Correlation between copy number variation genes (focal events) and molecular subtypes
Esophageal Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1KH0KXN
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1KH0KXN
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 71 focal events and 8 molecular subtypes across 103 patients, 20 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_3q26.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p13.33 cnv correlated to 'CN_CNMF'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF'.

  • del_3p14.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 focal 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, 20 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
amp 3q26 2 70 (68%) 33 1.49e-10
(8.48e-08) 		4.31e-05
(0.024) 		0.00163
(0.867) 		8.57e-06
(0.00482) 		7.2e-06
(0.00405) 		3.2e-07
(0.000181) 		7.63e-05
(0.0424) 		3.2e-07
(0.000181)
del 3p14 3 71 (69%) 32 0.000142
(0.0782) 		0.00167
(0.887) 		0.022
(1.00) 		0.000142
(0.0785) 		0.000222
(0.122) 		1.23e-05
(0.00691) 		0.00207
(1.00) 		1.23e-05
(0.00691)
del 9p21 3 78 (76%) 25 2.04e-06
(0.00115) 		0.103
(1.00) 		0.045
(1.00) 		0.000969
(0.524) 		0.00774
(1.00) 		0.00011
(0.0609) 		0.000953
(0.517) 		0.00011
(0.0609)
del 16q23 1 45 (44%) 58 2.5e-06
(0.00141) 		0.00039
(0.214) 		0.0014
(0.748) 		0.00083
(0.451) 		0.0017
(0.902) 		0.000737
(0.402) 		0.0154
(1.00) 		0.000737
(0.402)
amp 12p13 33 42 (41%) 61 1.52e-05
(0.00848) 		0.0286
(1.00) 		0.0359
(1.00) 		0.00963
(1.00) 		0.0129
(1.00) 		0.00932
(1.00) 		0.115
(1.00) 		0.00932
(1.00)
amp 12p12 1 48 (47%) 55 2.08e-05
(0.0116) 		0.136
(1.00) 		0.336
(1.00) 		0.0576
(1.00) 		0.0207
(1.00) 		0.0307
(1.00) 		0.0667
(1.00) 		0.0307
(1.00)
del 16p13 3 30 (29%) 73 0.000135
(0.0747) 		0.00228
(1.00) 		0.0728
(1.00) 		0.023
(1.00) 		0.0669
(1.00) 		0.0621
(1.00) 		0.129
(1.00) 		0.0621
(1.00)
amp 1p34 2 20 (19%) 83 0.228
(1.00) 		0.0908
(1.00) 		0.808
(1.00) 		0.883
(1.00) 		0.783
(1.00) 		0.587
(1.00) 		0.803
(1.00) 		0.587
(1.00)
amp 1q21 3 52 (50%) 51 0.00401
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.859
(1.00) 		0.93
(1.00) 		0.552
(1.00) 		0.854
(1.00) 		0.552
(1.00)
amp 2q14 2 34 (33%) 69 0.545
(1.00) 		1
(1.00) 		0.581
(1.00) 		0.378
(1.00) 		0.422
(1.00) 		0.776
(1.00) 		0.446
(1.00) 		0.776
(1.00)
amp 5p15 33 59 (57%) 44 0.00172
(0.911) 		0.0329
(1.00) 		0.0517
(1.00) 		0.00244
(1.00) 		0.0124
(1.00) 		0.00613
(1.00) 		0.0465
(1.00) 		0.00613
(1.00)
amp 6p21 1 35 (34%) 68 0.00401
(1.00) 		0.525
(1.00) 		0.276
(1.00) 		0.287
(1.00) 		0.435
(1.00) 		0.46
(1.00) 		0.36
(1.00) 		0.46
(1.00)
amp 7p22 3 70 (68%) 33 0.154
(1.00) 		0.59
(1.00) 		0.00149
