Correlation between copy number variations of arm-level result and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1P26X1V
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1P26X1V
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 8 molecular subtypes across 370 patients, 69 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 2p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 12p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 18p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 19q gain cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 22q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 3p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 7q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 15q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 69 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
16q loss 145 (39%) 225 1e-05
(0.0064) 		5e-05
(0.0298) 		1e-05
(0.0064) 		1e-05
(0.0064) 		0.168
(1.00) 		1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064)
16p loss 109 (29%) 261 3e-05
(0.0181) 		0.0187
(1.00) 		1e-05
(0.0064) 		1e-05
(0.0064) 		0.00382
(1.00) 		1e-05
(0.0064) 		1e-05
(0.0064) 		1e-05
(0.0064)
1q gain 222 (60%) 148 1e-05
(0.0064) 		2e-05
(0.0122) 		1e-05
(0.0064) 		5e-05
(0.0298) 		0.156
(1.00) 		0.00524
(1.00) 		0.414
(1.00) 		0.0525
(1.00)
14q loss 107 (29%) 263 1e-05
(0.0064) 		0.0512
(1.00) 		3e-05
(0.0181) 		1e-05
(0.0064) 		0.48
(1.00) 		0.176
(1.00) 		0.00038
(0.218) 		0.0164
(1.00)
8q gain 188 (51%) 182 1e-05
(0.0064) 		0.49
(1.00) 		5e-05
(0.0298) 		0.00629
(1.00) 		0.0285
(1.00) 		0.00365
(1.00) 		0.132
(1.00) 		0.0003
(0.173)
19q gain 72 (19%) 298 0.396
(1.00) 		0.00053
(0.299) 		2e-05
(0.0122) 		0.00074
(0.414) 		0.00034
(0.196) 		0.00089
(0.492) 		4e-05
(0.024) 		0.00073
(0.41)
20p gain 108 (29%) 262 1e-05
(0.0064) 		0.00589
(1.00) 		0.0106
(1.00) 		0.00017
(0.0993) 		0.169
(1.00) 		0.032
(1.00) 		0.0001
(0.0591) 		0.075
(1.00)
20q gain 112 (30%) 258 1e-05
(0.0064) 		0.0113
(1.00) 		0.012
(1.00) 		0.0001
(0.0591) 		0.307
(1.00) 		0.0753
(1.00) 		5e-05
(0.0298) 		0.0868
(1.00)
22q gain 48 (13%) 322 4e-05
(0.024) 		0.183
(1.00) 		0.00012
(0.0706) 		1e-05
(0.0064) 		0.606
(1.00) 		0.737
(1.00) 		0.00219
(1.00) 		0.136
(1.00)
10q loss 76 (21%) 294 0.00919
(1.00) 		0.302
(1.00) 		2e-05
(0.0122) 		0.0926
(1.00) 		0.312
(1.00) 		3e-05
(0.0181) 		0.453
(1.00) 		2e-05
(0.0122)
6p gain 117 (32%) 253 1e-05
(0.0064) 		0.00039
(0.223) 		0.00149
(0.805) 		0.0079
(1.00) 		0.145
(1.00) 		0.00297
(1.00) 		0.325
