Lung Adenocarcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level results and 10 molecular subtypes across 472 patients, 88 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' and 'METHLYATION_CNMF'.

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

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

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

  • 10p gain cnv correlated to 'METHLYATION_CNMF'.

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

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

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

  • 16p gain cnv correlated to 'METHLYATION_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

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

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • Xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'METHLYATION_CNMF'.

  • 3p loss cnv correlated to 'METHLYATION_CNMF'.

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

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

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

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

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  '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, 88 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
21q loss 66 (14%) 406 3.03e-12
(2.2e-09) 		1e-07
(7.04e-05) 		0.103
(1.00) 		0.0176
(1.00) 		6.6e-09
(4.71e-06) 		2.76e-07
(0.000194) 		1.48e-05
(0.01) 		2.31e-05
(0.0155)
7p gain 154 (33%) 318 0.754
(1.00) 		0.523
(1.00) 		3.08e-18
(2.25e-15) 		1.97e-06
(0.00137) 		8.93e-05
(0.0589) 		0.00948
(1.00) 		2.92e-08
(2.07e-05) 		0.000105
(0.069) 		0.000756
(0.474) 		0.00347
(1.00)
8q gain 144 (31%) 328 0.0641
(1.00) 		0.191
(1.00) 		1.9e-21
(1.39e-18) 		3.32e-07
(0.000233) 		0.0357
(1.00) 		0.00424
(1.00) 		0.00097
(0.6) 		0.00139
(0.852) 		1.68e-05
(0.0113) 		1.46e-05
(0.00989)
4p loss 38 (8%) 434 1.26e-05
(0.00854) 		6.44e-05
(0.0427) 		0.192
(1.00) 		0.248
(1.00) 		9.99e-05
(0.0657) 		4.91e-06
(0.00336) 		0.00183
(1.00) 		0.0599
(1.00)
4q loss 45 (10%) 427 0.00605
(1.00) 		0.00706
(1.00) 		2.2e-10
(1.59e-07) 		4.24e-07
(0.000297) 		0.469
(1.00) 		0.578
(1.00) 		6.64e-09
(4.74e-06) 		1.87e-09
(1.34e-06) 		0.00153
(0.933) 		0.000724
(0.456)
15q loss 95 (20%) 377 0.405
(1.00) 		0.219
(1.00) 		5.26e-12
(3.81e-09) 		1.41e-09
(1.02e-06) 		0.481
(1.00) 		0.0188
(1.00) 		0.00132
(0.813) 		3.6e-05
(0.024) 		0.00078
(0.488) 		9.74e-05
