Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1BG2M6W
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/C1BG2M6W
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 403 patients, 69 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_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 'METHLYATION_CNMF'.

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

  • 10p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

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

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 6q loss cnv correlated to 'METHLYATION_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q 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_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 69 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
21q loss 58 (14%) 345 7.78e-09
(5.58e-06) 		1.56e-05
(0.0109) 		0.0544
(1.00) 		0.0118
(1.00) 		6.6e-09
(4.74e-06) 		2.76e-07
(0.000196) 		1.48e-05
(0.0103) 		2.31e-05
(0.0159)
7p gain 138 (34%) 265 0.754
(1.00) 		0.523
(1.00) 		7.4e-17
(5.43e-14) 		0.0278
(1.00) 		2.06e-05
(0.0142) 		0.0061
(1.00) 		8.28e-08
(5.91e-05) 		0.000152
(0.103) 		0.000375
(0.25) 		0.00218
(1.00)
8q gain 120 (30%) 283 0.0641
(1.00) 		0.191
(1.00) 		2.69e-11
(1.96e-08) 		1.01e-06
(0.000716) 		0.0105
(1.00) 		0.000508
(0.334) 		0.000289
(0.194) 		0.000919
(0.592) 		1.68e-05
(0.0117) 		1.46e-05
(0.0102)
4q loss 39 (10%) 364 0.00605
(1.00) 		0.00706
(1.00) 		1.38e-08
(9.85e-06) 		0.000226
(0.152) 		0.332
(1.00) 		0.838
(1.00) 		6.64e-09
(4.77e-06) 		1.87e-09
(1.35e-06) 		0.00153
(0.966) 		0.000724
(0.473)
15q loss 80 (20%) 323 0.405
(1.00) 		0.219
(1.00) 		1.99e-10
(1.44e-07) 		5.28e-06
(0.00371) 		0.607
(1.00) 		0.0248
(1.00) 		0.000764
(0.496) 		6.48e-05
(0.0443) 		0.00121
(0.77) 		0.00012
(0.0815)
22q loss 80 (20%) 323 0.75
(1.00) 		0.591
(1.00) 		9.39e-11
(6.81e-08) 		2.59e-05
(0.0178) 		0.00759
(1.00) 		0.0555
(1.00) 		0.000322
(0.216) 		0.000506
(0.334) 		0.00333
(1.00) 		0.00019
(0.128)
7q gain 101 (25%) 302 0.388
(1.00) 		0.702
(1.00) 		6.63e-11
(4.82e-08) 		0.597
(1.00) 		0.0122
(1.00) 		0.124
(1.00) 		1.37e-05
(0.00957) 		8.87e-05
(0.0605) 		0.0525
(1.00) 		0.081
(1.00)
2p gain 45 (11%) 358 0.0312
(1.00) 		0.0151
(1.00) 		1.25e-06
(0.000878) 		0.000336
(0.225) 		0.0437
(1.00) 		0.125
(1.00) 		0.0321
(1.00) 		0.000783
(0.508) 		0.00186
(1.00) 		0.00503
(1.00)
8p gain 44 (11%) 359 0.000226
(0.152) 		0.000327
(0.219) 		0.374
(1.00) 		0.448
(1.00) 		0.00325
(1.00) 		0.0162
(1.00) 		0.792
(1.00) 		0.0841
(1.00)
11q gain 45 (11%) 358 0.12
(1.00) 		0.157
(1.00) 		1.33e-05
(0.00928) 		0.0864
(1.00) 		0.000348
(0.232) 		0.00773
(1.00) 		0.0519
(1.00) 		0.00288
(1.00) 		0.00431
(1.00) 		0.00801
(1.00)
20q gain 68 (17%) 335 0.00237
(1.00) 		0.00219
(1.00) 		3.56e-08
(2.54e-05) 		0.0163
(1.00) 		0.0047
(1.00) 		0.214