(1.00) 		0.103
(1.00)
18p gain 36 (10%) 334 0.0224
(1.00) 		0.117
(1.00) 		0.00029
(0.168) 		0.00017
(0.0993) 		0.768
(1.00) 		0.192
(1.00) 		0.0873
(1.00) 		0.457
(1.00)
1p loss 81 (22%) 289 0.00284
(1.00) 		1e-05
(0.0064) 		4e-05
(0.024) 		0.00177
(0.942) 		0.00424
(1.00) 		0.00774
(1.00) 		0.00063
(0.354) 		0.0042
(1.00)
4q loss 148 (40%) 222 1e-05
(0.0064) 		0.00342
(1.00) 		0.00114
(0.625) 		0.00573
(1.00) 		0.248
(1.00) 		0.006
(1.00) 		3e-05
(0.0181) 		0.00887
(1.00)
15q loss 67 (18%) 303 0.057
(1.00) 		0.278
(1.00) 		0.00483
(1.00) 		1e-05
(0.0064) 		0.154
(1.00) 		0.25
(1.00) 		3e-05
(0.0181) 		0.0175
(1.00)
17p loss 185 (50%) 185 1e-05
(0.0064) 		0.0281
(1.00) 		0.0144
(1.00) 		0.518
(1.00) 		0.00351
(1.00) 		0.00042
(0.24) 		0.446
(1.00) 		0.0005
(0.284)
2p gain 44 (12%) 326 0.161
(1.00) 		0.232
(1.00) 		0.02
(1.00) 		0.00013
(0.0762) 		0.553
(1.00) 		0.939
(1.00) 		0.00982
(1.00) 		0.384
(1.00)
5p gain 135 (36%) 235 0.0002
(0.116) 		0.00087
(0.483) 		0.511
(1.00) 		0.416
(1.00) 		0.226
(1.00) 		0.177
(1.00) 		0.3
(1.00) 		0.583
(1.00)
8p gain 80 (22%) 290 2e-05
(0.0122) 		0.156
(1.00) 		0.129
(1.00) 		0.283
(1.00) 		0.0111
(1.00) 		0.114
(1.00) 		0.147
(1.00) 		0.0161
(1.00)
10p gain 61 (16%) 309 0.00057
(0.321) 		0.00122
(0.665) 		0.0008
(0.446) 		0.00038
(0.218) 		0.275
(1.00) 		0.42
(1.00) 		0.022
(1.00) 		0.0181
(1.00)
10q gain 37 (10%) 333 0.00103
(0.566) 		0.0005
(0.284) 		1e-05
(0.0064) 		0.00507
(1.00) 		0.0643
(1.00) 		0.0411
(1.00) 		0.0378
(1.00) 		0.033
(1.00)
12p gain 41 (11%) 329 0.0168
(1.00) 		0.128
(1.00) 		0.00256
(1.00) 		1e-05
(0.0064) 		0.784
(1.00) 		0.37
(1.00) 		0.00145
(0.784) 		0.0236
(1.00)
12q gain 47 (13%) 323 0.0233
(1.00) 		0.42
(1.00) 		0.00203
(1.00) 		1e-05
(0.0064) 		0.341
(1.00) 		0.622
(1.00) 		0.00058
(0.327) 		0.0709
(1.00)
18q gain 28 (8%) 342 0.0201
(1.00) 		0.353
(1.00) 		0.00444
(1.00) 		0.00026
(0.151) 		0.83
(1.00) 		0.0545
(1.00) 		0.0193
(1.00) 		0.284
(1.00)
19p gain 56 (15%) 314 0.581
(1.00) 		0.00233
(1.00) 		9e-05
(0.0533) 		0.00174
(0.927) 		0.0143
(1.00) 		0.00505
(1.00) 		0.00077
(0.43) 		0.0375
(1.00)
3p loss 52 (14%) 318 0.0324
(1.00) 		0.43
(1.00) 		0.00154
(0.83) 		0.00011
(0.0648) 		0.00791
(1.00) 		0.322
(1.00) 		0.00173
(0.924) 		0.0497
(1.00)
4p loss 107 (29%) 263 1e-05
(0.0064) 		0.0134
(1.00) 		0.00281
(1.00) 		0.0159
(1.00) 		0.988
(1.00) 		0.0187
(1.00) 		0.0049
(1.00) 		0.00288
(1.00)
7q loss 21 (6%) 349 0.435
(1.00) 		0.132
(1.00) 		0.0254
(1.00) 		0.488
(1.00) 		0.562
(1.00) 		0.0267
