Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1H70CWB
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/C1H70CWB
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level results and 12 molecular subtypes across 493 patients, 110 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', and 'MRNASEQ_CNMF'.

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

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF'.

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

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

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

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

  • 10p gain cnv correlated to 'METHLYATION_CNMF'.

  • 10q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 16p gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

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

  • Xq gain cnv correlated to 'CN_CNMF'.

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

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

  • 3q loss cnv correlated to 'METHLYATION_CNMF'.

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

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

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

  • 6q loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 8q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 110 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
21q loss 0 (0%) 425 1.36e-09
(1.21e-06) 		3.65e-06
(0.00309) 		0.103
(1.00) 		0.0176
(1.00) 		1.42e-06
(0.00122) 		4.44e-07
(0.000384) 		3.11e-05
(0.0259) 		8.05e-07
(0.000694) 		0.00761
(1.00) 		3.02e-05
(0.0253)
2q gain 0 (0%) 448 0.0302
(1.00) 		0.0253
(1.00) 		2.09e-06
(0.00178) 		1.77e-08
(1.56e-05) 		0.252
(1.00) 		0.276
(1.00) 		0.000184
(0.147) 		0.0183
(1.00) 		0.000162
(0.13) 		0.0021
(1.00) 		0.000152
(0.123) 		0.00869
(1.00)
7p gain 0 (0%) 334 0.754
(1.00) 		0.523
(1.00) 		3.51e-21
(3.14e-18) 		0.000385
(0.301) 		8.93e-05
(0.073) 		0.00948
(1.00) 		1.24e-06
(0.00106) 		4.98e-07
(0.000431) 		0.000283
(0.224) 		0.00263
(1.00) 		0.0016
(1.00) 		0.000772
(0.592)
8q gain 0 (0%) 344 0.0641
(1.00) 		0.191
(1.00) 		1.84e-23
(1.65e-20) 		1.26e-07
(0.00011) 		0.0272
(1.00) 		0.00408
(1.00) 		0.000913
(0.693) 		0.000777
(0.595) 		8.05e-08
(7.05e-05) 		1.67e-07
(0.000145) 		0.00168
(1.00) 		1.46e-05
(0.0123)
15q loss 0 (0%) 395 0.405
(1.00) 		0.219
(1.00) 		7.75e-14
(6.93e-11) 		3.7e-08
(3.25e-05) 		0.481
(1.00) 		0.0188
(1.00) 		6.09e-05
(0.0503) 		0.000418
(0.325) 		0.000269
(0.213) 		0.000239
(0.19) 		0.0177
(1.00) 		0.00605
(1.00)
12p gain 0 (0%) 434 0.565
(1.00) 		0.132
(1.00) 		4.74e-08
(4.16e-05) 		3.97e-05
(0.033) 		0.18
(1.00) 		0.115
(1.00) 		0.000964
(0.73) 		0.000375
(0.294) 		0.000257
(0.204) 		0.00357
(1.00) 		0.000154
(0.125) 		0.0184
(1.00)
20p gain 0 (0%) 430 0.0235
(1.00) 		0.0127
(1.00) 		1.88e-06
(0.0016) 		2.27e-06
(0.00193) 		0.0249
(1.00) 		0.687
(1.00) 		5.74e-05
(0.0475) 		0.000135
(0.11) 		0.0189
(1.00) 		0.00772
(1.00) 		0.0179
(1.00) 		0.0672
(1.00)
20q gain 0 (0%) 415 0.00237
(1.00) 		0.00219
(1.00) 		3.11e-07
(0.00027) 		4.31e-09
(3.81e-06) 		0.000839
(0.639) 		0.092
(1.00) 		3.26e-06
(0.00276) 		3.94e-05
(0.0328) 		0.0019
(1.00) 		0.00265
(1.00) 		0.00937
(1.00) 		0.0114
(1.00)
4q loss 0 (0%) 446 0.00605
(1.00) 		0.00706
(1.00) 		1.23e-10
(1.09e-07) 		3.26e-06
(0.00276) 		0.469
(1.00) 		0.578
(1.00) 		9.1e-05