(1.00) 		1.96e-05
(0.0136) 		0.000632
(0.414) 		0.00235
(1.00) 		0.00704
(1.00)
4p loss 34 (8%) 369 0.00287
(1.00) 		0.0105
(1.00) 		0.124
(1.00) 		0.476
(1.00) 		9.99e-05
(0.0679) 		4.91e-06
(0.00345) 		0.00183
(1.00) 		0.0599
(1.00)
5q loss 54 (13%) 349 0.0235
(1.00) 		0.0127
(1.00) 		9.4e-06
(0.00659) 		3.5e-05
(0.024) 		0.0778
(1.00) 		0.35
(1.00) 		0.00293
(1.00) 		0.017
(1.00) 		0.026
(1.00) 		0.0496
(1.00)
13q loss 91 (23%) 312 0.142
(1.00) 		0.145
(1.00) 		1.02e-14
(7.49e-12) 		8.94e-05
(0.0609) 		0.37
(1.00) 		0.0246
(1.00) 		0.116
(1.00) 		0.000411
(0.273) 		0.00381
(1.00) 		0.0232
(1.00)
19p loss 102 (25%) 301 0.649
(1.00) 		0.688
(1.00) 		8.15e-09
(5.84e-06) 		0.00152
(0.963) 		0.692
(1.00) 		0.625
(1.00) 		0.000459
(0.305) 		0.00613
(1.00) 		0.000184
(0.124) 		0.0427
(1.00)
1p gain 49 (12%) 354 1
(1.00) 		1
(1.00) 		3.69e-09
(2.67e-06) 		0.0371
(1.00) 		0.0604
(1.00) 		0.0129
(1.00) 		0.205
(1.00) 		0.417
(1.00) 		0.425
(1.00) 		0.889
(1.00)
2q gain 40 (10%) 363 0.0302
(1.00) 		0.0253
(1.00) 		2.35e-06
(0.00166) 		0.0094
(1.00) 		0.163
(1.00) 		0.444
(1.00) 		0.11
(1.00) 		0.0171
(1.00) 		0.00557
(1.00) 		0.0439
(1.00)
5p gain 154 (38%) 249 0.487
(1.00) 		0.419
(1.00) 		1.22e-14
(8.92e-12) 		0.762
(1.00) 		0.417
(1.00) 		0.476
(1.00) 		0.0517
(1.00) 		0.0814
(1.00) 		0.298
(1.00) 		0.503
(1.00)
6p gain 61 (15%) 342 0.292
(1.00) 		0.0507
(1.00) 		0.000207
(0.14) 		0.00568
(1.00) 		0.00703
(1.00) 		0.236
(1.00) 		0.0242
(1.00) 		0.144
(1.00) 		0.0597
(1.00) 		0.0763
(1.00)
10p gain 43 (11%) 360 0.0043
(1.00) 		3.07e-05
(0.0211) 		0.248
(1.00) 		0.304
(1.00) 		0.349
(1.00) 		0.279
(1.00) 		0.138
(1.00) 		0.622
(1.00)
12p gain 50 (12%) 353 0.565
(1.00) 		0.132
(1.00) 		6.6e-13
(4.82e-10) 		0.00715
(1.00) 		0.15
(1.00) 		0.107
(1.00) 		0.0103
(1.00) 		0.000737
(0.48) 		0.00622
(1.00) 		0.0065
(1.00)
12q gain 40 (10%) 363 0.565
(1.00) 		0.132
(1.00) 		5.85e-11
(4.26e-08) 		0.0065
(1.00) 		0.133
(1.00) 		0.105
(1.00) 		0.0145
(1.00) 		0.00218
(1.00) 		0.0217
(1.00) 		0.00394
(1.00)
14q gain 51 (13%) 352 1.16e-06
(0.00082) 		0.000865
(0.559) 		0.285
(1.00) 		0.599
(1.00) 		0.000519
(0.341) 		0.00678
(1.00) 		0.0126
(1.00) 		0.00562
(1.00)
17q gain 69 (17%) 334 0.0447
(1.00) 		0.702
(1.00) 		7.55e-07
(0.000534) 		0.00667
(1.00) 		0.437
(1.00) 		0.136
(1.00) 		0.026
(1.00) 		0.0338
(1.00) 		0.0503
(1.00) 		0.0861
(1.00)
18p gain 35 (9%) 368 3.19e-05
(0.0219) 		0.0605
(1.00) 		0.0558
(1.00) 		0.548
(1.00) 		0.466
(1.00) 		0.145
(1.00) 		0.0559
(1.00) 		0.0435
(1.00)
18q gain 23 (6%) 380 2.74e-07
(0.000195) 		0.409
(1.00) 		0.121
(1.00) 		0.361
(1.00) 		0.0367
(1.00) 		0.0127
(1.00) 		0.137
(1.00) 		0.00733
(1.00)
20p gain 56 (14%) 347 0.0235
(1.00) 		0.0127
(1.00) 		6.15e-07
(0.000436) 		0.0871
(1.00) 		0.0241
(1.00) 		0.528
(1.00) 		0.000866
(0.559) 		0.00111
(0.707) 		0.075
(1.00) 		0.0216