(1.00) 		0.00014
(0.0819) 		0.0053
(1.00)
8p loss 190 (51%) 180 0.00012
(0.0706) 		0.0184
(1.00) 		0.0353
(1.00) 		0.4
(1.00) 		0.243
(1.00) 		0.0294
(1.00) 		0.452
(1.00) 		0.438
(1.00)
9p loss 118 (32%) 252 6e-05
(0.0356) 		0.016
(1.00) 		0.0108
(1.00) 		0.00463
(1.00) 		0.108
(1.00) 		0.00921
(1.00) 		0.0305
(1.00) 		0.0121
(1.00)
9q loss 107 (29%) 263 0.00031
(0.179) 		0.00212
(1.00) 		0.0452
(1.00) 		0.00088
(0.488) 		0.273
(1.00) 		0.0162
(1.00) 		0.114
(1.00) 		0.00167
(0.893)
13q loss 122 (33%) 248 0.00017
(0.0993) 		0.495
(1.00) 		0.0227
(1.00) 		0.00462
(1.00) 		0.00304
(1.00) 		0.00471
(1.00) 		0.019
(1.00) 		0.00126
(0.685)
19p loss 55 (15%) 315 1e-05
(0.0064) 		0.258
(1.00) 		0.083
(1.00) 		0.155
(1.00) 		0.149
(1.00) 		0.08
(1.00) 		0.284
(1.00) 		0.00343
(1.00)
19q loss 39 (11%) 331 1e-05
(0.0064) 		0.227
(1.00) 		0.00982
(1.00) 		0.0939
(1.00) 		0.0309
(1.00) 		0.153
(1.00) 		0.47
(1.00) 		0.246
(1.00)
1p gain 57 (15%) 313 0.291
(1.00) 		0.722
(1.00) 		0.162
(1.00) 		0.0918
(1.00) 		0.966
(1.00) 		0.0396
(1.00) 		0.111
(1.00) 		0.0226
(1.00)
2q gain 41 (11%) 329 0.0846
(1.00) 		0.0843
(1.00) 		0.0118
(1.00) 		0.00046
(0.262) 		0.695
(1.00) 		0.76
(1.00) 		0.00317
(1.00) 		0.374
(1.00)
3p gain 35 (9%) 335 0.0379
(1.00) 		0.5
(1.00) 		0.298
(1.00) 		0.204
(1.00) 		0.134
(1.00) 		0.519
(1.00) 		0.0232
(1.00) 		0.254
(1.00)
3q gain 38 (10%) 332 0.298
(1.00) 		0.673
(1.00) 		0.401
(1.00) 		0.311
(1.00) 		0.215
(1.00) 		0.51
(1.00) 		0.0148
(1.00) 		0.612
(1.00)
4p gain 27 (7%) 343 0.0151
(1.00) 		0.0336
(1.00) 		0.0711
(1.00) 		0.0219
(1.00) 		0.299
(1.00) 		0.443
(1.00) 		0.0677
(1.00) 		0.203
(1.00)
4q gain 7 (2%) 363 0.8
(1.00) 		0.57
(1.00) 		0.46
(1.00) 		0.309
(1.00) 		0.245
(1.00) 		0.849
(1.00) 		0.277
(1.00) 		0.555
(1.00)
5q gain 107 (29%) 263 0.00393
(1.00) 		0.0145
(1.00) 		0.163
(1.00) 		0.981
(1.00) 		0.643
(1.00) 		0.852
(1.00) 		0.928
(1.00) 		0.892
(1.00)
6q gain 67 (18%) 303 0.00079
(0.441) 		0.0975
(1.00) 		0.0156
(1.00) 		0.0589
(1.00) 		0.201
(1.00) 		0.187
(1.00) 		0.203
(1.00) 		0.387
(1.00)
7p gain 111 (30%) 259 0.0458
(1.00) 		0.272
(1.00) 		0.505
(1.00) 		0.0319
(1.00) 		0.0429
(1.00) 		0.0726
(1.00) 		0.258
(1.00) 		0.336
(1.00)
7q gain 111 (30%) 259 0.376
(1.00) 		0.0354
(1.00) 		0.881
(1.00) 		0.0552
(1.00) 		0.219
(1.00) 		0.209
(1.00) 		0.523
(1.00) 		0.339
(1.00)
9p gain 19 (5%) 351 0.466
(1.00) 		0.526
(1.00) 		0.445
(1.00) 		0.558
(1.00) 		0.706
(1.00) 		0.399
(1.00) 		0.0981
(1.00) 		0.365
(1.00)
9q gain 21 (6%) 349 0.0849
(1.00) 		0.661
