.00)
2q loss 0 (0%) 468 0.149
(1.00) 		0.227
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.544
(1.00) 		0.797
(1.00)
3q loss 0 (0%) 416 0.554
(1.00) 		0.418
(1.00) 		0.0107
(1.00) 		0.00335
(1.00) 		0.341
(1.00) 		0.933
(1.00) 		0.14
(1.00) 		0.448
(1.00) 		0.429
(1.00) 		0.0242
(1.00)
5p loss 0 (0%) 457 0.00645
(1.00) 		0.008
(1.00) 		0.306
(1.00) 		0.777
(1.00) 		0.64
(1.00) 		0.0348
(1.00) 		0.17
(1.00) 		0.227
(1.00)
6p loss 0 (0%) 434 0.335
(1.00) 		0.308
(1.00) 		0.0252
(1.00) 		0.0374
(1.00) 		0.202
(1.00) 		0.537
(1.00) 		0.162
(1.00) 		0.973
(1.00) 		0.239
(1.00) 		0.745
(1.00)
7p loss 0 (0%) 458 0.554
(1.00) 		0.418
(1.00) 		0.00723
(1.00) 		0.312
(1.00) 		0.522
(1.00) 		0.938
(1.00) 		0.0244
(1.00) 		0.067
(1.00) 		0.1
(1.00) 		0.801
(1.00)
7q loss 0 (0%) 455 0.53
(1.00) 		0.186
(1.00) 		0.0305
(1.00) 		0.411
(1.00) 		0.687
(1.00) 		0.821
(1.00) 		0.315
(1.00) 		0.272
(1.00) 		1
(1.00) 		0.734
(1.00)
8q loss 0 (0%) 455 0.000943
(0.574) 		0.09
(1.00) 		0.00124
(0.747) 		0.00526
(1.00) 		0.328
(1.00) 		0.0477
(1.00) 		0.951
(1.00) 		0.69
(1.00)
10p loss 0 (0%) 437 0.901
(1.00) 		0.818
(1.00) 		0.000707
(0.435) 		0.000889
(0.544) 		0.0525
(1.00) 		0.0991
(1.00) 		0.0832
(1.00) 		0.51
(1.00) 		0.0453
(1.00) 		0.0128
(1.00)
10q loss 0 (0%) 427 0.75
(1.00) 		0.591
(1.00) 		0.00124
(0.747) 		0.00454
(1.00) 		0.0157
(1.00) 		0.0585
(1.00) 		0.0258
(1.00) 		0.609
(1.00) 		0.311
(1.00) 		0.0264
(1.00)
11p loss 0 (0%) 440 0.335
(1.00) 		0.102
(1.00) 		0.00053
(0.331) 		0.846
(1.00) 		0.00454
(1.00) 		0.0268
(1.00) 		0.042
(1.00) 		0.054
(1.00) 		0.159
(1.00) 		0.0977
(1.00)
11q loss 0 (0%) 443 0.474
(1.00) 		0.157
(1.00) 		0.00271
(1.00) 		0.5
(1.00) 		0.0102
(1.00) 		0.0251
(1.00) 		0.452
(1.00) 		0.211
(1.00) 		0.384
(1.00) 		0.827
(1.00)
12p loss 0 (0%) 435 0.728
(1.00) 		0.818
(1.00) 		0.229
(1.00) 		0.000653
(0.404) 		0.819
(1.00) 		0.534
(1.00) 		0.072
(1.00) 		0.593
(1.00) 		0.269
(1.00) 		0.711
(1.00)
12q loss 0 (0%) 449 0.0787
(1.00) 		0.131
(1.00) 		0.886
(1.00) 		0.305
(1.00) 		0.404
(1.00) 		0.921
(1.00) 		0.386
(1.00) 		0.822
(1.00)
14q loss 0 (0%) 426 0.401
(1.00) 		0.418
(1.00) 		0.0631
(1.00) 		0.0245
(1.00) 		0.0306
(1.00) 		0.00488
(1.00) 		0.0971
(1.00) 		0.665
(1.00) 		0.0755
(1.00) 		0.167
(1.00)
17q loss 0 (0%) 455 0.155
(1.00) 		0.0222
(1.00) 		0.0661
(1.00) 		0.897
(1.00) 		0.476
(1.00) 		0.198
(1.00) 		0.854
(1.00) 		0.0271
(1.00)
20q loss 0 (0%) 448 0.262
(1.00) 		0.139
(1.00) 		0.325
(1.00) 		0.306
(1.00) 		0.419
(1.00) 		0.333
(1.00) 		0.635
(1.00) 		0.555
(1.00)
Xq loss 0 (0%) 461 0.253
(1.00) 		0.281
(1.00) 		0.74
(1.00) 		0.572
(1.00) 		0.0554
(1.00) 		0.363
(1.00) 		0.794
(1.00) 		0.35
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 3.6e-08 (Fisher's exact test), Q value = 2.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
1P GAIN CNV 39 9 6 4
1P GAIN WILD-TYPE 109 179 81 45