(0.0642)
22q loss 90 (19%) 382 0.308
(1.00) 		0.321
(1.00) 		5.75e-10
(4.14e-07) 		4.56e-05
(0.0304) 		0.00909
(1.00) 		0.011
(1.00) 		0.000364
(0.234) 		0.000476
(0.304) 		0.00221
(1.00) 		0.00017
(0.111)
7q gain 111 (24%) 361 0.388
(1.00) 		0.702
(1.00) 		5.86e-09
(4.19e-06) 		0.000472
(0.302) 		0.0789
(1.00) 		0.298
(1.00) 		1.37e-05
(0.00931) 		8.87e-05
(0.0586) 		0.0525
(1.00) 		0.081
(1.00)
20q gain 76 (16%) 396 0.00237
(1.00) 		0.00219
(1.00) 		4.8e-07
(0.000336) 		5.01e-09
(3.58e-06) 		0.00132
(0.809) 		0.0914
(1.00) 		6.84e-05
(0.0453) 		0.00141
(0.864) 		0.0053
(1.00) 		0.0106
(1.00)
19p loss 112 (24%) 360 0.649
(1.00) 		0.688
(1.00) 		1.56e-09
(1.12e-06) 		7.15e-08
(5.05e-05) 		0.867
(1.00) 		0.69
(1.00) 		0.000632
(0.4) 		0.0183
(1.00) 		0.00024
(0.156) 		0.0562
(1.00)
2p gain 50 (11%) 422 0.0312
(1.00) 		0.0151
(1.00) 		7e-08
(4.95e-05) 		3.89e-06
(0.00268) 		0.0781
(1.00) 		0.0301
(1.00) 		0.0321
(1.00) 		0.000783
(0.489) 		0.00186
(1.00) 		0.00503
(1.00)
2q gain 45 (10%) 427 0.0302
(1.00) 		0.0253
(1.00) 		1.69e-06
(0.00118) 		7.92e-07
(0.000553) 		0.252
(1.00) 		0.276
(1.00) 		0.11
(1.00) 		0.0171
(1.00) 		0.00557
(1.00) 		0.0439
(1.00)
12p gain 57 (12%) 415 0.565
(1.00) 		0.132
(1.00) 		3.02e-14
(2.2e-11) 		8.57e-05
(0.0568) 		0.18
(1.00) 		0.115
(1.00) 		0.0103
(1.00) 		0.000737
(0.464) 		0.00622
(1.00) 		0.0065
(1.00)
12q gain 46 (10%) 426 0.565
(1.00) 		0.132
(1.00) 		2.9e-12
(2.1e-09) 		0.000184
(0.12) 		0.158
(1.00) 		0.0893
(1.00) 		0.0229
(1.00) 		0.00454
(1.00) 		0.0217
(1.00) 		0.00394
(1.00)
14q gain 56 (12%) 416 4.9e-06
(0.00336) 		2.98e-06
(0.00206) 		0.127
(1.00) 		0.518
(1.00) 		0.000519
(0.331) 		0.00678
(1.00) 		0.0126
(1.00) 		0.00562
(1.00)
17q gain 78 (17%) 394 0.0447
(1.00) 		0.702
(1.00) 		4.69e-08
(3.32e-05) 		1.39e-06
(0.000969) 		0.423
(1.00) 		0.199
(1.00) 		0.00954
(1.00) 		0.0447
(1.00) 		0.0601
(1.00) 		0.0706
(1.00)
20p gain 61 (13%) 411 0.0235
(1.00) 		0.0127
(1.00) 		3.06e-06
(0.00211) 		2.78e-05
(0.0186) 		0.0249
(1.00) 		0.687
(1.00) 		0.000465
(0.298) 		0.000826
(0.514) 		0.0699
(1.00) 		0.0221
(1.00)
21q gain 41 (9%) 431 0.192
(1.00) 		0.157
(1.00) 		5e-05
(0.0332) 		3.42e-05
(0.0229) 		0.0914
(1.00) 		0.0523
(1.00) 		0.438
(1.00) 		0.0584
(1.00) 		0.423
(1.00) 		0.39
(1.00)
5q loss 58 (12%) 414 0.0235
(1.00) 		0.0127
(1.00) 		3.4e-05
(0.0228) 		1.01e-05
(0.00686) 		0.0388
(1.00) 		0.0986
(1.00) 		0.00144
(0.882) 		0.00827
(1.00) 		0.00593