(1.00)
21q gain 36 (9%) 367 0.192
(1.00) 		0.157
(1.00) 		0.000148
(0.101) 		0.0535
(1.00) 		0.0658
(1.00) 		0.0363
(1.00) 		0.438
(1.00) 		0.0584
(1.00) 		0.423
(1.00) 		0.39
(1.00)
1p loss 28 (7%) 375 2.27e-05
(0.0157) 		0.148
(1.00) 		0.1
(1.00) 		0.365
(1.00) 		0.00739
(1.00) 		0.072
(1.00) 		0.465
(1.00) 		0.489
(1.00)
3p loss 77 (19%) 326 0.208
(1.00) 		0.176
(1.00) 		4.86e-05
(0.0333) 		0.0187
(1.00) 		0.147
(1.00) 		0.495
(1.00) 		0.0302
(1.00) 		0.00978
(1.00) 		0.0193
(1.00) 		0.0879
(1.00)
6q loss 90 (22%) 313 0.803
(1.00) 		0.722
(1.00) 		0.0227
(1.00) 		8.45e-11
(6.14e-08) 		0.229
(1.00) 		0.0153
(1.00) 		0.0156
(1.00) 		0.772
(1.00) 		0.245
(1.00) 		0.739
(1.00)
8p loss 104 (26%) 299 0.104
(1.00) 		0.173
(1.00) 		4.06e-11
(2.96e-08) 		0.0383
(1.00) 		0.154
(1.00) 		0.0965
(1.00) 		0.00357
(1.00) 		0.0155
(1.00) 		0.0302
(1.00) 		0.0159
(1.00)
9p loss 122 (30%) 281 0.0512
(1.00) 		0.0702
(1.00) 		1.57e-07
(0.000112) 		0.178
(1.00) 		0.203
(1.00) 		0.0383
(1.00) 		0.106
(1.00) 		0.00431
(1.00) 		0.791
(1.00) 		0.348
(1.00)
9q loss 102 (25%) 301 0.203
(1.00) 		0.222
(1.00) 		5.95e-09
(4.28e-06) 		0.00196
(1.00) 		0.215
(1.00) 		0.16
(1.00) 		0.0262
(1.00) 		0.00128
(0.814) 		0.0947
(1.00) 		0.00252
(1.00)
16q loss 51 (13%) 352 0.0159
(1.00) 		1
(1.00) 		1.01e-05
(0.00707) 		0.00392
(1.00) 		0.00307
(1.00) 		0.0138
(1.00) 		0.00891
(1.00) 		0.186
(1.00) 		0.0243
(1.00) 		0.122
(1.00)
18p loss 60 (15%) 343 0.12
(1.00) 		0.102
(1.00) 		5.08e-05
(0.0347) 		0.038
(1.00) 		0.926
(1.00) 		0.313
(1.00) 		0.367
(1.00) 		0.639
(1.00) 		0.853
(1.00) 		0.56
(1.00)
18q loss 90 (22%) 313 0.42
(1.00) 		0.412
(1.00) 		5.78e-09
(4.17e-06) 		0.00144
(0.915) 		0.347
(1.00) 		0.152
(1.00) 		0.259
(1.00) 		0.178
(1.00) 		0.502
(1.00) 		0.917
(1.00)
1q gain 155 (38%) 248 0.597
(1.00) 		1
(1.00) 		0.0322
(1.00) 		0.000729
(0.475) 		0.0948
(1.00) 		0.0807
(1.00) 		0.0731
(1.00) 		0.555
(1.00) 		0.503
(1.00) 		0.112
(1.00)
3p gain 12 (3%) 391 0.0524
(1.00) 		0.0677
(1.00) 		0.0998
(1.00) 		0.17
(1.00) 		0.0198
(1.00) 		0.171
(1.00) 		0.72
(1.00) 		0.298
(1.00)
3q gain 23 (6%) 380 0.0012
(0.765) 		0.0275
(1.00) 		0.0199
(1.00) 		0.0249
(1.00) 		0.0327
(1.00) 		0.343
(1.00) 		0.0647
(1.00) 		0.122
(1.00)
4p gain 26 (6%) 377 0.554
(1.00) 		0.418
(1.00) 		0.0111
(1.00) 		0.886
(1.00) 		0.074
(1.00) 		0.0659
(1.00) 		0.715
(1.00) 		0.199
(1.00) 		0.276
(1.00) 		0.128
(1.00)
4q gain 8 (2%) 395 0.127
(1.00) 		1
(1.00) 		0.194
(1.00) 		0.396
(1.00) 		0.159
(1.00) 		0.112
(1.00) 		0.207
(1.00) 		0.0217
(1.00)
5q gain 47 (12%) 356 0.0177
(1.00) 		0.644
(1.00) 		0.0448
(1.00) 		0.0211
(1.00) 		0.482
(1.00) 		0.0877
(1.00) 		0.0169
(1.00) 		0.141
(1.00) 		0.156
(1.00) 		0.617
(1.00)
6q gain 17 (4%) 386 0.124
(1.00) 		0.0269
(1.00) 		0.139
(1.00) 		0.0821
(1.00) 		0.505
(1.00) 		0.703
(1.00) 		0.0444