(1.00) 		0.0961
(1.00) 		0.0411
(1.00) 		0.767
(1.00) 		0.413
(1.00) 		0.112
(1.00) 		0.231
(1.00)
11p gain 17 (5%) 353 0.473
(1.00) 		0.191
(1.00) 		0.394
(1.00) 		0.0695
(1.00) 		0.302
(1.00) 		0.47
(1.00) 		0.0151
(1.00) 		0.274
(1.00)
11q gain 18 (5%) 352 0.912
(1.00) 		0.722
(1.00) 		0.667
(1.00) 		0.421
(1.00) 		0.367
(1.00) 		0.701
(1.00) 		0.178
(1.00) 		0.344
(1.00)
13q gain 23 (6%) 347 0.00958
(1.00) 		0.184
(1.00) 		0.00161
(0.863) 		0.124
(1.00) 		0.0776
(1.00) 		0.294
(1.00) 		0.181
(1.00) 		0.214
(1.00)
14q gain 23 (6%) 347 0.453
(1.00) 		0.29
(1.00) 		0.0537
(1.00) 		0.177
(1.00) 		0.76
(1.00) 		0.149
(1.00) 		0.0669
(1.00) 		0.651
(1.00)
15q gain 33 (9%) 337 0.647
(1.00) 		0.537
(1.00) 		0.385
(1.00) 		0.326
(1.00) 		0.849
(1.00) 		0.287
(1.00) 		0.53
(1.00) 		0.83
(1.00)
16p gain 31 (8%) 339 0.174
(1.00) 		0.962
(1.00) 		0.577
(1.00) 		0.913
(1.00) 		0.769
(1.00) 		0.254
(1.00) 		0.101
(1.00) 		0.318
(1.00)
16q gain 17 (5%) 353 0.907
(1.00) 		0.0604
(1.00) 		0.00802
(1.00) 		0.511
(1.00) 		0.125
(1.00) 		0.913
(1.00) 		0.159
(1.00) 		0.706
(1.00)
17p gain 30 (8%) 340 0.101
(1.00) 		0.0343
(1.00) 		0.0412
(1.00) 		0.00918
(1.00) 		0.399
(1.00) 		0.757
(1.00) 		0.0526
(1.00) 		0.141
(1.00)
17q gain 95 (26%) 275 0.00158
(0.848) 		0.009
(1.00) 		0.413
(1.00) 		0.00669
(1.00) 		0.0196
(1.00) 		0.00044
(0.251) 		0.608
(1.00) 		0.0232
(1.00)
21q gain 26 (7%) 344 0.179
(1.00) 		0.17
(1.00) 		0.0386
(1.00) 		0.0195
(1.00) 		0.925
(1.00) 		0.227
(1.00) 		0.249
(1.00) 		0.525
(1.00)
xq gain 62 (17%) 308 0.00044
(0.251) 		0.0367
(1.00) 		0.067
(1.00) 		0.0979
(1.00) 		0.00843
(1.00) 		0.00341
(1.00) 		0.212
(1.00) 		0.00095
(0.524)
1q loss 22 (6%) 348 0.37
(1.00) 		0.687
(1.00) 		0.109
(1.00) 		0.18
(1.00) 		0.355
(1.00) 		0.244
(1.00) 		0.287
(1.00) 		0.0619
(1.00)
2p loss 33 (9%) 337 0.0596
(1.00) 		1
(1.00) 		0.336
(1.00) 		0.0482
(1.00) 		0.376
(1.00) 		0.709
(1.00) 		0.198
(1.00) 		0.268
(1.00)
2q loss 38 (10%) 332 0.185
(1.00) 		1
(1.00) 		0.241
(1.00) 		0.0237
(1.00) 		0.256
(1.00) 		0.595
(1.00) 		0.603
(1.00) 		0.406
(1.00)
3q loss 40 (11%) 330 0.328
(1.00) 		0.674
(1.00) 		0.0126
(1.00) 		0.0111
(1.00) 		0.0782
(1.00) 		0.316
(1.00) 		0.00525
(1.00) 		0.272
(1.00)
5p loss 28 (8%) 342 0.0249
(1.00) 		0.719
(1.00) 		0.135
(1.00) 		0.125
(1.00) 		0.264
(1.00) 		0.098
(1.00) 		0.00899
(1.00) 		0.0189
(1.00)
5q loss 39 (11%) 331 0.00287
(1.00) 		0.0382
(1.00) 		0.0132
(1.00) 		0.00154
(0.83) 		0.535
(1.00) 		0.046
(1.00) 		0.00095
(0.524) 		0.00134
(0.728)