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.88e-05 (Chi-square test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
1Q GAIN CNV 37 41 42 17 15
1Q GAIN WILD-TYPE 53 53 53 83 10

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

'2p gain' versus 'CN_CNMF'

P value = 7e-08 (Fisher's exact test), Q value = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
2P GAIN CNV 21 3 15 11
2P GAIN WILD-TYPE 127 185 72 38

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 3.89e-06 (Chi-square test), Q value = 0.0027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
2P GAIN CNV 4 22 8 2 4
2P GAIN WILD-TYPE 86 72 87 98 21

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.000256 (Chi-square test), Q value = 0.16

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
2P GAIN CNV 7 3 15 7 1 10 1 1 0
2P GAIN WILD-TYPE 68 52 41 35 28 38 38 23 23

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
2P GAIN CNV 10 35 5
2P GAIN WILD-TYPE 161 163 93

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.0012

Table S7.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
2Q GAIN CNV 13 5 15 12
2Q GAIN WILD-TYPE 135 183 72 37

Figure S7.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 7.92e-07 (Chi-square test), Q value = 0.00055

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
2Q GAIN CNV 5 22 8 0 3
2Q GAIN WILD-TYPE 85 72 87 100 22

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.000184 (Chi-square test), Q value = 0.12

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
2Q GAIN CNV 5 4 14 9 1 6 0 1 0
2Q GAIN WILD-TYPE 70 51 42 33 28 42 39 23 23

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.1

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
2Q GAIN CNV 10 32 3
2Q GAIN WILD-TYPE 161 166 95

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 9.1e-15 (Fisher's exact test), Q value = 6.7e-12

Table S11.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
5P GAIN CNV 93 39 24 22
5P GAIN WILD-TYPE 55 149 63 27

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 3.77e-06 (Chi-square test), Q value = 0.0026

Table S12.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
6P GAIN CNV 13 27 8 4 7
6P GAIN WILD-TYPE 77 67 87 96 18

Figure S12.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3.08e-18 (Fisher's exact test), Q value = 2.3e-15

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
7P GAIN CNV 89 26 28 11
7P GAIN WILD-TYPE 59 162 59 38

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1.97e-06 (Chi-square test), Q value = 0.0014

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
7P GAIN CNV 25 35 38 20 19
7P GAIN WILD-TYPE 65 59 57 80 6

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 8.93e-05 (Fisher's exact test), Q value = 0.059

Table S15.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 75
7P GAIN CNV 38 13 35
7P GAIN WILD-TYPE 47 62 40

Figure S15.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3.89e-06 (Chi-square test), Q value = 0.0027

Table S16.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
7P GAIN CNV 40 27 19 6 4 12 13 10 2
7P GAIN WILD-TYPE 35 28 37 36 25 36 26 14 21

Figure S16.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.47e-07 (Fisher's exact test), Q value = 0.00052

Table S17.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
7P GAIN CNV 39 58 36
7P GAIN WILD-TYPE 119 47 92

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 5.86e-09 (Fisher's exact test), Q value = 4.2e-06

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
7Q GAIN CNV 61 22 20 8
7Q GAIN WILD-TYPE 87 166 67 41

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.68e-05 (Chi-square test), Q value = 0.011

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
7Q GAIN CNV 35 16 13 4 3 7 9 9 2
7Q GAIN WILD-TYPE 40 39 43 38 26 41 30 15 21

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.0083

Table S20.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
7Q GAIN CNV 29 45 24
7Q GAIN WILD-TYPE 129 60 104

Figure S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 3.74e-10 (Fisher's exact test), Q value = 2.7e-07