(0.796) 		0.00883
(1.00) 		0.389
(1.00) 		0.394
(1.00) 		0.864
(1.00) 		0.394
(1.00)
amp 7p11 2 70 (68%) 33 0.507
(1.00) 		0.435
(1.00) 		0.0427
(1.00) 		0.303
(1.00) 		0.103
(1.00) 		0.235
(1.00) 		0.287
(1.00) 		0.235
(1.00)
amp 7q21 2 66 (64%) 37 0.0671
(1.00) 		0.146
(1.00) 		0.95
(1.00) 		1
(1.00) 		0.304
(1.00) 		0.418
(1.00) 		0.669
(1.00) 		0.418
(1.00)
amp 8p11 21 49 (48%) 54 0.214
(1.00) 		0.776
(1.00) 		0.236
(1.00) 		1
(1.00) 		0.904
(1.00) 		0.681
(1.00) 		0.719
(1.00) 		0.681
(1.00)
amp 8q24 21 83 (81%) 20 0.00211
(1.00) 		0.0129
(1.00) 		0.169
(1.00) 		0.035
(1.00) 		0.306
(1.00) 		0.0237
(1.00) 		0.024
(1.00) 		0.0237
(1.00)
amp 9p13 3 22 (21%) 81 0.44
(1.00) 		0.312
(1.00) 		0.335
(1.00) 		0.593
(1.00) 		0.121
(1.00) 		0.599
(1.00) 		0.852
(1.00) 		0.599
(1.00)
amp 10p11 21 29 (28%) 74 0.703
(1.00) 		0.18
(1.00) 		0.922
(1.00) 		0.862
(1.00) 		0.924
(1.00) 		0.802
(1.00) 		0.898
(1.00) 		0.802
(1.00)
amp 11p13 28 (27%) 75 0.73
(1.00) 		0.863
(1.00) 		0.243
(1.00) 		0.72
(1.00) 		0.535
(1.00) 		0.463
(1.00) 		0.492
(1.00) 		0.463
(1.00)
amp 11q13 3 57 (55%) 46 0.00214
(1.00) 		0.0507
(1.00) 		0.181
(1.00) 		0.0644
(1.00) 		0.104
(1.00) 		0.0208
(1.00) 		0.173
(1.00) 		0.0208
(1.00)
amp 13q22 1 36 (35%) 67 0.0522
(1.00) 		0.232
(1.00) 		0.299
(1.00) 		0.104
(1.00) 		0.0311
(1.00) 		0.0644
(1.00) 		0.0842
(1.00) 		0.0644
(1.00)
amp 15q26 3 33 (32%) 70 0.249
(1.00) 		0.0279
(1.00) 		0.299
(1.00) 		0.0888
(1.00) 		0.126
(1.00) 		0.0793
(1.00) 		0.124
(1.00) 		0.0793
(1.00)
amp 17q12 38 (37%) 65 0.00142
(0.76) 		0.191
(1.00) 		0.339
(1.00) 		0.024
(1.00) 		0.0475
(1.00) 		0.101
(1.00) 		0.17
(1.00) 		0.101
(1.00)
amp 18p11 32 37 (36%) 66 0.00477
(1.00) 		0.546
(1.00) 		0.778
(1.00) 		0.505
(1.00) 		0.662
(1.00) 		0.634
(1.00) 		0.462
(1.00) 		0.634
(1.00)
amp 18q11 2 31 (30%) 72 0.522
(1.00) 		0.0375
(1.00) 		0.345
(1.00) 		0.149
(1.00) 		0.283
(1.00) 		0.208
(1.00) 		0.531
(1.00) 		0.208
(1.00)
amp 19p13 2 18 (17%) 85 0.106
(1.00) 		0.204
(1.00) 		0.219
(1.00) 		0.272
(1.00) 		0.0508
(1.00) 		0.301
(1.00) 		0.0366
(1.00) 		0.301
(1.00)
amp 19q12 29 (28%) 74 0.00104
(0.558) 		0.177
(1.00) 		0.427
(1.00) 		0.258
(1.00) 		0.283
(1.00) 		0.208
(1.00) 		0.0461
(1.00) 		0.208
(1.00)
del 1p36 13 33 (32%) 70 0.0487
(1.00) 		0.0931
(1.00) 		0.316
(1.00) 		0.192
(1.00) 		0.374
(1.00) 		0.319
(1.00) 		0.67
(1.00) 		0.319
(1.00)
del 1p13 2 34 (33%) 69 0.0461
(1.00) 		0.628
(1.00) 		0.255
(1.00) 		0.365
(1.00) 		0.836
(1.00) 		0.795
(1.00) 		0.688
(1.00) 		0.795
(1.00)
del 1q44 13 (13%) 90 0.219
(1.00) 		0.824
(1.00) 		0.262
(1.00) 		0.594
(1.00) 		0.466
(1.00) 		0.391
(1.00) 		0.704
(1.00) 		0.391
(1.00)
del 2q22 1 32 (31%) 71 0.0928