(0.0743) 		9.39e-08
(8.21e-05) 		0.000386
(0.301) 		0.000579
(0.449) 		0.0081
(1.00) 		0.00235
(1.00)
2p gain 0 (0%) 443 0.0312
(1.00) 		0.0151
(1.00) 		2.28e-08
(2.01e-05) 		1.26e-06
(0.00108) 		0.0781
(1.00) 		0.0301
(1.00) 		0.000162
(0.13) 		0.000766
(0.588) 		0.000405
(0.315) 		0.00765
(1.00) 		0.00295
(1.00) 		0.0382
(1.00)
7q gain 0 (0%) 381 0.388
(1.00) 		0.702
(1.00) 		3.13e-10
(2.78e-07) 		0.0207
(1.00) 		0.0789
(1.00) 		0.298
(1.00) 		1.68e-05
(0.0141) 		1.22e-05
(0.0102) 		0.142
(1.00) 		0.238
(1.00) 		0.0293
(1.00) 		0.117
(1.00)
12q gain 0 (0%) 445 0.565
(1.00) 		0.132
(1.00) 		8.62e-06
(0.00727) 		0.000125
(0.102) 		0.158
(1.00) 		0.0893
(1.00) 		0.000189
(0.151) 		0.00123
(0.931) 		0.00744
(1.00) 		0.0757
(1.00) 		0.00547
(1.00) 		0.158
(1.00)
4p loss 0 (0%) 453 1.22e-05
(0.0102) 		0.000376
(0.294) 		0.192
(1.00) 		0.248
(1.00) 		0.000668
(0.515) 		4.13e-05
(0.0343) 		0.000102
(0.0831) 		0.0081
(1.00) 		0.00765
(1.00) 		0.0336
(1.00)
5q loss 0 (0%) 433 0.0235
(1.00) 		0.0127
(1.00) 		1.84e-06
(0.00157) 		8.48e-05
(0.0695) 		0.0388
(1.00) 		0.0986
(1.00) 		0.000176
(0.142) 		0.0468
(1.00) 		0.0212
(1.00) 		0.0105
(1.00) 		0.0278
(1.00) 		0.0434
(1.00)
19p loss 0 (0%) 374 0.649
(1.00) 		0.688
(1.00) 		5.57e-05
(0.0461) 		5.9e-07
(0.00051) 		0.867
(1.00) 		0.69
(1.00) 		7.53e-05
(0.0619) 		0.116
(1.00) 		0.00603
(1.00) 		0.0143
(1.00) 		0.0233
(1.00) 		0.0535
(1.00)
8p gain 0 (0%) 432 1
(1.00) 		0.418
(1.00) 		7.74e-11
(6.89e-08) 		0.00371
(1.00) 		0.449
(1.00) 		0.542
(1.00) 		4.65e-05
(0.0386) 		0.00568
(1.00) 		0.189
(1.00) 		0.101
(1.00) 		0.85
(1.00) 		0.0649
(1.00)
14q gain 0 (0%) 434 5.1e-07
(0.000441) 		2.98e-06
(0.00254) 		0.127
(1.00) 		0.518
(1.00) 		0.000566
(0.439) 		0.0184
(1.00) 		0.0072
(1.00) 		0.000355
(0.279) 		0.00234
(1.00) 		0.0211
(1.00)
17p gain 0 (0%) 464 4.76e-06
(0.00403) 		8.48e-05
(0.0695) 		0.665
(1.00) 		0.533
(1.00) 		0.544
(1.00) 		0.356
(1.00) 		0.0413
(1.00) 		0.184
(1.00) 		0.24
(1.00) 		0.558
(1.00)
17q gain 0 (0%) 413 0.0447
(1.00) 		0.702
(1.00) 		4.62e-10
(4.1e-07) 		1.59e-07
(0.000138) 		0.423
(1.00) 		0.199
(1.00) 		0.00575
(1.00) 		0.0595
(1.00) 		0.0218
(1.00) 		0.0298
(1.00) 		0.0774
(1.00) 		0.109
(1.00)
18p gain 0 (0%) 449 3.57e-07
(0.00031) 		0.00016
(0.129) 		0.148
(1.00) 		0.338
(1.00) 		0.209
(1.00) 		0.0517
(1.00) 		0.0112
(1.00) 		0.0197
(1.00) 		0.0151
(1.00) 		0.0044
(1.00)
1p loss 0 (0%) 464 2.16e-05
(0.0181) 		0.000175
(0.141) 		0.111
(1.00) 		0.199
(1.00) 		0.113
(1.00) 		0.189
(1.00) 		0.789
(1.00) 		0.146
(1.00) 		0.299
(1.00) 		0.557
(1.00)
3p loss 0 (0%) 397 0.208
(1.00) 		0.176
(1.00) 		1.86e-06
(0.00159) 		3.24e-06
(0.00275) 		0.124
(1.00) 		0.259
(1.00) 		0.513
(1.00) 		0.0387
(1.00) 		0.0288
(1.00) 		0.0184
(1.00) 		0.00383
(1.00) 		0.19
(1.00)
8p loss 0 (0%) 371 0.104
(1.00) 		0.173
(1.00) 		1.72e-20
(1.54e-17) 		6.27e-05
(0.0518) 		0.259
(1.00) 		0.0547
(1.00) 		0.0868
(1.00) 		0.00209
(1.00) 		0.0184
(1.00) 		0.0126
(1.00) 		0.011
(1.00) 		0.0752
(1.00)
9p loss 0 (0%) 351 0.0512
(1.00) 		0.0702
(1.00) 		5.55e-05
(0.046) 		9.99e-06
(0.00841) 		0.272
(1.00) 		0.0382
(1.00) 		0.00598
(1.00) 		0.0168
(1.00) 		0.817
(1.00) 		0.722
(1.00) 		0.675
(1.00) 		0.773
(1.00)
9q loss 0 (0%) 373 0.203
(1.00) 		0.222
(1.00) 		1.04e-06
(0.000898) 		5.05e-08
(4.43e-05) 		0.39
(1.00) 		0.198
(1.00) 		0.0262
(1.00) 		0.0127
(1.00) 		0.124
(1.00) 		0.222
(1.00) 		0.173
(1.00) 		0.333
(1.00)