(1.00) 		0.0533
(1.00)
8p loss 118 (25%) 354 0.104
(1.00) 		0.173
(1.00) 		4.75e-14
(3.45e-11) 		2e-06
(0.00139) 		0.173
(1.00) 		0.0281
(1.00) 		0.00325
(1.00) 		0.0256
(1.00) 		0.0618
(1.00) 		0.0241
(1.00)
9p loss 139 (29%) 333 0.155
(1.00) 		0.206
(1.00) 		2.7e-08
(1.92e-05) 		2.59e-05
(0.0173) 		0.345
(1.00) 		0.049
(1.00) 		0.16
(1.00) 		0.00726
(1.00) 		0.757
(1.00) 		0.309
(1.00)
9q loss 117 (25%) 355 0.462
(1.00) 		0.475
(1.00) 		8.17e-08
(5.76e-05) 		1.07e-08
(7.62e-06) 		0.323
(1.00) 		0.144
(1.00) 		0.0564
(1.00) 		0.00652
(1.00) 		0.147
(1.00) 		0.00352
(1.00)
13q loss 109 (23%) 363 0.0846
(1.00) 		0.0411
(1.00) 		3.55e-21
(2.6e-18) 		6.46e-07
(0.000452) 		0.285
(1.00) 		0.00936
(1.00) 		0.106
(1.00) 		0.000598
(0.379) 		0.00424
(1.00) 		0.0299
(1.00)
18q loss 108 (23%) 364 0.42
(1.00) 		0.412
(1.00) 		1.68e-09
(1.21e-06) 		0.00016
(0.105) 		0.301
(1.00) 		0.129
(1.00) 		0.216
(1.00) 		0.16
(1.00) 		0.632
(1.00) 		0.988
(1.00)
1p gain 58 (12%) 414 1
(1.00) 		1
(1.00) 		3.6e-08
(2.55e-05) 		0.000565
(0.359) 		0.0815
(1.00) 		0.0241
(1.00) 		0.23
(1.00) 		0.433
(1.00) 		0.542
(1.00) 		0.89
(1.00)
1q gain 177 (38%) 295 0.465
(1.00) 		0.885
(1.00) 		0.0352
(1.00) 		1.88e-05
(0.0127) 		0.131
(1.00) 		0.146
(1.00) 		0.0824
(1.00) 		0.376
(1.00) 		0.491
(1.00) 		0.122
(1.00)
5p gain 178 (38%) 294 0.487
(1.00) 		0.419
(1.00) 		9.1e-15
(6.64e-12) 		0.156
(1.00) 		0.233
(1.00) 		0.636
(1.00) 		0.0502
(1.00) 		0.129
(1.00) 		0.501
(1.00) 		0.668
(1.00)
6p gain 71 (15%) 401 0.292
(1.00) 		0.0507
(1.00) 		0.0199
(1.00) 		3.77e-06
(0.0026) 		0.00936
(1.00) 		0.261
(1.00) 		0.0446
(1.00) 		0.229
(1.00) 		0.141
(1.00) 		0.0973
(1.00)
8p gain 59 (12%) 413 3.74e-10
(2.7e-07) 		0.00323
(1.00) 		0.598
(1.00) 		0.842
(1.00) 		0.0058
(1.00) 		0.00922
(1.00) 		0.859
(1.00) 		0.0845
(1.00)
10p gain 49 (10%) 423 0.0417
(1.00) 		0.00011
(0.0723) 		0.169
(1.00) 		0.16
(1.00) 		0.327
(1.00) 		0.378
(1.00) 		0.132
(1.00) 		0.657
(1.00)
16p gain 67 (14%) 405 0.358
(1.00) 		0.322
(1.00) 		0.328
(1.00) 		0.000349
(0.226) 		0.0878
(1.00) 		0.448
(1.00) 		0.042
(1.00) 		0.0484
(1.00) 		0.0136
(1.00) 		0.0365
(1.00)
17p gain 28 (6%) 444 8.73e-06
(0.00596) 		0.000427
(0.275) 		0.665
(1.00) 		0.533
(1.00) 		0.485
(1.00) 		0.881
(1.00) 		0.129
(1.00) 		0.569
(1.00)
18p gain 42 (9%) 430 2.13e-06
(0.00148) 		0.00112
(0.691) 		0.0711
(1.00) 		0.209
(1.00) 		0.224
(1.00) 		0.0652
(1.00) 		0.0242
(1.00) 		0.0281
(1.00)
18q gain 26 (6%) 446 2.2e-05