(1.00) 		0.000387
(0.257)
9p gain 11 (3%) 392 0.00526
(1.00) 		0.00666
(1.00) 		0.832
(1.00) 		0.789
(1.00) 		0.0119
(1.00) 		1
(1.00) 		0.918
(1.00) 		0.591
(1.00)
9q gain 7 (2%) 396 0.0694
(1.00) 		0.192
(1.00) 		0.256
(1.00) 		0.277
(1.00) 		0.0143
(1.00) 		0.392
(1.00) 		0.439
(1.00) 		0.345
(1.00)
10q gain 25 (6%) 378 0.0743
(1.00) 		0.349
(1.00) 		0.647
(1.00) 		0.187
(1.00) 		0.16
(1.00) 		0.164
(1.00) 		0.701
(1.00) 		0.181
(1.00)
11p gain 32 (8%) 371 0.0054
(1.00) 		0.335
(1.00) 		0.0699
(1.00) 		0.437
(1.00) 		0.583
(1.00) 		0.157
(1.00) 		0.0635
(1.00) 		0.0521
(1.00)
13q gain 15 (4%) 388 0.192
(1.00) 		0.157
(1.00) 		0.117
(1.00) 		0.926
(1.00) 		0.177
(1.00) 		0.288
(1.00) 		0.316
(1.00) 		0.0634
(1.00) 		0.345
(1.00) 		0.839
(1.00)
15q gain 14 (3%) 389 0.0788
(1.00) 		0.833
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.106
(1.00) 		0.341
(1.00) 		0.929
(1.00) 		0.351
(1.00)
16p gain 58 (14%) 345 0.358
(1.00) 		0.322
(1.00) 		0.183
(1.00) 		0.0125
(1.00) 		0.149
(1.00) 		0.726
(1.00) 		0.0647
(1.00) 		0.0582
(1.00) 		0.0396
(1.00) 		0.0526
(1.00)
16q gain 39 (10%) 364 0.192
(1.00) 		0.0514
(1.00) 		0.433
(1.00) 		0.0642
(1.00) 		0.0346
(1.00) 		0.0506
(1.00) 		0.196
(1.00) 		0.312
(1.00) 		0.221
(1.00) 		0.00291
(1.00)
17p gain 25 (6%) 378 0.00115
(0.732) 		0.0684
(1.00) 		0.665
(1.00) 		0.965
(1.00) 		0.485
(1.00) 		0.881
(1.00) 		0.187
(1.00) 		0.773
(1.00)
19p gain 8 (2%) 395 0.815
(1.00) 		0.265
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.807
(1.00) 		0.772
(1.00) 		0.207
(1.00) 		0.733
(1.00)
19q gain 21 (5%) 382 0.026
(1.00) 		0.274
(1.00) 		0.547
(1.00) 		0.0465
(1.00) 		0.995
(1.00) 		1
(1.00) 		0.0139
(1.00) 		0.0584
(1.00)
22q gain 20 (5%) 383 0.0888
(1.00) 		0.826
(1.00) 		0.426
(1.00) 		0.349
(1.00) 		0.615
(1.00) 		0.597
(1.00) 		0.0181
(1.00) 		0.129
(1.00)
Xq gain 18 (4%) 385 0.75
(1.00) 		0.591
(1.00) 		0.000478
(0.316) 		0.0318
(1.00) 		0.694
(1.00) 		0.672
(1.00) 		0.0224
(1.00) 		0.416
(1.00) 		0.255
(1.00) 		0.0818
(1.00)
1q loss 10 (2%) 393 0.0411
(1.00) 		0.9
(1.00) 		0.196
(1.00) 		0.0348
(1.00) 		0.188
(1.00) 		0.0739
(1.00) 		0.341
(1.00) 		0.374
(1.00)
2p loss 5 (1%) 398 0.927
(1.00) 		0.305
(1.00) 		1
(1.00) 		0.725
(1.00) 		0.655
(1.00) 		0.579
(1.00) 		0.369
(1.00) 		1
(1.00)
2q loss 3 (1%) 400 0.0927
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.487
(1.00)
3q loss 45 (11%) 358 0.554
(1.00) 		0.418
(1.00) 		0.00187
(1.00) 		0.00134
(0.852) 		0.229
(1.00) 		0.943
(1.00) 		0.0093
(1.00) 		0.375
(1.00) 		0.0651
(1.00) 		0.627
(1.00)
5p loss 13 (3%) 390 0.00334
(1.00) 		0.000959
(0.616) 		0.593
(1.00) 		0.937
(1.00) 		0.106
(1.00) 		0.00634
(1.00) 		0.0553
(1.00) 		0.00254
(1.00)
6p loss 34 (8%) 369 0.335
(1.00) 		0.308
(1.00) 		0.0167
(1.00) 		0.000835
(0.54) 		0.229
(1.00) 		0.274
(1.00) 		0.441
(1.00) 		0.751
(1.00) 		0.212