10p loss 0 (0%) 455 0.901
(1.00) 		0.818
(1.00) 		2.07e-05
(0.0173) 		0.00677
(1.00) 		0.0525
(1.00) 		0.0991
(1.00) 		0.0832
(1.00) 		0.51
(1.00) 		0.0453
(1.00) 		0.0128
(1.00) 		0.000784
(0.599) 		0.000201
(0.161)
13q loss 0 (0%) 378 0.142
(1.00) 		0.145
(1.00) 		6.37e-27
(5.72e-24) 		0.000122
(0.0993) 		0.322
(1.00) 		0.0124
(1.00) 		0.00124
(0.933) 		0.0819
(1.00) 		0.00468
(1.00) 		0.0404
(1.00) 		0.0879
(1.00) 		0.0715
(1.00)
18q loss 0 (0%) 381 0.42
(1.00) 		0.412
(1.00) 		9.98e-13
(8.91e-10) 		0.000865
(0.657) 		0.351
(1.00) 		0.126
(1.00) 		0.000254
(0.202) 		0.0242
(1.00) 		0.135
(1.00) 		0.95
(1.00) 		0.0404
(1.00) 		0.504
(1.00)
22q loss 0 (0%) 396 0.308
(1.00) 		0.321
(1.00) 		4.23e-11
(3.77e-08) 		0.000234
(0.187) 		0.00909
(1.00) 		0.011
(1.00) 		0.0202
(1.00) 		0.00747
(1.00) 		0.000398
(0.31) 		0.00182
(1.00) 		0.0081
(1.00) 		0.000346
(0.273)
1p gain 0 (0%) 435 1
(1.00) 		1
(1.00) 		1.63e-07
(0.000141) 		0.0155
(1.00) 		0.0815
(1.00) 		0.0241
(1.00) 		0.0243
(1.00) 		0.31
(1.00) 		0.635
(1.00) 		0.763
(1.00) 		1
(1.00) 		0.386
(1.00)
1q gain 0 (0%) 302 0.465
(1.00) 		0.885
(1.00) 		0.0337
(1.00) 		1.67e-06
(0.00143) 		0.131
(1.00) 		0.146
(1.00) 		0.00063
(0.486) 		0.642
(1.00) 		0.494
(1.00) 		0.604
(1.00) 		0.444
(1.00) 		0.0744
(1.00)
4p gain 0 (0%) 463 0.554
(1.00) 		0.418
(1.00) 		0.000114
(0.0926) 		0.044
(1.00) 		0.0948
(1.00) 		0.0347
(1.00) 		0.851
(1.00) 		0.382
(1.00) 		0.564
(1.00) 		0.447
(1.00) 		0.633
(1.00) 		0.442
(1.00)
5p gain 0 (0%) 309 0.487
(1.00) 		0.419
(1.00) 		5.03e-12
(4.49e-09) 		0.0423
(1.00) 		0.182
(1.00) 		0.612
(1.00) 		0.013
(1.00) 		0.0219
(1.00) 		0.119
(1.00) 		0.081
(1.00) 		0.289
(1.00) 		0.203
(1.00)
6p gain 0 (0%) 420 0.292
(1.00) 		0.0507
(1.00) 		0.00917
(1.00) 		9.48e-08
(8.28e-05) 		0.00936
(1.00) 		0.261
(1.00) 		0.00282
(1.00) 		0.261
(1.00) 		0.0703
(1.00) 		0.342
(1.00) 		0.154
(1.00) 		0.0965
(1.00)
10p gain 0 (0%) 442 0.00243
(1.00) 		0.000309
(0.244) 		0.169
(1.00) 		0.16
(1.00) 		0.00333
(1.00) 		0.0867
(1.00) 		0.0612
(1.00) 		0.22
(1.00) 		0.00376
(1.00) 		0.0756
(1.00)
10q gain 0 (0%) 463 0.251
(1.00) 		0.000806
(0.615) 		0.501
(1.00) 		0.157
(1.00) 		7.06e-06
(0.00596) 		0.316
(1.00) 		0.782
(1.00) 		0.363
(1.00) 		0.495
(1.00) 		0.196
(1.00)
11q gain 0 (0%) 442 0.12
(1.00) 		0.157
(1.00) 		0.000187
(0.15) 		0.0207
(1.00) 		0.00159
(1.00) 		0.0354
(1.00) 		0.00705
(1.00) 		0.00271
(1.00) 		0.00467
(1.00) 		0.0243
(1.00) 		0.00447
(1.00) 		0.0523
(1.00)
16p gain 0 (0%) 422 0.358
(1.00) 		0.322
(1.00) 		0.00333
(1.00) 		0.000357
(0.28) 		0.0647
(1.00) 		0.561
(1.00) 		0.000111
(0.0902) 		0.0163
(1.00) 		0.218
(1.00) 		0.149
(1.00) 		0.168
(1.00) 		0.527
(1.00)
18q gain 0 (0%) 466 2.24e-06
(0.00191) 		0.000947
(0.718) 		0.09
(1.00) 		0.0373
(1.00) 		0.0284
(1.00) 		0.00497
(1.00) 		0.0853
(1.00) 		0.0716
(1.00) 		0.0517
(1.00) 		0.00703
(1.00)
21q gain 0 (0%) 450 0.192
(1.00) 		0.157
(1.00) 		0.000224
(0.179) 		0.0026
(1.00) 		0.0914
(1.00) 		0.0523
(1.00) 		0.23
(1.00) 		0.17
(1.00) 		0.0596
(1.00) 		0.38
(1.00) 		0.619
(1.00) 		0.67
(1.00)
Xq gain 0 (0%) 476 0.75
(1.00) 		0.591
(1.00) 		8.37e-05
(0.0687) 		0.44
(1.00) 		0.636
(1.00) 		0.345
(1.00) 		0.284
(1.00) 		0.421
(1.00) 		0.452
(1.00) 		0.465
(1.00) 		0.139
(1.00) 		0.248
(1.00)
3q loss 0 (0%) 437 0.554
(1.00) 		0.418
(1.00) 		0.000368
(0.289) 		0.000166
(0.134) 		0.341
(1.00) 		0.933
(1.00) 		0.161
(1.00) 		0.612