6p loss 28 (8%) 342 0.645
(1.00) 		0.592
(1.00) 		0.133
(1.00) 		0.671
(1.00) 		0.675
(1.00) 		0.721
(1.00) 		0.27
(1.00) 		0.241
(1.00)
6q loss 92 (25%) 278 0.184
(1.00) 		0.375
(1.00) 		0.00483
(1.00) 		0.458
(1.00) 		0.523
(1.00) 		0.141
(1.00) 		0.671
(1.00) 		0.831
(1.00)
7p loss 16 (4%) 354 0.364
(1.00) 		0.142
(1.00) 		0.424
(1.00) 		0.925
(1.00) 		0.879
(1.00) 		0.225
(1.00) 		0.00634
(1.00) 		0.0392
(1.00)
8q loss 43 (12%) 327 0.00141
(0.764) 		0.593
(1.00) 		0.326
(1.00) 		0.642
(1.00) 		0.763
(1.00) 		0.935
(1.00) 		0.691
(1.00) 		0.902
(1.00)
10p loss 45 (12%) 325 0.0243
(1.00) 		0.176
(1.00) 		0.0154
(1.00) 		0.245
(1.00) 		0.613
(1.00) 		0.00636
(1.00) 		0.394
(1.00) 		0.0204
(1.00)
11p loss 65 (18%) 305 0.463
(1.00) 		0.843
(1.00) 		0.0311
(1.00) 		0.00917
(1.00) 		0.644
(1.00) 		0.175
(1.00) 		0.00121
(0.661) 		0.0053
(1.00)
11q loss 73 (20%) 297 0.144
(1.00) 		0.294
(1.00) 		0.144
(1.00) 		0.0523
(1.00) 		0.658
(1.00) 		0.302
(1.00) 		0.00315
(1.00) 		0.0165
(1.00)
12p loss 65 (18%) 305 0.00082
(0.456) 		0.036
(1.00) 		0.0256
(1.00) 		0.492
(1.00) 		0.408
(1.00) 		0.162
(1.00) 		0.622
(1.00) 		0.432
(1.00)
12q loss 36 (10%) 334 0.088
(1.00) 		0.512
(1.00) 		0.0418
(1.00) 		0.853
(1.00) 		0.877
(1.00) 		0.914
(1.00) 		0.696
(1.00) 		0.934
(1.00)
17q loss 39 (11%) 331 0.371
(1.00) 		0.776
(1.00) 		0.332
(1.00) 		0.571
(1.00) 		0.178
(1.00) 		0.626
(1.00) 		0.269
(1.00) 		0.462
(1.00)
18p loss 74 (20%) 296 0.0488
(1.00) 		0.00371
(1.00) 		0.549
(1.00) 		0.31
(1.00) 		0.527
(1.00) 		0.711
(1.00) 		0.069
(1.00) 		0.223
(1.00)
18q loss 79 (21%) 291 0.00423
(1.00) 		0.00115
(0.629) 		0.592
(1.00) 		0.335
(1.00) 		0.205
(1.00) 		0.405
(1.00) 		0.116
(1.00) 		0.305
(1.00)
20p loss 26 (7%) 344 0.265
(1.00) 		0.216
(1.00) 		0.529
(1.00) 		0.16
(1.00) 		0.087
(1.00) 		0.854
(1.00) 		0.714
(1.00) 		0.304
(1.00)
20q loss 13 (4%) 357 0.35
(1.00) 		0.386
(1.00) 		0.263
(1.00) 		0.232
(1.00) 		0.464
(1.00) 		0.639
(1.00) 		0.0137
(1.00) 		0.255
(1.00)
21q loss 110 (30%) 260 0.00052
(0.294) 		0.873
(1.00) 		0.00107
(0.587) 		0.00636
(1.00) 		0.497
(1.00) 		0.932
(1.00) 		0.121
(1.00) 		0.309
(1.00)
22q loss 70 (19%) 300 0.0364
(1.00) 		0.352
(1.00) 		0.00578
(1.00) 		0.317
(1.00) 		0.507
(1.00) 		0.462
(1.00) 		0.105
(1.00) 		0.875
(1.00)
xq loss 73 (20%) 297 0.00531
(1.00) 		0.253
(1.00) 		0.561
(1.00) 		0.821
(1.00) 		0.444
(1.00) 		0.759
(1.00) 		0.22
(1.00) 		0.831
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
1Q GAIN MUTATED 82 87 53
1Q GAIN WILD-TYPE 27 37 84