(0.0148) 		0.000608
(0.386) 		0.09
(1.00) 		0.0373
(1.00) 		0.0139
(1.00) 		0.00682
(1.00) 		0.0991
(1.00) 		0.0114
(1.00)
Xq gain 19 (4%) 453 0.75
(1.00) 		0.591
(1.00) 		0.000237
(0.154) 		0.0425
(1.00) 		0.433
(1.00) 		0.598
(1.00) 		0.058
(1.00) 		0.48
(1.00) 		0.378
(1.00) 		0.179
(1.00)
1p loss 28 (6%) 444 0.00445
(1.00) 		0.000214
(0.139) 		0.111
(1.00) 		0.199
(1.00) 		0.00732
(1.00) 		0.12
(1.00) 		0.465
(1.00) 		0.489
(1.00)
3p loss 93 (20%) 379 0.208
(1.00) 		0.176
(1.00) 		0.000456
(0.294) 		1.53e-05
(0.0104) 		0.156
(1.00) 		0.402
(1.00) 		0.0426
(1.00) 		0.0059
(1.00) 		0.00962
(1.00) 		0.0625
(1.00)
6q loss 105 (22%) 367 0.803
(1.00) 		0.722
(1.00) 		0.0704
(1.00) 		4.4e-06
(0.00303) 		0.104
(1.00) 		0.0335
(1.00) 		0.0154
(1.00) 		0.686
(1.00) 		0.244
(1.00) 		0.664
(1.00)
16p loss 37 (8%) 435 0.000307
(0.199) 		0.00182
(1.00) 		0.0447
(1.00) 		0.281
(1.00) 		0.0106
(1.00) 		0.0755
(1.00) 		0.0415
(1.00) 		0.0521
(1.00)
16q loss 56 (12%) 416 0.0159
(1.00) 		1
(1.00) 		4.64e-06
(0.00319) 		0.00148
(0.905) 		0.00595
(1.00) 		0.00855
(1.00) 		0.0179
(1.00) 		0.148
(1.00) 		0.0116
(1.00) 		0.122
(1.00)
17p loss 109 (23%) 363 0.13
(1.00) 		0.301
(1.00) 		5.86e-06
(0.00401) 		0.00353
(1.00) 		0.0572
(1.00) 		0.21
(1.00) 		0.2
(1.00) 		0.709
(1.00) 		0.819
(1.00) 		0.465
(1.00)
18p loss 75 (16%) 397 0.42
(1.00) 		0.412
(1.00) 		1.14e-05
(0.00779) 		0.0198
(1.00) 		0.88
(1.00) 		0.223
(1.00) 		0.442
(1.00) 		0.69
(1.00) 		0.889
(1.00) 		0.545
(1.00)
19q loss 67 (14%) 405 0.71
(1.00) 		0.722
(1.00) 		0.00019
(0.124) 		0.0288
(1.00) 		0.778
(1.00) 		0.433
(1.00) 		0.0738
(1.00) 		0.0981
(1.00) 		0.0203
(1.00) 		0.0826
(1.00)
20p loss 61 (13%) 411 0.192
(1.00) 		0.412
(1.00) 		0.000194
(0.126) 		0.0535
(1.00) 		0.00631
(1.00) 		0.0252
(1.00) 		0.137
(1.00) 		0.0518
(1.00) 		0.614
(1.00) 		0.423
(1.00)
3p gain 13 (3%) 459 0.0322
(1.00) 		0.0462
(1.00) 		0.137
(1.00) 		0.271
(1.00) 		0.0198
(1.00) 		0.171
(1.00) 		0.72
(1.00) 		0.298
(1.00)
3q gain 29 (6%) 443 0.0025
(1.00) 		0.00235
(1.00) 		0.0783
(1.00) 		0.0222
(1.00) 		0.0577
(1.00) 		0.502
(1.00) 		0.104
(1.00) 		0.218
(1.00)
4p gain 30 (6%) 442 0.554
(1.00) 		0.418
(1.00) 		0.00352
(1.00) 		0.0102
(1.00) 		0.0727
(1.00) 		0.035
(1.00) 		0.753
(1.00) 		0.172
(1.00) 		0.211
(1.00) 		0.128
(1.00)
4q gain 11 (2%) 461 0.0379
(1.00) 		0.838
(1.00) 		0.222
(1.00) 		0.271
(1.00) 		0.251
(1.00) 		0.0894
(1.00) 		0.101
(1.00) 		0.0413
(1.00)