(1.00) 		0.44
(1.00) 		0.0451
(1.00) 		0.00488
(1.00) 		0.342
(1.00)
6q loss 0 (0%) 381 0.803
(1.00) 		0.722
(1.00) 		0.0376
(1.00) 		1.33e-07
(0.000116) 		0.153
(1.00) 		0.0437
(1.00) 		0.00705
(1.00) 		0.194
(1.00) 		0.431
(1.00) 		0.879
(1.00) 		0.326
(1.00) 		0.0168
(1.00)
8q loss 0 (0%) 472 0.000285
(0.225) 		0.648
(1.00) 		0.00257
(1.00) 		0.0275
(1.00) 		0.0529
(1.00) 		0.0109
(1.00) 		0.634
(1.00) 		0.619
(1.00) 		0.507
(1.00) 		0.0947
(1.00)
11p loss 0 (0%) 457 0.335
(1.00) 		0.102
(1.00) 		0.000306
(0.241) 		0.546
(1.00) 		0.00454
(1.00) 		0.0268
(1.00) 		0.0712
(1.00) 		0.025
(1.00) 		0.0798
(1.00) 		0.0511
(1.00) 		0.0159
(1.00) 		0.156
(1.00)
16p loss 0 (0%) 454 7.15e-05
(0.0588) 		0.0169
(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) 		0.154
(1.00) 		0.225
(1.00)
16q loss 0 (0%) 436 0.0159
(1.00) 		1
(1.00) 		6.8e-09
(6e-06) 		0.00432
(1.00) 		0.00928
(1.00) 		0.0112
(1.00) 		0.00612
(1.00) 		0.172
(1.00) 		0.0182
(1.00) 		0.292
(1.00) 		0.00916
(1.00) 		0.255
(1.00)
17p loss 0 (0%) 375 0.399
(1.00) 		0.631
(1.00) 		3.35e-08
(2.95e-05) 		0.000593
(0.459) 		0.0572
(1.00) 		0.21
(1.00) 		0.4
(1.00) 		0.567
(1.00) 		0.656
(1.00) 		0.528
(1.00) 		0.542
(1.00) 		0.348
(1.00)
18p loss 0 (0%) 413 0.42
(1.00) 		0.412
(1.00) 		5.92e-09
(5.23e-06) 		0.0163
(1.00) 		0.904
(1.00) 		0.228
(1.00) 		0.0367
(1.00) 		0.353
(1.00) 		0.583
(1.00) 		0.92
(1.00) 		0.0224
(1.00) 		0.345
(1.00)
20p loss 0 (0%) 427 0.192
(1.00) 		0.412
(1.00) 		7.02e-05
(0.0579) 		0.0142
(1.00) 		0.00399
(1.00) 		0.0158
(1.00) 		0.158
(1.00) 		0.243
(1.00) 		0.791
(1.00) 		0.0725
(1.00) 		0.79
(1.00) 		0.891
(1.00)
3p gain 0 (0%) 480 0.0167
(1.00) 		0.12
(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) 		0.758
(1.00) 		0.436
(1.00)
3q gain 0 (0%) 463 0.00235
(1.00) 		0.0107
(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) 		0.0892
(1.00) 		0.105
(1.00)
4q gain 0 (0%) 483 0.0225
(1.00) 		0.955
(1.00) 		0.325
(1.00) 		0.253
(1.00) 		0.532
(1.00) 		0.348
(1.00) 		0.129
(1.00) 		0.223
(1.00) 		0.313
(1.00) 		0.0363
(1.00)
5q gain 0 (0%) 433 0.0177
(1.00) 		0.644
(1.00) 		0.0774
(1.00) 		0.00132
(0.996) 		0.498
(1.00) 		0.164
(1.00) 		0.00644
(1.00) 		0.0375
(1.00) 		0.447
(1.00) 		0.146
(1.00) 		0.306
(1.00) 		0.247
(1.00)
6q gain 0 (0%) 474 0.0835
(1.00) 		0.00258
(1.00) 		0.108
(1.00) 		0.0645
(1.00) 		0.118
(1.00) 		0.605
(1.00) 		0.104
(1.00) 		0.0327
(1.00) 		0.283
(1.00) 		0.0647
(1.00)
9p gain 0 (0%) 477 0.104
(1.00) 		0.00706
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.253
(1.00) 		0.216
(1.00) 		0.303
(1.00) 		0.157
(1.00) 		0.0454
(1.00) 		0.24
(1.00)
9q gain 0 (0%) 485 0.0242
(1.00) 		0.279
(1.00) 		0.392
(1.00) 		0.269
(1.00) 		0.201
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.249
(1.00) 		0.0322
(1.00) 		0.167
(1.00)
11p gain 0 (0%) 457 0.0152
(1.00) 		0.0456
(1.00) 		0.188
(1.00) 		0.602
(1.00) 		0.0613
(1.00) 		0.349
(1.00) 		0.0313
(1.00) 		0.109
(1.00) 		0.0361
(1.00) 		0.247
(1.00)
13q gain 0 (0%) 477 0.192
(1.00) 		0.157
(1.00) 		0.565
(1.00) 		0.00487
(1.00) 		0.288
(1.00) 		0.196
(1.00) 		0.151
(1.00) 		0.103
(1.00) 		0.792
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.442
(1.00)
15q gain 0 (0%) 479 0.723
(1.00) 		0.221
(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) 		0.696
(1.00) 		0.15
(1.00)
16q gain 0 (0%) 450 0.192
(1.00) 		0.0514
(1.00) 		0.0175
(1.00) 		0.0268
(1.00) 		0.0317