(1.00) 		0.617
(1.00)
7p loss 12 (3%) 391 0.554
(1.00) 		0.418
(1.00) 		0.0297
(1.00) 		0.562
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.0543
(1.00) 		0.115
(1.00) 		1
(1.00) 		0.872
(1.00)
7q loss 13 (3%) 390 0.53
(1.00) 		0.186
(1.00) 		0.162
(1.00) 		1
(1.00) 		0.593
(1.00) 		0.822
(1.00) 		0.29
(1.00) 		0.186
(1.00) 		0.738
(1.00) 		0.726
(1.00)
8q loss 16 (4%) 387 0.00578
(1.00) 		0.618
(1.00) 		0.00048
(0.317) 		0.00315
(1.00) 		0.488
(1.00) 		0.0673
(1.00) 		0.881
(1.00) 		0.473
(1.00)
10p loss 34 (8%) 369 0.901
(1.00) 		0.818
(1.00) 		0.000479
(0.317) 		0.106
(1.00) 		0.034
(1.00) 		0.108
(1.00) 		0.153
(1.00) 		0.0539
(1.00) 		0.0404
(1.00) 		0.22
(1.00)
10q loss 40 (10%) 363 0.75
(1.00) 		0.591
(1.00) 		0.000818
(0.53) 		0.031
(1.00) 		0.0111
(1.00) 		0.0804
(1.00) 		0.0779
(1.00) 		0.314
(1.00) 		0.269
(1.00) 		0.669
(1.00)
11p loss 27 (7%) 376 0.335
(1.00) 		0.102
(1.00) 		0.000542
(0.356) 		0.604
(1.00) 		0.00611
(1.00) 		0.0983
(1.00) 		0.00344
(1.00) 		0.00875
(1.00) 		0.0444
(1.00) 		0.138
(1.00)
11q loss 23 (6%) 380 0.474
(1.00) 		0.157
(1.00) 		0.0905
(1.00) 		0.358
(1.00) 		0.00348
(1.00) 		0.0716
(1.00) 		0.0675
(1.00) 		0.124
(1.00) 		0.373
(1.00) 		0.892
(1.00)
12p loss 34 (8%) 369 0.728
(1.00) 		0.818
(1.00) 		0.0337
(1.00) 		0.000953
(0.613) 		0.922
(1.00) 		0.362
(1.00) 		0.00366
(1.00) 		0.515
(1.00) 		0.66
(1.00) 		0.403
(1.00)
12q loss 21 (5%) 382 0.151
(1.00) 		0.235
(1.00) 		0.943
(1.00) 		0.534
(1.00) 		0.909
(1.00) 		0.839
(1.00) 		0.86
(1.00) 		0.416
(1.00)
14q loss 41 (10%) 362 0.401
(1.00) 		0.418
(1.00) 		0.28
(1.00) 		0.0974
(1.00) 		0.0329
(1.00) 		0.0272
(1.00) 		0.545
(1.00) 		0.657
(1.00) 		0.211
(1.00) 		0.432
(1.00)
16p loss 31 (8%) 372 0.00105
(0.674) 		0.0358
(1.00) 		0.0404
(1.00) 		0.425
(1.00) 		0.00583
(1.00) 		0.123
(1.00) 		0.0297
(1.00) 		0.0255
(1.00)
17p loss 94 (23%) 309 0.13
(1.00) 		0.301
(1.00) 		0.000693
(0.453) 		0.00655
(1.00) 		0.151
(1.00) 		0.433
(1.00) 		0.122
(1.00) 		0.878
(1.00) 		0.85
(1.00) 		0.697
(1.00)
17q loss 14 (3%) 389 0.378
(1.00) 		0.0228
(1.00) 		0.0605
(1.00) 		0.577
(1.00) 		0.05
(1.00) 		0.159
(1.00) 		0.658
(1.00) 		0.697
(1.00)
19q loss 60 (15%) 343 0.71
(1.00) 		0.722
(1.00) 		0.00252
(1.00) 		0.017
(1.00) 		0.975
(1.00) 		0.56
(1.00) 		0.0615
(1.00) 		0.085
(1.00) 		0.0133
(1.00) 		0.116
(1.00)
20p loss 53 (13%) 350 0.192
(1.00) 		0.412
(1.00) 		0.00181
(1.00) 		0.764
(1.00) 		0.00138
(0.878) 		0.00609
(1.00) 		0.105
(1.00) 		0.0349
(1.00) 		0.591
(1.00) 		0.509
(1.00)
20q loss 20 (5%) 383 0.81
(1.00) 		0.256
(1.00) 		0.322
(1.00) 		0.367
(1.00) 		0.276
(1.00) 		0.871
(1.00) 		0.951
(1.00) 		0.141
(1.00)
Xq loss 9 (2%) 394 0.0847
(1.00) 		0.168
(1.00) 		0.738
(1.00) 		0.665
(1.00) 		0.324
(1.00) 		0.255
(1.00) 		0.66
(1.00) 		0.693
(1.00)
'1p gain mutation analysis' versus 'CN_CNMF'