Table S21.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
8P GAIN CNV 14 11 11 23
8P GAIN WILD-TYPE 134 177 76 26

Figure S21.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 4.32e-05 (Chi-square test), Q value = 0.029

Table S22.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
8P GAIN CNV 3 6 5 5 2 17 2 3 2
8P GAIN WILD-TYPE 72 49 51 37 27 31 37 21 21

Figure S22.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.9e-21 (Fisher's exact test), Q value = 1.4e-18

Table S23.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
8Q GAIN CNV 56 17 34 37
8Q GAIN WILD-TYPE 92 171 53 12

Figure S23.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 3.32e-07 (Chi-square test), Q value = 0.00023

Table S24.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
8Q GAIN CNV 17 48 34 16 8
8Q GAIN WILD-TYPE 73 46 61 84 17

Figure S24.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 3.06e-07 (Fisher's exact test), Q value = 0.00022

Table S25.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
8Q GAIN CNV 27 81 34
8Q GAIN WILD-TYPE 144 117 64

Figure S25.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.97e-07 (Fisher's exact test), Q value = 0.00028

Table S26.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 244 59
8Q GAIN CNV 27 100 15
8Q GAIN WILD-TYPE 137 144 44

Figure S26.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Chi-square test), Q value = 0.072

Table S27.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
10P GAIN CNV 4 17 18 3 1
10P GAIN WILD-TYPE 86 77 77 97 24

Figure S27.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 1.67e-05 (Chi-square test), Q value = 0.011

Table S28.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
10Q GAIN CNV 3 0 3 11 2 3 1 1 0
10Q GAIN WILD-TYPE 72 55 53 31 27 45 38 23 23

Figure S28.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 3.02e-14 (Fisher's exact test), Q value = 2.2e-11

Table S29.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
12P GAIN CNV 16 3 32 6
12P GAIN WILD-TYPE 132 185 55 43

Figure S29.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 8.57e-05 (Chi-square test), Q value = 0.056

Table S30.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
12P GAIN CNV 1 22 9 10 3
12P GAIN WILD-TYPE 89 72 86 90 22

Figure S30.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.24

Table S31.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
12P GAIN CNV 9 12 27
12P GAIN WILD-TYPE 149 93 101

Figure S31.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.16

Table S32.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
12P GAIN CNV 9 37 10
12P GAIN WILD-TYPE 162 161 88

Figure S32.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 2.9e-12 (Fisher's exact test), Q value = 2.1e-09

Table S33.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
12Q GAIN CNV 9 3 27 7
12Q GAIN WILD-TYPE 139 185 60 42

Figure S33.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.000184 (Chi-square test), Q value = 0.12

Table S34.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
12Q GAIN CNV 1 18 5 7 3
12Q GAIN WILD-TYPE 89 76 90 93 22

Figure S34.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.000189 (Chi-square test), Q value = 0.12

Table S35.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
12Q GAIN CNV 7 1 5 3 4 14 5 0 0
12Q GAIN WILD-TYPE 68 54 51 39 25 34 34 24 23

Figure S35.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 4.9e-06 (Fisher's exact test), Q value = 0.0034

Table S36.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
14Q GAIN CNV 19 9 12 16
14Q GAIN WILD-TYPE 129 179 75 33

Figure S36.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 2.98e-06 (Chi-square test), Q value = 0.0021

Table S37.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
14Q GAIN CNV 8 26 8 4 6
14Q GAIN WILD-TYPE 82 68 87 96 19

Figure S37.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000355 (Fisher's exact test), Q value = 0.22

Table S38.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 244 59
14Q GAIN CNV 7 38 10
14Q GAIN WILD-TYPE 157 206 49

Figure S38.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.000349 (Chi-square test), Q value = 0.22

Table S39.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
16P GAIN CNV 23 10 9 7 7
16P GAIN WILD-TYPE 67 84 86 93 18

Figure S39.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000179 (Chi-square test), Q value = 0.12

Table S40.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
16P GAIN CNV 8 20 2 5 3 5 7 5 2
16P GAIN WILD-TYPE 67 35 54 37 26 43 32 19 21

Figure S40.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 8.73e-06 (Fisher's exact test), Q value = 0.006

Table S41.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
17P GAIN CNV 5 3 13 7
17P GAIN WILD-TYPE 143 185 74 42