(1.00) 		0.0383
(1.00) 		0.0088
(1.00) 		0.236
(1.00) 		0.254
(1.00) 		0.137
(1.00) 		0.33
(1.00) 		0.794
(1.00)
19p gain 0 (0%) 487 1
(1.00) 		0.254
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.482
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.862
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 0 (0%) 469 0.000818
(0.623) 		0.0625
(1.00) 		0.198
(1.00) 		0.00772
(1.00) 		0.00689
(1.00) 		0.0194
(1.00) 		0.112
(1.00) 		0.0426
(1.00) 		0.0819
(1.00) 		0.199
(1.00)
22q gain 0 (0%) 473 0.00294
(1.00) 		0.085
(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) 		0.0714
(1.00) 		0.229
(1.00)
1q loss 0 (0%) 483 0.000693
(0.533) 		0.0924
(1.00) 		0.222
(1.00) 		0.0151
(1.00) 		0.34
(1.00) 		0.212
(1.00) 		0.452
(1.00) 		0.165
(1.00) 		0.5
(1.00) 		0.158
(1.00)
2p loss 0 (0%) 487 0.867
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.617
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.862
(1.00) 		0.846
(1.00) 		1
(1.00)
2q loss 0 (0%) 489 0.0421
(1.00) 		0.218
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.544
(1.00) 		0.797
(1.00) 		0.831
(1.00) 		0.778
(1.00)
5p loss 0 (0%) 482 0.0262
(1.00) 		0.146
(1.00) 		0.838
(1.00) 		0.881
(1.00) 		0.354
(1.00) 		0.00768
(1.00) 		0.0147
(1.00) 		0.0286
(1.00) 		0.0231
(1.00) 		0.0391
(1.00)
6p loss 0 (0%) 450 0.335
(1.00) 		0.308
(1.00) 		0.00149
(1.00) 		0.0334
(1.00) 		0.107
(1.00) 		0.488
(1.00) 		0.199
(1.00) 		0.896
(1.00) 		0.357
(1.00) 		0.612
(1.00) 		0.159
(1.00) 		0.168
(1.00)
7p loss 0 (0%) 479 0.554
(1.00) 		0.418
(1.00) 		0.0119
(1.00) 		0.418
(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) 		0.917
(1.00) 		0.898
(1.00)
7q loss 0 (0%) 476 0.53
(1.00) 		0.186
(1.00) 		0.614
(1.00) 		0.494
(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) 		0.339
(1.00) 		0.246
(1.00)
10q loss 0 (0%) 444 0.75
(1.00) 		0.591
(1.00) 		0.000447
(0.348) 		0.000613
(0.474) 		0.0157
(1.00) 		0.0585
(1.00) 		0.0227
(1.00) 		0.601
(1.00) 		0.298
(1.00) 		0.0288
(1.00) 		0.111
(1.00) 		0.00598
(1.00)
11q loss 0 (0%) 462 0.474
(1.00) 		0.157
(1.00) 		0.000754
(0.579) 		0.526
(1.00) 		0.0102
(1.00) 		0.0251
(1.00) 		0.394
(1.00) 		0.262
(1.00) 		0.289
(1.00) 		0.773
(1.00) 		0.456
(1.00) 		0.505
(1.00)
12p loss 0 (0%) 453 0.728
(1.00) 		0.818
(1.00) 		0.728
(1.00) 		0.00231
(1.00) 		0.819
(1.00) 		0.534
(1.00) 		0.072
(1.00) 		0.593
(1.00) 		0.269
(1.00) 		0.711
(1.00) 		0.0315
(1.00) 		0.965
(1.00)
12q loss 0 (0%) 469 0.0956
(1.00) 		0.439
(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) 		0.136
(1.00) 		0.951
(1.00)
14q loss 0 (0%) 446 0.401
(1.00) 		0.418
(1.00) 		0.026
(1.00) 		0.157
(1.00) 		0.00875
(1.00) 		0.00808
(1.00) 		0.195
(1.00) 		0.559
(1.00) 		0.0463
(1.00) 		0.225
(1.00) 		0.0202
(1.00) 		0.704
(1.00)
17q loss 0 (0%) 474 0.103
(1.00) 		0.0365
(1.00) 		0.0494
(1.00) 		0.759
(1.00) 		0.572
(1.00) 		0.0777
(1.00) 		0.587
(1.00) 		0.0091
(1.00) 		0.721
(1.00) 		0.231
(1.00)
19q loss 0 (0%) 421 0.71
(1.00) 		0.722
(1.00) 		0.000732
(0.563) 		0.0333
(1.00) 		0.658
(1.00) 		0.357
(1.00) 		0.0124
(1.00) 		0.361
(1.00) 		0.0129
(1.00) 		0.0516
(1.00) 		0.0126
(1.00) 		0.0648
(1.00)
20q loss 0 (0%) 468 0.0877
(1.00) 		0.106
(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) 		0.722
(1.00) 		0.605
(1.00)
Xq loss 0 (0%) 482 0.477
(1.00) 		0.316
(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) 		0.411
(1.00) 		0.275
(1.00)
'1p gain' versus 'CN_CNMF'