P value = 3.69e-09 (Fisher's exact test), Q value = 2.7e-06

Table S1.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
1P GAIN MUTATED 35 6 4 4
1P GAIN WILD-TYPE 87 151 66 50

Figure S1.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00088

Table S2.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
2P GAIN MUTATED 17 3 15 10
2P GAIN WILD-TYPE 105 154 55 44

Figure S2.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000336 (Fisher's exact test), Q value = 0.22

Table S3.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
2P GAIN MUTATED 4 23 6
2P GAIN WILD-TYPE 74 89 106

Figure S3.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.0017

Table S4.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
2Q GAIN MUTATED 12 3 14 11
2Q GAIN WILD-TYPE 110 154 56 43

Figure S4.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 1.22e-14 (Fisher's exact test), Q value = 8.9e-12

Table S5.  Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
5P GAIN MUTATED 80 30 20 24
5P GAIN WILD-TYPE 42 127 50 30

Figure S5.  Get High-res Image Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.14

Table S6.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
6P GAIN MUTATED 20 16 6 19
6P GAIN WILD-TYPE 102 141 64 35

Figure S6.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 7.4e-17 (Fisher's exact test), Q value = 5.4e-14

Table S7.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
7P GAIN MUTATED 76 20 25 17
7P GAIN WILD-TYPE 46 137 45 37

Figure S7.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'RPPA_CNMF'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.014

Table S8.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 75 71
7P GAIN MUTATED 42 12 32
7P GAIN WILD-TYPE 47 63 39

Figure S8.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.28e-08 (Chi-square test), Q value = 5.9e-05

Table S9.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
7P GAIN MUTATED 53 9 13 26 20
7P GAIN WILD-TYPE 45 66 41 55 24

Figure S9.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000152 (Fisher's exact test), Q value = 0.1

Table S10.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
7P GAIN MUTATED 39 33 49
7P GAIN WILD-TYPE 113 72 46

Figure S10.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.25

Table S11.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
7P GAIN MUTATED 40 66 31
7P GAIN WILD-TYPE 118 117 26

Figure S11.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 6.63e-11 (Fisher's exact test), Q value = 4.8e-08

Table S12.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
7Q GAIN MUTATED 57 16 18 10
7Q GAIN WILD-TYPE 65 141 52 44

Figure S12.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.37e-05 (Chi-square test), Q value = 0.0096

Table S13.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
7Q GAIN MUTATED 39 7 10 16 17
7Q GAIN WILD-TYPE 59 68 44 65 27

Figure S13.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.87e-05 (Fisher's exact test), Q value = 0.06

Table S14.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
7Q GAIN MUTATED 27 22 40
7Q GAIN WILD-TYPE 125 83 55

Figure S14.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000226 (Fisher's exact test), Q value = 0.15

Table S15.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
8P GAIN MUTATED 10 9 10 15
8P GAIN WILD-TYPE 112 148 60 39

Figure S15.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000327 (Fisher's exact test), Q value = 0.22

Table S16.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
8P GAIN MUTATED 6 22 4
8P GAIN WILD-TYPE 72 90 108

Figure S16.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 2.69e-11 (Fisher's exact test), Q value = 2e-08

Table S17.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
8Q GAIN MUTATED 41 19 28 32
8Q GAIN WILD-TYPE 81 138 42 22

Figure S17.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00072

Table S18.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
8Q GAIN MUTATED 12 53 24
8Q GAIN WILD-TYPE 66 59 88

Figure S18.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000289 (Chi-square test), Q value = 0.19

Table S19.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
8Q GAIN MUTATED 33 14 12 39 9
8Q GAIN WILD-TYPE 65 61 42 42 35

Figure S19.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'8q gain mutation analysis' versus 'MIRSEQ_CNMF'

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

Table S20.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
8Q GAIN MUTATED 27 73 18
8Q GAIN WILD-TYPE 131 110 39

Figure S20.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'8q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.01

Table S21.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
8Q GAIN MUTATED 31 33 54
8Q GAIN WILD-TYPE 132 82 66

Figure S21.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.021

Table S22.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
10P GAIN MUTATED 3 24 5
10P GAIN WILD-TYPE 75 88 107

Figure S22.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 1.33e-05 (Fisher's exact test), Q value = 0.0093

Table S23.  Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
11Q GAIN MUTATED 22 4 13 6
11Q GAIN WILD-TYPE 100 153 57 48

Figure S23.  Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q gain mutation analysis' versus 'RPPA_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.23

Table S24.  Gene #22: '11q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 75 71
11Q GAIN MUTATED 10 2 17
11Q GAIN WILD-TYPE 79 73 54

Figure S24.  Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 6.6e-13 (Fisher's exact test), Q value = 4.8e-10