Figure S41.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 4.69e-08 (Fisher's exact test), Q value = 3.3e-05

Table S42.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
17Q GAIN CNV 37 9 22 10
17Q GAIN WILD-TYPE 111 179 65 39

Figure S42.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1.39e-06 (Chi-square test), Q value = 0.00097

Table S43.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
17Q GAIN CNV 9 26 20 3 9
17Q GAIN WILD-TYPE 81 68 75 97 16

Figure S43.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 2.13e-06 (Fisher's exact test), Q value = 0.0015

Table S44.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
18P GAIN CNV 22 5 4 11
18P GAIN WILD-TYPE 126 183 83 38

Figure S44.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 2.2e-05 (Fisher's exact test), Q value = 0.015

Table S45.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
18Q GAIN CNV 12 2 3 9
18Q GAIN WILD-TYPE 136 186 84 40

Figure S45.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 3.06e-06 (Fisher's exact test), Q value = 0.0021

Table S46.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
20P GAIN CNV 15 11 22 13
20P GAIN WILD-TYPE 133 177 65 36

Figure S46.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 2.78e-05 (Chi-square test), Q value = 0.019

Table S47.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
20P GAIN CNV 7 26 9 6 5
20P GAIN WILD-TYPE 83 68 86 94 20

Figure S47.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 5.74e-05 (Chi-square test), Q value = 0.038

Table S48.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
20P GAIN CNV 7 4 19 6 3 12 2 1 1
20P GAIN WILD-TYPE 68 51 37 36 26 36 37 23 22

Figure S48.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.088

Table S49.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
20P GAIN CNV 15 8 32
20P GAIN WILD-TYPE 143 97 96

Figure S49.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 4.8e-07 (Fisher's exact test), Q value = 0.00034

Table S50.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
20Q GAIN CNV 27 11 26 12
20Q GAIN WILD-TYPE 121 177 61 37

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.01e-09 (Chi-square test), Q value = 3.6e-06

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
20Q GAIN CNV 8 30 9 7 11
20Q GAIN WILD-TYPE 82 64 86 93 14

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 5.59e-06 (Chi-square test), Q value = 0.0038

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
20Q GAIN CNV 8 7 24 5 5 14 3 3 1
20Q GAIN WILD-TYPE 67 48 32 37 24 34 36 21 22

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.041

Table S53.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
20Q GAIN CNV 20 11 39
20Q GAIN WILD-TYPE 138 94 89

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S54.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
21Q GAIN CNV 27 8 4 2
21Q GAIN WILD-TYPE 121 180 83 47

Figure S54.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 3.42e-05 (Chi-square test), Q value = 0.023

Table S55.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
21Q GAIN CNV 8 7 11 1 8
21Q GAIN WILD-TYPE 82 87 84 99 17

Figure S55.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Xq gain' versus 'CN_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.15

Table S56.  Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
XQ GAIN CNV 10 0 6 3
XQ GAIN WILD-TYPE 138 188 81 46

Figure S56.  Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.000214 (Chi-square test), Q value = 0.14

Table S57.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
1P LOSS CNV 5 15 3 1 1
1P LOSS WILD-TYPE 85 79 92 99 24

Figure S57.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.53e-05 (Chi-square test), Q value = 0.01

Table S58.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
3P LOSS CNV 14 33 22 6 6
3P LOSS WILD-TYPE 76 61 73 94 19

Figure S58.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0085

Table S59.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
4P LOSS CNV 12 4 11 11
4P LOSS WILD-TYPE 136 184 76 38

Figure S59.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 6.44e-05 (Chi-square test), Q value = 0.042

Table S60.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
4P LOSS CNV 2 17 5 3 4
4P LOSS WILD-TYPE 88 77 90 97 21

Figure S60.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.13e-05 (Fisher's exact test), Q value = 0.028

Table S61.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
4P LOSS CNV 4 7 22
4P LOSS WILD-TYPE 154 98 106

Figure S61.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.067

Table S62.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
4P LOSS CNV 7 28 2
4P LOSS WILD-TYPE 164 170 96

Figure S62.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 2.2e-10 (Fisher's exact test), Q value = 1.6e-07

Table S63.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
4Q LOSS CNV 15 1 17 12
4Q LOSS WILD-TYPE 133 187 70 37