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

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

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

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
1Q GAIN CNV 37 49 51 16
1Q GAIN WILD-TYPE 49 59 59 84

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

'2p gain' versus 'CN_CNMF'

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

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

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

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
2P GAIN CNV 4 25 8 2
2P GAIN WILD-TYPE 82 83 102 98

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.000162 (Chi-square test), Q value = 0.13

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 6 3 15 7 1 10 1 1 0
2P GAIN WILD-TYPE 69 52 41 35 28 38 38 23 23

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

'2q gain' versus 'CN_CNMF'

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

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

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

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

'2q gain' versus 'METHLYATION_CNMF'

P value = 1.77e-08 (Fisher's exact test), Q value = 1.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
2Q GAIN CNV 4 25 9 0
2Q GAIN WILD-TYPE 82 83 101 100

Figure S7.  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 = 0.15

Table S8.  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 S8.  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 = 0.13

Table S9.  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 S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000152 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 174 73
2Q GAIN CNV 8 29 2
2Q GAIN WILD-TYPE 149 145 71

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'CN_CNMF'

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

Table S11.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S11.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

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

Table S12.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S12.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 9.48e-08 (Fisher's exact test), Q value = 8.3e-05

Table S13.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
6P GAIN CNV 13 33 10 3
6P GAIN WILD-TYPE 73 75 100 97

Figure S13.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

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

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 8.93e-05 (Fisher's exact test), Q value = 0.073

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 = 1.24e-06 (Chi-square test), Q value = 0.0011

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 29 19 6 4 12 13 10 2
7P GAIN WILD-TYPE 35 26 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 = 4.98e-07 (Fisher's exact test), Q value = 0.00043

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 40 59 36
7P GAIN WILD-TYPE 118 46 92

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

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.000283 (Fisher's exact test), Q value = 0.22