Table S25.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
12P GAIN MUTATED 12 4 29 5
12P GAIN WILD-TYPE 110 153 41 49

Figure S25.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q gain mutation analysis' versus 'CN_CNMF'

P value = 5.85e-11 (Fisher's exact test), Q value = 4.3e-08

Table S26.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
12Q GAIN MUTATED 8 3 24 5
12Q GAIN WILD-TYPE 114 154 46 49

Figure S26.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q gain mutation analysis' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00082

Table S27.  Gene #26: '14q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
14Q GAIN MUTATED 15 9 7 20
14Q GAIN WILD-TYPE 107 148 63 34

Figure S27.  Get High-res Image Gene #26: '14q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 7.55e-07 (Fisher's exact test), Q value = 0.00053

Table S28.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
17Q GAIN MUTATED 32 8 15 14
17Q GAIN WILD-TYPE 90 149 55 40

Figure S28.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p gain mutation analysis' versus 'CN_CNMF'

P value = 3.19e-05 (Fisher's exact test), Q value = 0.022

Table S29.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
18P GAIN MUTATED 17 4 3 11
18P GAIN WILD-TYPE 105 153 67 43

Figure S29.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q gain mutation analysis' versus 'CN_CNMF'

P value = 2.74e-07 (Fisher's exact test), Q value = 2e-04

Table S30.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
18Q GAIN MUTATED 9 0 3 11
18Q GAIN WILD-TYPE 113 157 67 43

Figure S30.  Get High-res Image Gene #33: '18q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 6.15e-07 (Fisher's exact test), Q value = 0.00044

Table S31.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
20P GAIN MUTATED 14 8 16 18
20P GAIN WILD-TYPE 108 149 54 36

Figure S31.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 3.56e-08 (Fisher's exact test), Q value = 2.5e-05

Table S32.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
20Q GAIN MUTATED 21 8 20 19
20Q GAIN WILD-TYPE 101 149 50 35

Figure S32.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.96e-05 (Chi-square test), Q value = 0.014

Table S33.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
20Q GAIN MUTATED 9 6 8 28 10
20Q GAIN WILD-TYPE 89 69 46 53 34

Figure S33.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'21q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.1

Table S34.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
21Q GAIN MUTATED 23 6 3 4
21Q GAIN WILD-TYPE 99 151 67 50

Figure S34.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.016

Table S35.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
1P LOSS MUTATED 3 5 9 11
1P LOSS WILD-TYPE 119 152 61 43

Figure S35.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3p loss mutation analysis' versus 'CN_CNMF'

P value = 4.86e-05 (Fisher's exact test), Q value = 0.033

Table S36.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
3P LOSS MUTATED 25 14 21 17
3P LOSS WILD-TYPE 97 143 49 37

Figure S36.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.99e-05 (Chi-square test), Q value = 0.068

Table S37.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
4P LOSS MUTATED 5 1 5 17 2
4P LOSS WILD-TYPE 93 74 49 64 42

Figure S37.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.91e-06 (Fisher's exact test), Q value = 0.0035

Table S38.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
4P LOSS MUTATED 4 21 5
4P LOSS WILD-TYPE 148 84 90

Figure S38.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 1.38e-08 (Fisher's exact test), Q value = 9.8e-06

Table S39.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
4Q LOSS MUTATED 9 2 16 12
4Q LOSS WILD-TYPE 113 155 54 42

Figure S39.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000226 (Fisher's exact test), Q value = 0.15

Table S40.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
4Q LOSS MUTATED 2 20 5
4Q LOSS WILD-TYPE 76 92 107

Figure S40.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.64e-09 (Chi-square test), Q value = 4.8e-06

Table S41.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
4Q LOSS MUTATED 4 2 4 24 2
4Q LOSS WILD-TYPE 94 73 50 57 42

Figure S41.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'4q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.87e-09 (Fisher's exact test), Q value = 1.4e-06

Table S42.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
4Q LOSS MUTATED 5 28 3
4Q LOSS WILD-TYPE 147 77 92

Figure S42.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 9.4e-06 (Fisher's exact test), Q value = 0.0066

Table S43.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
5Q LOSS MUTATED 20 6 15 13
5Q LOSS WILD-TYPE 102 151 55 41

Figure S43.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.5e-05 (Fisher's exact test), Q value = 0.024

Table S44.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
5Q LOSS MUTATED 8 29 6
5Q LOSS WILD-TYPE 70 83 106

Figure S44.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'6q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.45e-11 (Fisher's exact test), Q value = 6.1e-08

Table S45.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
6Q LOSS MUTATED 22 45 5
6Q LOSS WILD-TYPE 56 67 107

Figure S45.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 4.06e-11 (Fisher's exact test), Q value = 3e-08

Table S46.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
8P LOSS MUTATED 53 13 23 15
8P LOSS WILD-TYPE 69 144 47 39