Figure S63.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 4.24e-07 (Chi-square test), Q value = 3e-04

Table S64.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
4Q LOSS CNV 2 21 4 4 5
4Q LOSS WILD-TYPE 88 73 91 96 20

Figure S64.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 9.1e-05 (Chi-square test), Q value = 0.06

Table S65.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
4Q LOSS CNV 5 1 11 2 1 13 3 3 0
4Q LOSS WILD-TYPE 70 54 45 40 28 35 36 21 23

Figure S65.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.39e-08 (Fisher's exact test), Q value = 6.7e-05

Table S66.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
4Q LOSS CNV 5 5 29
4Q LOSS WILD-TYPE 153 100 99

Figure S66.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.000386 (Fisher's exact test), Q value = 0.24

Table S67.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
4Q LOSS CNV 7 31 6
4Q LOSS WILD-TYPE 164 167 92

Figure S67.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.023

Table S68.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
5Q LOSS CNV 23 8 19 8
5Q LOSS WILD-TYPE 125 180 68 41

Figure S68.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Chi-square test), Q value = 0.0069

Table S69.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
5Q LOSS CNV 5 24 13 3 5
5Q LOSS WILD-TYPE 85 70 82 97 20

Figure S69.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.000124 (Chi-square test), Q value = 0.081

Table S70.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
5Q LOSS CNV 16 2 16 5 5 5 0 2 0
5Q LOSS WILD-TYPE 59 53 40 37 24 43 39 22 23

Figure S70.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 4.4e-06 (Chi-square test), Q value = 0.003

Table S71.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
6Q LOSS CNV 29 29 27 4 4
6Q LOSS WILD-TYPE 61 65 68 96 21

Figure S71.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 4.75e-14 (Fisher's exact test), Q value = 3.5e-11

Table S72.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
8P LOSS CNV 69 18 24 7
8P LOSS WILD-TYPE 79 170 63 42

Figure S72.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 2e-06 (Chi-square test), Q value = 0.0014

Table S73.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
8P LOSS CNV 17 25 33 10 14
8P LOSS WILD-TYPE 73 69 62 90 11

Figure S73.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.7e-08 (Fisher's exact test), Q value = 1.9e-05

Table S74.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
9P LOSS CNV 50 35 46 8
9P LOSS WILD-TYPE 98 153 41 41

Figure S74.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2.59e-05 (Chi-square test), Q value = 0.017

Table S75.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
9P LOSS CNV 26 43 27 13 10
9P LOSS WILD-TYPE 64 51 68 87 15

Figure S75.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 8.17e-08 (Fisher's exact test), Q value = 5.8e-05

Table S76.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
9Q LOSS CNV 44 22 37 14
9Q LOSS WILD-TYPE 104 166 50 35

Figure S76.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.07e-08 (Chi-square test), Q value = 7.7e-06

Table S77.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
9Q LOSS CNV 18 43 17 9 10
9Q LOSS WILD-TYPE 72 51 78 91 15

Figure S77.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3.55e-21 (Fisher's exact test), Q value = 2.6e-18

Table S78.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
13Q LOSS CNV 58 4 31 16
13Q LOSS WILD-TYPE 90 184 56 33

Figure S78.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 6.46e-07 (Chi-square test), Q value = 0.00045

Table S79.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
13Q LOSS CNV 18 25 21 8 15
13Q LOSS WILD-TYPE 72 69 74 92 10

Figure S79.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 5.26e-12 (Fisher's exact test), Q value = 3.8e-09

Table S80.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
15Q LOSS CNV 48 9 22 16
15Q LOSS WILD-TYPE 100 179 65 33

Figure S80.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1.41e-09 (Chi-square test), Q value = 1e-06

Table S81.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
15Q LOSS CNV 11 32 21 4 13
15Q LOSS WILD-TYPE 79 62 74 96 12

Figure S81.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 6.09e-05 (Chi-square test), Q value = 0.04

Table S82.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
15Q LOSS CNV 23 17 16 1 3 14 3 1 2
15Q LOSS WILD-TYPE 52 38 40 41 26 34 36 23 21

Figure S82.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.17

Table S83.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
15Q LOSS CNV 19 55 20
15Q LOSS WILD-TYPE 152 143 78

Figure S83.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000239 (Fisher's exact test), Q value = 0.15