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
7P GAIN CNV 39 71 45
7P GAIN WILD-TYPE 132 127 53

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'CN_CNMF'

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

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S19.  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 = 0.014

Table S20.  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 S20.  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 = 0.01

Table S21.  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 S21.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

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

Table S22.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S22.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 4.65e-05 (Chi-square test), Q value = 0.039

Table S23.  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 6 4 2 17 2 3 2
8P GAIN WILD-TYPE 72 49 50 38 27 31 37 21 21

Figure S23.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'CN_CNMF'

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

Table S24.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S24.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1.26e-07 (Fisher's exact test), Q value = 0.00011

Table S25.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
8Q GAIN CNV 15 52 40 16
8Q GAIN WILD-TYPE 71 56 70 84

Figure S25.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 8.05e-08 (Fisher's exact test), Q value = 7.1e-05

Table S26.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 198 98
8Q GAIN CNV 26 82 34
8Q GAIN WILD-TYPE 145 116 64

Figure S26.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-07 (Fisher's exact test), Q value = 0.00014

Table S27.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 244 59
8Q GAIN CNV 27 101 14
8Q GAIN WILD-TYPE 137 143 45

Figure S27.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.012

Table S28.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 46 205
8Q GAIN CNV 28 12 84
8Q GAIN WILD-TYPE 125 34 121

Figure S28.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.24

Table S29.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
10P GAIN CNV 4 19 17 3
10P GAIN WILD-TYPE 82 89 93 97

Figure S29.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 7.06e-06 (Chi-square test), Q value = 0.006

Table S30.  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 2 11 2 3 1 1 0
10Q GAIN WILD-TYPE 72 55 54 31 27 45 38 23 23

Figure S30.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'CN_CNMF'

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

Table S31.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S31.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 4.74e-08 (Fisher's exact test), Q value = 4.2e-05

Table S32.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S32.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3.97e-05 (Fisher's exact test), Q value = 0.033

Table S33.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
12P GAIN CNV 2 25 10 8
12P GAIN WILD-TYPE 84 83 100 92

Figure S33.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.2

Table S34.  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 S34.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.12

Table S35.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 157 174 73
12P GAIN CNV 6 31 8
12P GAIN WILD-TYPE 151 143 65

Figure S35.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 8.62e-06 (Fisher's exact test), Q value = 0.0073

Table S36.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S36.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.000125 (Fisher's exact test), Q value = 0.1

Table S37.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
12Q GAIN CNV 1 20 7 6
12Q GAIN WILD-TYPE 85 88 103 94

Figure S37.  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 = 0.15

Table S38.  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 S38.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'CN_CNMF'

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

Table S39.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S39.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 2.98e-06 (Fisher's exact test), Q value = 0.0025

Table S40.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
14Q GAIN CNV 8 30 10 4
14Q GAIN WILD-TYPE 78 78 100 96

Figure S40.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000111 (Chi-square test), Q value = 0.09

Table S41.  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 7 20 2 5 3 5 7 5 2
16P GAIN WILD-TYPE 68 35 54 37 26 43 32 19 21

Figure S41.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

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

Table S42.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S42.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 8.48e-05 (Fisher's exact test), Q value = 0.07

Table S43.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
17P GAIN CNV 3 16 3 1
17P GAIN WILD-TYPE 83 92 107 99

Figure S43.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

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

Table S44.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S44.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1.59e-07 (Fisher's exact test), Q value = 0.00014

Table S45.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
17Q GAIN CNV 7 33 23 4
17Q GAIN WILD-TYPE 79 75 87 96

Figure S45.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

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

Table S46.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S46.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S47.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
18P GAIN CNV 3 22 11 4
18P GAIN WILD-TYPE 83 86 99 96

Figure S47.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'CN_CNMF'

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

Table S48.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S48.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

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

Table S49.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S49.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 2.27e-06 (Fisher's exact test), Q value = 0.0019

Table S50.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
20P GAIN CNV 7 31 10 5
20P GAIN WILD-TYPE 79 77 100 95

Figure S50.  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 = 0.048

Table S51.  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 S51.  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 = 0.11

Table S52.  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 S52.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S53.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 4.31e-09 (Fisher's exact test), Q value = 3.8e-06

Table S54.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
20Q GAIN CNV 7 39 12 6
20Q GAIN WILD-TYPE 79 69 98 94

Figure S54.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 3.26e-06 (Chi-square test), Q value = 0.0028

Table S55.  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 6 24 5 5 14 3 3 1
20Q GAIN WILD-TYPE 67 49 32 37 24 34 36 21 22

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.94e-05 (Fisher's exact test), Q value = 0.033

Table S56.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 105 128
20Q GAIN CNV 19 11 39
20Q GAIN WILD-TYPE 139 94 89

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

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

Table S57.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S57.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'Xq gain' versus 'CN_CNMF'

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

Table S58.  Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S58.  Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