5q gain 56 (12%) 416 0.0177
(1.00) 		0.644
(1.00) 		0.0451
(1.00) 		0.000742
(0.466) 		0.541
(1.00) 		0.187
(1.00) 		0.034
(1.00) 		0.106
(1.00) 		0.136
(1.00) 		0.587
(1.00)
6q gain 20 (4%) 452 0.41
(1.00) 		0.00965
(1.00) 		0.108
(1.00) 		0.0645
(1.00) 		0.746
(1.00) 		0.594
(1.00) 		0.0606
(1.00) 		0.00198
(1.00)
9p gain 14 (3%) 458 0.0173
(1.00) 		0.0112
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.0146
(1.00) 		0.913
(1.00) 		0.72
(1.00) 		0.398
(1.00)
9q gain 7 (1%) 465 0.274
(1.00) 		0.59
(1.00) 		0.392
(1.00) 		0.269
(1.00) 		0.0143
(1.00) 		0.392
(1.00) 		0.439
(1.00) 		0.345
(1.00)
10q gain 28 (6%) 444 0.107
(1.00) 		0.0237
(1.00) 		0.555
(1.00) 		0.188
(1.00) 		0.16
(1.00) 		0.164
(1.00) 		0.701
(1.00) 		0.181
(1.00)
11p gain 35 (7%) 437 0.0527
(1.00) 		0.0419
(1.00) 		0.101
(1.00) 		0.476
(1.00) 		0.583
(1.00) 		0.157
(1.00) 		0.0773
(1.00) 		0.0574
(1.00)
11q gain 51 (11%) 421 0.12
(1.00) 		0.157
(1.00) 		0.000915
(0.568) 		0.0131
(1.00) 		0.000824
(0.514) 		0.0196
(1.00) 		0.0304
(1.00) 		0.00182
(1.00) 		0.0033
(1.00) 		0.00566
(1.00)
13q gain 15 (3%) 457 0.226
(1.00) 		0.0272
(1.00) 		0.433
(1.00) 		0.294
(1.00) 		0.455
(1.00) 		0.13
(1.00) 		0.398
(1.00) 		0.938
(1.00)
15q gain 14 (3%) 458 0.263
(1.00) 		0.542
(1.00) 		0.819
(1.00) 		0.578
(1.00) 		0.106
(1.00) 		0.341
(1.00) 		0.929
(1.00) 		0.351
(1.00)
16q gain 42 (9%) 430 0.192
(1.00) 		0.0514
(1.00) 		0.428
(1.00) 		0.00977
(1.00) 		0.0253
(1.00) 		0.0252
(1.00) 		0.157
(1.00) 		0.224
(1.00) 		0.132
(1.00) 		0.00183
(1.00)
19p gain 6 (1%) 466 0.773
(1.00) 		0.372
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.864
(1.00) 		0.21
(1.00) 		0.589
(1.00)
19q gain 22 (5%) 450 0.000461
(0.296) 		0.176
(1.00) 		0.402
(1.00) 		0.0144
(1.00) 		0.992
(1.00) 		0.722
(1.00) 		0.0237
(1.00) 		0.104
(1.00)
22q gain 20 (4%) 452 0.061
(1.00) 		0.13
(1.00) 		0.782
(1.00) 		0.172
(1.00) 		0.559
(1.00) 		0.806
(1.00) 		0.0224
(1.00) 		0.179
(1.00)
1q loss 11 (2%) 461 0.0619
(1.00) 		0.0811
(1.00) 		0.222
(1.00) 		0.0151
(1.00) 		0.394
(1.00) 		0.0949
(1.00) 		0.204
(1.00) 		0.294
(1.00)
2p loss 6 (1%) 466 0.931
(1.00) 		0.466
(1.00) 		1
(1.00) 		0.617
(1.00) 		0.655
(1.00) 		0.579
(1.00) 		0.369
(1.00) 		1
(1.00)
2q loss 4 (1%) 468 0.149
(1.00) 		0.227
(1.00) 		1
(1.00) 		0.487
(1.00)
3q loss 56 (12%) 416 0.554
(1.00) 		0.418
(1.00) 		0.0107
(1.00) 		0.00335
(1.00) 		0.341
(1.00) 		0.933
(1.00) 		0.0103
(1.00) 		0.296
(1.00) 		0.0366
(1.00) 		0.575