Table S84.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 244 59
15Q LOSS CNV 17 64 13
15Q LOSS WILD-TYPE 147 180 46

Figure S84.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.000307 (Fisher's exact test), Q value = 0.19

Table S85.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
16P LOSS CNV 15 4 13 5
16P LOSS WILD-TYPE 133 184 74 44

Figure S85.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 4.64e-06 (Fisher's exact test), Q value = 0.0032

Table S86.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
16Q LOSS CNV 28 6 15 7
16Q LOSS WILD-TYPE 120 182 72 42

Figure S86.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 5.86e-06 (Fisher's exact test), Q value = 0.004

Table S87.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
17P LOSS CNV 53 23 20 13
17P LOSS WILD-TYPE 95 165 67 36

Figure S87.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0078

Table S88.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
18P LOSS CNV 35 14 22 4
18P LOSS WILD-TYPE 113 174 65 45

Figure S88.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1.68e-09 (Fisher's exact test), Q value = 1.2e-06

Table S89.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
18Q LOSS CNV 52 22 31 3
18Q LOSS WILD-TYPE 96 166 56 46

Figure S89.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Chi-square test), Q value = 0.1

Table S90.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
18Q LOSS CNV 23 21 29 11 13
18Q LOSS WILD-TYPE 67 73 66 89 12

Figure S90.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.000254 (Chi-square test), Q value = 0.16

Table S91.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
18Q LOSS CNV 24 21 14 2 10 5 8 3 2
18Q LOSS WILD-TYPE 51 34 42 40 19 43 31 21 21

Figure S91.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1.56e-09 (Fisher's exact test), Q value = 1.1e-06

Table S92.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
19P LOSS CNV 32 22 41 17
19P LOSS WILD-TYPE 116 166 46 32

Figure S92.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 7.15e-08 (Chi-square test), Q value = 5.1e-05

Table S93.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
19P LOSS CNV 20 39 15 6 5
19P LOSS WILD-TYPE 70 55 80 94 20

Figure S93.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 7.53e-05 (Chi-square test), Q value = 0.05

Table S94.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
19P LOSS CNV 16 14 16 23 7 14 6 3 0
19P LOSS WILD-TYPE 59 41 40 19 22 34 33 21 23

Figure S94.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S95.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
19Q LOSS CNV 27 12 21 7
19Q LOSS WILD-TYPE 121 176 66 42

Figure S95.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.000194 (Fisher's exact test), Q value = 0.13

Table S96.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
20P LOSS CNV 30 11 16 4
20P LOSS WILD-TYPE 118 177 71 45

Figure S96.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 3.03e-12 (Fisher's exact test), Q value = 2.2e-09

Table S97.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
21Q LOSS CNV 13 8 30 15
21Q LOSS WILD-TYPE 135 180 57 34

Figure S97.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-07 (Chi-square test), Q value = 7.1e-05

Table S98.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
21Q LOSS CNV 8 31 8 6 3
21Q LOSS WILD-TYPE 82 63 87 94 22

Figure S98.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1.42e-06 (Chi-square test), Q value = 0.00099

Table S99.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 75 55 56 42 29 48 39 24 23
21Q LOSS CNV 4 4 11 6 5 20 5 2 0
21Q LOSS WILD-TYPE 71 51 45 36 24 28 34 22 23

Figure S99.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.44e-07 (Fisher's exact test), Q value = 0.00031

Table S100.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
21Q LOSS CNV 13 7 37
21Q LOSS WILD-TYPE 145 98 91

Figure S100.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 3.11e-05 (Fisher's exact test), Q value = 0.021

Table S101.  Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
21Q LOSS CNV 12 44 8
21Q LOSS WILD-TYPE 159 154 90

Figure S101.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.05e-07 (Fisher's exact test), Q value = 0.00056

Table S102.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 244 59
21Q LOSS CNV 11 52 1
21Q LOSS WILD-TYPE 153 192 58

Figure S102.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 5.75e-10 (Fisher's exact test), Q value = 4.2e-07

Table S103.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
22Q LOSS CNV 39 10 24 17
22Q LOSS WILD-TYPE 109 178 63 32

Figure S103.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.56e-05 (Chi-square test), Q value = 0.03

Table S104.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
22Q LOSS CNV 12 32 14 9 7
22Q LOSS WILD-TYPE 78 62 81 91 18

Figure S104.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 472

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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