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
1Q GAIN MUTATED 26 79 57
1Q GAIN WILD-TYPE 50 47 25

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
1Q GAIN MUTATED 19 20 37 22 19 30
1Q GAIN WILD-TYPE 13 44 9 6 29 14

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
1Q GAIN MUTATED 64 55 28
1Q GAIN WILD-TYPE 30 75 10

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.076

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
2P GAIN MUTATED 23 7 4
2P GAIN WILD-TYPE 71 123 34

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S6.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
5P GAIN MUTATED 47 56 32
5P GAIN WILD-TYPE 62 68 105

Figure S6.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S7.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
6P GAIN MUTATED 37 58 22
6P GAIN WILD-TYPE 72 66 115

Figure S7.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.22

Table S8.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
6P GAIN MUTATED 10 46 30
6P GAIN WILD-TYPE 66 80 52

Figure S8.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S9.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
8P GAIN MUTATED 39 25 16
8P GAIN WILD-TYPE 70 99 121

Figure S9.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S10.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
8Q GAIN MUTATED 97 61 30
8Q GAIN WILD-TYPE 12 63 107

Figure S10.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S11.  Gene #16: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
8Q GAIN MUTATED 17 17 28 21 19 26
8Q GAIN WILD-TYPE 15 47 18 7 29 18

Figure S11.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.17

Table S12.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
8Q GAIN MUTATED 42 29 56 14 35
8Q GAIN WILD-TYPE 25 57 43 21 18

Figure S12.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.22

Table S13.  Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
10P GAIN MUTATED 27 11 7
10P GAIN WILD-TYPE 67 119 31

Figure S13.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S14.  Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
10Q GAIN MUTATED 0 3 17 1 2 6
10Q GAIN WILD-TYPE 32 61 29 27 46 38

Figure S14.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S15.  Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
12P GAIN MUTATED 26 8 2
12P GAIN WILD-TYPE 68 122 36

Figure S15.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S16.  Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
12Q GAIN MUTATED 27 10 2
12Q GAIN WILD-TYPE 67 120 36

Figure S16.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.17

Table S17.  Gene #32: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
18P GAIN MUTATED 4 1 10 4 7 0
18P GAIN WILD-TYPE 28 63 36 24 41 44