(1.00)
5p loss 15 (3%) 457 0.00645
(1.00) 		0.008
(1.00) 		0.306
(1.00) 		0.777
(1.00) 		0.162
(1.00) 		0.0403
(1.00) 		0.0888
(1.00) 		0.0292
(1.00)
6p loss 38 (8%) 434 0.335
(1.00) 		0.308
(1.00) 		0.0252
(1.00) 		0.0374
(1.00) 		0.202
(1.00) 		0.537
(1.00) 		0.361
(1.00) 		0.863
(1.00) 		0.334
(1.00) 		0.76
(1.00)
7p loss 14 (3%) 458 0.554
(1.00) 		0.418
(1.00) 		0.00723
(1.00) 		0.312
(1.00) 		0.522
(1.00) 		0.938
(1.00) 		0.0543
(1.00) 		0.115
(1.00) 		1
(1.00) 		0.872
(1.00)
7q loss 17 (4%) 455 0.53
(1.00) 		0.186
(1.00) 		0.0305
(1.00) 		0.411
(1.00) 		0.687
(1.00) 		0.821
(1.00) 		0.29
(1.00) 		0.186
(1.00) 		0.738
(1.00) 		0.726
(1.00)
8q loss 17 (4%) 455 0.000943
(0.585) 		0.09
(1.00) 		0.00124
(0.766) 		0.00526
(1.00) 		0.552
(1.00) 		0.0492
(1.00) 		0.721
(1.00) 		0.677
(1.00)
10p loss 35 (7%) 437 0.901
(1.00) 		0.818
(1.00) 		0.000707
(0.446) 		0.000889
(0.553) 		0.0525
(1.00) 		0.0991
(1.00) 		0.141
(1.00) 		0.0443
(1.00) 		0.0234
(1.00) 		0.146
(1.00)
10q loss 45 (10%) 427 0.75
(1.00) 		0.591
(1.00) 		0.00124
(0.766) 		0.00454
(1.00) 		0.0157
(1.00) 		0.0585
(1.00) 		0.0779
(1.00) 		0.314
(1.00) 		0.269
(1.00) 		0.669
(1.00)
11p loss 32 (7%) 440 0.335
(1.00) 		0.102
(1.00) 		0.00053
(0.337) 		0.846
(1.00) 		0.00454
(1.00) 		0.0268
(1.00) 		0.0132
(1.00) 		0.00201
(1.00) 		0.0793
(1.00) 		0.177
(1.00)
11q loss 29 (6%) 443 0.474
(1.00) 		0.157
(1.00) 		0.00271
(1.00) 		0.5
(1.00) 		0.0102
(1.00) 		0.0251
(1.00) 		0.21
(1.00) 		0.126
(1.00) 		0.326
(1.00) 		1
(1.00)
12p loss 37 (8%) 435 0.728
(1.00) 		0.818
(1.00) 		0.229
(1.00) 		0.000653
(0.413) 		0.819
(1.00) 		0.534
(1.00) 		0.00366
(1.00) 		0.515
(1.00) 		0.66
(1.00) 		0.403
(1.00)
12q loss 23 (5%) 449 0.0787
(1.00) 		0.131
(1.00) 		0.886
(1.00) 		0.305
(1.00) 		0.909
(1.00) 		0.839
(1.00) 		0.86
(1.00) 		0.416
(1.00)
14q loss 46 (10%) 426 0.401
(1.00) 		0.418
(1.00) 		0.0631
(1.00) 		0.0245
(1.00) 		0.0306
(1.00) 		0.00488
(1.00) 		0.53
(1.00) 		0.766
(1.00) 		0.236
(1.00) 		0.562
(1.00)
17q loss 17 (4%) 455 0.155
(1.00) 		0.0222
(1.00) 		0.0661
(1.00) 		0.897
(1.00) 		0.0589
(1.00) 		0.371
(1.00) 		0.673
(1.00) 		0.534
(1.00)
20q loss 24 (5%) 448 0.262
(1.00) 		0.139
(1.00) 		0.325
(1.00) 		0.306
(1.00) 		0.276
(1.00) 		0.871
(1.00) 		0.951
(1.00) 		0.141
(1.00)
Xq loss 11 (2%) 461 0.253
(1.00) 		0.281
(1.00) 		0.74
(1.00) 		0.572
(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 = 3.6e-08 (Fisher's exact test), Q value = 2.6e-05