Figure S46.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 1.57e-07 (Fisher's exact test), Q value = 0.00011

Table S47.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
9P LOSS MUTATED 37 28 40 17
9P LOSS WILD-TYPE 85 129 30 37

Figure S47.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 5.95e-09 (Fisher's exact test), Q value = 4.3e-06

Table S48.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
9Q LOSS MUTATED 32 17 34 19
9Q LOSS WILD-TYPE 90 140 36 35

Figure S48.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 1.02e-14 (Fisher's exact test), Q value = 7.5e-12

Table S49.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
13Q LOSS MUTATED 43 5 24 19
13Q LOSS WILD-TYPE 79 152 46 35

Figure S49.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.94e-05 (Fisher's exact test), Q value = 0.061

Table S50.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
13Q LOSS MUTATED 18 37 11
13Q LOSS WILD-TYPE 60 75 101

Figure S50.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 1.99e-10 (Fisher's exact test), Q value = 1.4e-07

Table S51.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
15Q LOSS MUTATED 36 7 17 20
15Q LOSS WILD-TYPE 86 150 53 34

Figure S51.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'15q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.28e-06 (Fisher's exact test), Q value = 0.0037

Table S52.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
15Q LOSS MUTATED 12 40 11
15Q LOSS WILD-TYPE 66 72 101

Figure S52.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'15q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.48e-05 (Fisher's exact test), Q value = 0.044

Table S53.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
15Q LOSS MUTATED 17 26 32
15Q LOSS WILD-TYPE 135 79 63

Figure S53.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.082

Table S54.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
15Q LOSS MUTATED 17 26 36
15Q LOSS WILD-TYPE 146 89 84

Figure S54.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss mutation analysis' versus 'CN_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0071

Table S55.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
16Q LOSS MUTATED 25 5 11 10
16Q LOSS WILD-TYPE 97 152 59 44

Figure S55.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 5.08e-05 (Fisher's exact test), Q value = 0.035

Table S56.  Gene #72: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
18P LOSS MUTATED 24 10 20 6
18P LOSS WILD-TYPE 98 147 50 48

Figure S56.  Get High-res Image Gene #72: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 5.78e-09 (Fisher's exact test), Q value = 4.2e-06

Table S57.  Gene #73: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
18Q LOSS MUTATED 41 16 28 5
18Q LOSS WILD-TYPE 81 141 42 49

Figure S57.  Get High-res Image Gene #73: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p loss mutation analysis' versus 'CN_CNMF'

P value = 8.15e-09 (Fisher's exact test), Q value = 5.8e-06

Table S58.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
19P LOSS MUTATED 23 23 37 19
19P LOSS WILD-TYPE 99 134 33 35

Figure S58.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000184 (Fisher's exact test), Q value = 0.12

Table S59.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
19P LOSS MUTATED 39 55 3
19P LOSS WILD-TYPE 119 128 54

Figure S59.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 7.78e-09 (Fisher's exact test), Q value = 5.6e-06

Table S60.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
21Q LOSS MUTATED 12 8 25 13
21Q LOSS WILD-TYPE 110 149 45 41

Figure S60.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.011

Table S61.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
21Q LOSS MUTATED 6 30 7
21Q LOSS WILD-TYPE 72 82 105

Figure S61.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'21q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.6e-09 (Chi-square test), Q value = 4.7e-06

Table S62.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
21Q LOSS MUTATED 7 4 8 30 3
21Q LOSS WILD-TYPE 91 71 46 51 41

Figure S62.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'21q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-07 (Fisher's exact test), Q value = 2e-04

Table S63.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
21Q LOSS MUTATED 11 33 8
21Q LOSS WILD-TYPE 141 72 87

Figure S63.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.01

Table S64.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
21Q LOSS MUTATED 11 42 3
21Q LOSS WILD-TYPE 147 141 54

Figure S64.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'21q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.016

Table S65.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
21Q LOSS MUTATED 12 12 32
21Q LOSS WILD-TYPE 151 103 88

Figure S65.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 9.39e-11 (Fisher's exact test), Q value = 6.8e-08

Table S66.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 157 70 54
22Q LOSS MUTATED 24 9 23 24
22Q LOSS WILD-TYPE 98 148 47 30

Figure S66.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.59e-05 (Fisher's exact test), Q value = 0.018

Table S67.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 112 112
22Q LOSS MUTATED 9 39 14
22Q LOSS WILD-TYPE 69 73 98

Figure S67.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000322 (Chi-square test), Q value = 0.22

Table S68.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
22Q LOSS MUTATED 20 10 10 31 4
22Q LOSS WILD-TYPE 78 65 44 50 40

Figure S68.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S69.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
22Q LOSS MUTATED 18 23 37
22Q LOSS WILD-TYPE 145 92 83

Figure S69.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 403

  • 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)
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