Figure S17.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.099

Table S18.  Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
18P GAIN MUTATED 19 7 0
18P GAIN WILD-TYPE 75 123 38

Figure S18.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.15

Table S19.  Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
18Q GAIN MUTATED 16 5 0
18Q GAIN WILD-TYPE 78 125 38

Figure S19.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.053

Table S20.  Gene #34: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
19P GAIN MUTATED 2 6 15 11 11 2
19P GAIN WILD-TYPE 30 58 31 17 37 42

Figure S20.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S21.  Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
19Q GAIN MUTATED 2 6 17 11 14 4
19Q GAIN WILD-TYPE 30 58 29 17 34 40

Figure S21.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.2

Table S22.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
19Q GAIN MUTATED 7 14 13 37
19Q GAIN WILD-TYPE 58 113 36 87

Figure S22.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S23.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
19Q GAIN MUTATED 23 24 7 12
19Q GAIN WILD-TYPE 69 63 112 30

Figure S23.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S24.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
20P GAIN MUTATED 28 58 22
20P GAIN WILD-TYPE 81 66 115

Figure S24.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.099

Table S25.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
20P GAIN MUTATED 42 30 5
20P GAIN WILD-TYPE 52 100 33

Figure S25.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.059

Table S26.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
20P GAIN MUTATED 34 23 20 22
20P GAIN WILD-TYPE 58 64 99 20

Figure S26.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S27.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
20Q GAIN MUTATED 30 59 23
20Q GAIN WILD-TYPE 79 65 114

Figure S27.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.059

Table S28.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
20Q GAIN MUTATED 42 32 4
20Q GAIN WILD-TYPE 52 98 34

Figure S28.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S29.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
20Q GAIN MUTATED 36 23 21 22
20Q GAIN WILD-TYPE 56 64 98 20

Figure S29.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S30.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
22Q GAIN MUTATED 13 29 6
22Q GAIN WILD-TYPE 96 95 131

Figure S30.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.071

Table S31.  Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
22Q GAIN MUTATED 2 7 15 0 12 3
22Q GAIN WILD-TYPE 30 57 31 28 36 41

Figure S31.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S32.  Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
22Q GAIN MUTATED 28 9 2
22Q GAIN WILD-TYPE 66 121 36

Figure S32.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S33.  Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
1P LOSS MUTATED 8 21 34
1P LOSS WILD-TYPE 68 105 48

Figure S33.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S34.  Gene #41: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
1P LOSS MUTATED 5 11 25 5 7 6
1P LOSS WILD-TYPE 27 53 21 23 41 38

Figure S34.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.065

Table S35.  Gene #45: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
3P LOSS MUTATED 28 10 5
3P LOSS WILD-TYPE 66 120 33

Figure S35.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S36.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
4P LOSS MUTATED 25 60 22
4P LOSS WILD-TYPE 84 64 115

Figure S36.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S37.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
4Q LOSS MUTATED 34 85 29
4Q LOSS WILD-TYPE 75 39 108

Figure S37.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S38.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
4Q LOSS MUTATED 49 33 32 26
4Q LOSS WILD-TYPE 43 54 87 16

Figure S38.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.082

Table S39.  Gene #54: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
7Q LOSS MUTATED 14 3 1 3
7Q LOSS WILD-TYPE 78 84 118 39

Figure S39.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.071

Table S40.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
8P LOSS MUTATED 66 73 51
8P LOSS WILD-TYPE 43 51 86

Figure S40.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S41.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
9P LOSS MUTATED 31 58 29
9P LOSS WILD-TYPE 78 66 108

Figure S41.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.18

Table S42.  Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
9Q LOSS MUTATED 28 52 27
9Q LOSS WILD-TYPE 81 72 110

Figure S42.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S43.  Gene #60: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
10Q LOSS MUTATED 18 15 3 5 14 5
10Q LOSS WILD-TYPE 14 49 43 23 34 39

Figure S43.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S44.  Gene #60: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
10Q LOSS MUTATED 10 34 7 23 2
10Q LOSS WILD-TYPE 34 61 49 99 46