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

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

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

'1q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S2.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S2.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 7e-08 (Fisher's exact test), Q value = 4.9e-05

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

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

Figure S3.  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 = 3.89e-06 (Chi-square test), Q value = 0.0027

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

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

Figure S4.  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 = 1.69e-06 (Fisher's exact test), Q value = 0.0012

Table S5.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S5.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S6.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S6.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 9.1e-15 (Fisher's exact test), Q value = 6.6e-12

Table S7.  Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S7.  Get High-res Image Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S8.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S8.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 3.08e-18 (Fisher's exact test), Q value = 2.2e-15

Table S9.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S9.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S10.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S10.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'RPPA_CNMF'

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

Table S11.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

Figure S11.  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 = 2.92e-08 (Chi-square test), Q value = 2.1e-05

Table S12.  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 8 13 26 20
7P GAIN WILD-TYPE 45 67 41 55 24

Figure S12.  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 = 0.000105 (Fisher's exact test), Q value = 0.069

Table S13.  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 38 33 49
7P GAIN WILD-TYPE 114 72 46

Figure S13.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

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

Table S14.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S14.  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 = 0.0093

Table S15.  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 S15.  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 = 0.059

Table S16.  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 S16.  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 = 3.74e-10 (Fisher's exact test), Q value = 2.7e-07

Table S17.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S17.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

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

Table S18.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S18.  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 = 3.32e-07 (Chi-square test), Q value = 0.00023

Table S19.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S19.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.011

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 = 0.0099

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

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

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

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

'12p gain mutation analysis' versus 'CN_CNMF'

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

Table S23.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S23.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.57e-05 (Chi-square test), Q value = 0.057

Table S24.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S24.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12q gain mutation analysis' versus 'CN_CNMF'

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

Table S25.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S25.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S26.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S26.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q gain mutation analysis' versus 'CN_CNMF'

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

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

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

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

'14q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S28.  Gene #26: '14q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S28.  Get High-res Image Gene #26: '14q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000349 (Chi-square test), Q value = 0.23

Table S29.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S29.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p gain mutation analysis' versus 'CN_CNMF'

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

Table S30.  Gene #30: '17p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S30.  Get High-res Image Gene #30: '17p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'CN_CNMF'

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

Table S31.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S31.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S32.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S32.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p gain mutation analysis' versus 'CN_CNMF'

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

Table S33.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S33.  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 = 2.2e-05 (Fisher's exact test), Q value = 0.015

Table S34.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S34.  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 = 3.06e-06 (Fisher's exact test), Q value = 0.0021

Table S35.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S35.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S36.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S36.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

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

Table S37.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S37.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S38.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S38.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.84e-05 (Chi-square test), Q value = 0.045

Table S39.  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 11 6 8 28 10
20Q GAIN WILD-TYPE 87 69 46 53 34

Figure S39.  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 = 5e-05 (Fisher's exact test), Q value = 0.033

Table S40.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S40.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S41.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S41.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Xq gain mutation analysis' versus 'CN_CNMF'

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

Table S42.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S42.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'METHLYATION_CNMF'