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

Table S59.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S59.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.14

Table S60.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
1P LOSS CNV 5 16 3 1
1P LOSS WILD-TYPE 81 92 107 99

Figure S60.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

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

Table S61.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S61.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.0027

Table S62.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
3P LOSS CNV 14 37 23 6
3P LOSS WILD-TYPE 72 71 87 94

Figure S62.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.13

Table S63.  Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
3Q LOSS CNV 13 22 13 2
3Q LOSS WILD-TYPE 73 86 97 98

Figure S63.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

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

Table S64.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S64.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.13e-05 (Fisher's exact test), Q value = 0.034

Table S65.  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 S65.  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 = 0.083

Table S66.  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 S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'CN_CNMF'

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

Table S67.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S67.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.0028

Table S68.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
4Q LOSS CNV 3 24 5 4
4Q LOSS WILD-TYPE 83 84 105 96

Figure S68.  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 = 0.074

Table S69.  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 S69.  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 = 8.2e-05

Table S70.  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 S70.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

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

Table S71.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S71.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 8.48e-05 (Fisher's exact test), Q value = 0.07

Table S72.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
5Q LOSS CNV 6 24 15 3
5Q LOSS WILD-TYPE 80 84 95 97

Figure S72.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.000176 (Chi-square test), Q value = 0.14

Table S73.  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 15 2 16 5 5 5 0 2 0
5Q LOSS WILD-TYPE 60 53 40 37 24 43 39 22 23

Figure S73.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 0.00012

Table S74.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
6Q LOSS CNV 28 27 33 4
6Q LOSS WILD-TYPE 58 81 77 96

Figure S74.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'CN_CNMF'

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

Table S75.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S75.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 6.27e-05 (Fisher's exact test), Q value = 0.052

Table S76.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
8P LOSS CNV 15 34 38 11
8P LOSS WILD-TYPE 71 74 72 89

Figure S76.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'CN_CNMF'

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

Table S77.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S77.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

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

Table S78.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S78.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 9.99e-06 (Fisher's exact test), Q value = 0.0084

Table S79.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
9P LOSS CNV 26 48 31 13
9P LOSS WILD-TYPE 60 60 79 87

Figure S79.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.04e-06 (Fisher's exact test), Q value = 9e-04

Table S80.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S80.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 5.05e-08 (Fisher's exact test), Q value = 4.4e-05

Table S81.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
9Q LOSS CNV 19 47 20 9
9Q LOSS WILD-TYPE 67 61 90 91

Figure S81.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

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

Table S82.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S82.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000201 (Fisher's exact test), Q value = 0.16

Table S83.  Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 46 205
10P LOSS CNV 4 10 17
10P LOSS WILD-TYPE 149 36 188

Figure S83.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

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

Table S84.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S84.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

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

Table S85.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S85.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.099

Table S86.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
13Q LOSS CNV 17 35 27 8
13Q LOSS WILD-TYPE 69 73 83 92

Figure S86.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

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

Table S87.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S87.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 3.7e-08 (Fisher's exact test), Q value = 3.3e-05

Table S88.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
15Q LOSS CNV 12 37 28 4
15Q LOSS WILD-TYPE 74 71 82 96

Figure S88.  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 = 0.05

Table S89.  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 S89.  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 = 0.21

Table S90.  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 S90.  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 = 0.19

Table S91.  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 S91.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

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

Table S92.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S92.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

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

Table S93.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S93.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

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

Table S94.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S94.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

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

Table S95.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S95.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

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

Table S96.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S96.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.000254 (Chi-square test), Q value = 0.2

Table S97.  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 S97.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'CN_CNMF'

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

Table S98.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S98.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 5.9e-07 (Fisher's exact test), Q value = 0.00051

Table S99.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
19P LOSS CNV 21 39 19 6
19P LOSS WILD-TYPE 65 69 91 94

Figure S99.  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 = 0.062

Table S100.  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 S100.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'CN_CNMF'

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

Table S101.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S101.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

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

Table S102.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S102.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 3.65e-06 (Fisher's exact test), Q value = 0.0031

Table S103.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
21Q LOSS CNV 8 32 10 6
21Q LOSS WILD-TYPE 78 76 100 94

Figure S103.  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 = 0.0012

Table S104.  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 S104.  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 = 0.00038

Table S105.  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 S105.  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 = 0.026

Table S106.  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 S106.  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 = 0.00069

Table S107.  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 S107.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.02e-05 (Fisher's exact test), Q value = 0.025

Table S108.  Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 153 46 205
21Q LOSS CNV 10 2 44
21Q LOSS WILD-TYPE 143 44 161

Figure S108.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

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

Table S109.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S109.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.19

Table S110.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 108 110 100
22Q LOSS CNV 11 34 20 9
22Q LOSS WILD-TYPE 75 74 90 91

Figure S110.  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 = 493

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

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)
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