Figure S44.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S45.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
10Q LOSS MUTATED 15 32 17 9 1
10Q LOSS WILD-TYPE 52 54 82 26 52

Figure S45.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.099

Table S46.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
13Q LOSS MUTATED 27 59 36
13Q LOSS WILD-TYPE 82 65 101

Figure S46.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S47.  Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
14Q LOSS MUTATED 17 64 26
14Q LOSS WILD-TYPE 92 60 111

Figure S47.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S48.  Gene #66: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
14Q LOSS MUTATED 19 10 20 7 17 6
14Q LOSS WILD-TYPE 13 54 26 21 31 38

Figure S48.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S49.  Gene #66: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
14Q LOSS MUTATED 48 25 6
14Q LOSS WILD-TYPE 46 105 32

Figure S49.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.22

Table S50.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
14Q LOSS MUTATED 40 29 20 13
14Q LOSS WILD-TYPE 52 58 99 29

Figure S50.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S51.  Gene #67: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
15Q LOSS MUTATED 36 13 6
15Q LOSS WILD-TYPE 58 117 32

Figure S51.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S52.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
15Q LOSS MUTATED 28 10 11 15
15Q LOSS WILD-TYPE 64 77 108 27

Figure S52.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S53.  Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
16P LOSS MUTATED 25 57 27
16P LOSS WILD-TYPE 84 67 110

Figure S53.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S54.  Gene #68: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
16P LOSS MUTATED 13 12 28 6 15 3
16P LOSS WILD-TYPE 19 52 18 22 33 41

Figure S54.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S55.  Gene #68: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
16P LOSS MUTATED 50 25 2
16P LOSS WILD-TYPE 44 105 36

Figure S55.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S56.  Gene #68: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
16P LOSS MUTATED 10 21 27 48 2
16P LOSS WILD-TYPE 34 74 29 74 46

Figure S56.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S57.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
16P LOSS MUTATED 39 22 16 27
16P LOSS WILD-TYPE 53 65 103 15

Figure S57.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S58.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
16P LOSS MUTATED 30 19 42 8 5
16P LOSS WILD-TYPE 37 67 57 27 48

Figure S58.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S59.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
16Q LOSS MUTATED 43 69 33
16Q LOSS WILD-TYPE 66 55 104

Figure S59.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S60.  Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 126 82
16Q LOSS MUTATED 17 42 46
16Q LOSS WILD-TYPE 59 84 36

Figure S60.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S61.  Gene #69: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 64 46 28 48 44
16Q LOSS MUTATED 21 20 34 6 11 5
16Q LOSS WILD-TYPE 11 44 12 22 37 39

Figure S61.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S62.  Gene #69: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 130 38
16Q LOSS MUTATED 54 40 3
16Q LOSS WILD-TYPE 40 90 35

Figure S62.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S63.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
16Q LOSS MUTATED 15 33 33 60 3
16Q LOSS WILD-TYPE 29 62 23 62 45

Figure S63.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S64.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
16Q LOSS MUTATED 53 31 28 27
16Q LOSS WILD-TYPE 39 56 91 15

Figure S64.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S65.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
16Q LOSS MUTATED 39 32 49 11 8
16Q LOSS WILD-TYPE 28 54 50 24 45

Figure S65.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S66.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
17P LOSS MUTATED 36 84 65
17P LOSS WILD-TYPE 73 40 72

Figure S66.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.24

Table S67.  Gene #70: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
17P LOSS MUTATED 34 54 23 52 21
17P LOSS WILD-TYPE 10 41 33 70 27

Figure S67.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S68.  Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
19P LOSS MUTATED 9 37 9
19P LOSS WILD-TYPE 100 87 128

Figure S68.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0064

Table S69.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
19Q LOSS MUTATED 6 29 4
19Q LOSS WILD-TYPE 103 95 133

Figure S69.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 370

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 8

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

Fisher's exact test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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