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

Table S43.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S43.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'3p loss mutation analysis' versus 'METHLYATION_CNMF'

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

Table S44.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S44.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

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

Table S45.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S45.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.44e-05 (Chi-square test), Q value = 0.043

Table S46.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S46.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.99e-05 (Chi-square test), Q value = 0.066

Table S47.  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 S47.  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 = 0.0034

Table S48.  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 S48.  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 = 2.2e-10 (Fisher's exact test), Q value = 1.6e-07

Table S49.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S49.  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 = 4.24e-07 (Chi-square test), Q value = 3e-04

Table S50.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S50.  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 = 4.7e-06

Table S51.  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 S51.  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 = 1.3e-06

Table S52.  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 S52.  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 = 3.4e-05 (Fisher's exact test), Q value = 0.023

Table S53.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S53.  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 = 1.01e-05 (Chi-square test), Q value = 0.0069

Table S54.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S54.  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 = 4.4e-06 (Chi-square test), Q value = 0.003

Table S55.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S55.  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 = 4.75e-14 (Fisher's exact test), Q value = 3.5e-11

Table S56.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S56.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S57.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

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

Table S58.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S58.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'METHLYATION_CNMF'

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

Table S59.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S59.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

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

Table S60.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S60.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.07e-08 (Chi-square test), Q value = 7.6e-06

Table S61.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S61.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

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

Table S62.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S62.  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 = 6.46e-07 (Chi-square test), Q value = 0.00045

Table S63.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S63.  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 = 5.26e-12 (Fisher's exact test), Q value = 3.8e-09

Table S64.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S64.  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 = 1.41e-09 (Chi-square test), Q value = 1e-06

Table S65.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S65.  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 = 3.6e-05 (Fisher's exact test), Q value = 0.024

Table S66.  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 33
15Q LOSS WILD-TYPE 135 79 62

Figure S66.  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 = 9.74e-05 (Fisher's exact test), Q value = 0.064

Table S67.  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 27 36
15Q LOSS WILD-TYPE 146 88 84

Figure S67.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000307 (Fisher's exact test), Q value = 0.2

Table S68.  Gene #68: '16p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S68.  Get High-res Image Gene #68: '16p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16q loss mutation analysis' versus 'CN_CNMF'

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

Table S69.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S69.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'CN_CNMF'

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

Table S70.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S70.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'CN_CNMF'

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

Table S71.  Gene #72: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S71.  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 = 1.68e-09 (Fisher's exact test), Q value = 1.2e-06

Table S72.  Gene #73: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S72.  Get High-res Image Gene #73: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00016 (Chi-square test), Q value = 0.11

Table S73.  Gene #73: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S73.  Get High-res Image Gene #73: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19p loss mutation analysis' versus 'CN_CNMF'

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

Table S74.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S74.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.15e-08 (Chi-square test), Q value = 5e-05

Table S75.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S75.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S76.  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 38 54 3
19P LOSS WILD-TYPE 120 129 54

Figure S76.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

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

Table S77.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S77.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p loss mutation analysis' versus 'CN_CNMF'

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

Table S78.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S78.  Get High-res Image Gene #76: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

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

Table S79.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S79.  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 = 1e-07 (Chi-square test), Q value = 7e-05

Table S80.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S80.  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 S81.  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 S81.  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 = 0.00019

Table S82.  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 S82.  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 S83.  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 S83.  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 S84.  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 S84.  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 = 5.75e-10 (Fisher's exact test), Q value = 4.1e-07

Table S85.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S85.  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 = 4.56e-05 (Chi-square test), Q value = 0.03

Table S86.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S86.  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 = 0.000364 (Chi-square test), Q value = 0.23

Table S87.  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 21 10 10 31 4
22Q LOSS WILD-TYPE 77 65 44 50 40

Figure S87.  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 = 0.00017 (Fisher's exact test), Q value = 0.11

Table S88.  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 24 37
22Q LOSS WILD-TYPE 145 91 83

Figure S88.  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 = 472

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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