(1.00) 		0.0072
(1.00) 		0.395
(1.00) 		0.187
(1.00) 		0.0829
(1.00) 		0.0578
(1.00) 		0.0796
(1.00) 		0.0578
(1.00)
del 2q33 3 17 (17%) 86 1
(1.00) 		0.0255
(1.00) 		0.261
(1.00) 		0.49
(1.00) 		0.128
(1.00) 		0.451
(1.00) 		0.31
(1.00) 		0.451
(1.00)
del 3p14 2 72 (70%) 31 0.00174
(0.919) 		0.0174
(1.00) 		0.309
(1.00) 		0.00629
(1.00) 		0.0187
(1.00) 		0.00101
(0.544) 		0.0511
(1.00) 		0.00101
(0.544)
del 3q11 1 17 (17%) 86 0.774
(1.00) 		0.887
(1.00) 		0.46
(1.00) 		0.523
(1.00) 		0.699
(1.00) 		0.583
(1.00) 		0.702
(1.00) 		0.583
(1.00)
del 3q26 31 8 (8%) 95 0.0534
(1.00) 		0.0733
(1.00) 		0.068
(1.00) 		0.0205
(1.00) 		0.0443
(1.00) 		0.0191
(1.00) 		0.0843
(1.00) 		0.0191
(1.00)
del 4p16 3 53 (51%) 50 0.702
(1.00) 		0.718
(1.00) 		0.362
(1.00) 		0.809
(1.00) 		0.193
(1.00) 		0.416
(1.00) 		0.267
(1.00) 		0.416
(1.00)
del 4p15 2 54 (52%) 49 0.0185
(1.00) 		0.399
(1.00) 		0.17
(1.00) 		0.537
(1.00) 		0.144
(1.00) 		0.233
(1.00) 		0.664
(1.00) 		0.233
(1.00)
del 4q21 23 50 (49%) 53 0.000746
(0.406) 		0.171
(1.00) 		0.0524
(1.00) 		0.489
(1.00) 		0.321
(1.00) 		0.694
(1.00) 		0.714
(1.00) 		0.694
(1.00)
del 4q22 1 53 (51%) 50 0.000472
(0.259) 		0.248
(1.00) 		0.0333
(1.00) 		0.5
(1.00) 		0.319
(1.00) 		0.615
(1.00) 		0.664
(1.00) 		0.615
(1.00)
del 5q11 2 58 (56%) 45 0.0717
(1.00) 		0.0283
(1.00) 		0.698
(1.00) 		0.698
(1.00) 		0.887
(1.00) 		0.684
(1.00) 		0.412
(1.00) 		0.684
(1.00)
del 6p25 3 37 (36%) 66 0.775
(1.00) 		0.154
(1.00) 		0.661
(1.00) 		0.483
(1.00) 		0.301
(1.00) 		0.271
(1.00) 		0.161
(1.00) 		0.271
(1.00)
del 6q16 1 29 (28%) 74 0.312
(1.00) 		0.6
(1.00) 		0.355
(1.00) 		0.478
(1.00) 		0.93
(1.00) 		1
(1.00) 		0.847
(1.00) 		1
(1.00)
del 6q26 25 (24%) 78 0.101
(1.00) 		0.384
(1.00) 		0.0741
(1.00) 		0.0489
(1.00) 		0.158
(1.00) 		0.0962
(1.00) 		0.312
(1.00) 		0.0962
(1.00)
del 7q31 1 30 (29%) 73 0.76
(1.00) 		0.589
(1.00) 		0.318
(1.00) 		0.627
(1.00) 		0.9
(1.00) 		0.801
(1.00) 		0.668
(1.00) 		0.801
(1.00)
del 7q36 2 38 (37%) 65 0.847
(1.00) 		0.6
(1.00) 		0.14
(1.00) 		0.901
(1.00) 		0.18
(1.00) 		0.756
(1.00) 		0.319
(1.00) 		0.756
(1.00)
del 8p23 2 46 (45%) 57 0.00399
(1.00) 		0.522
(1.00) 		0.0402
(1.00) 		0.221
(1.00) 		0.185
(1.00) 		0.069
(1.00) 		0.131
(1.00) 		0.069
(1.00)
del 10p15 1 28 (27%) 75 0.222
(1.00) 		0.565
(1.00) 		0.52
(1.00) 		0.168
(1.00) 		0.614
(1.00) 		0.577
(1.00) 		0.578
(1.00) 		0.577
(1.00)
del 10p11 21 23 (22%) 80 0.00191
(1.00) 		0.0015
(0.797) 		0.109
(1.00) 		0.02
(1.00) 		0.017
(1.00) 		0.0206
(1.00) 		0.0413
(1.00) 		0.0206
(1.00)
del 10q22 3 33 (32%) 70 0.00834
(1.00) 		0.00751
(1.00) 		0.203
(1.00) 		0.0307
(1.00) 		0.143
(1.00) 		0.0585
(1.00) 		0.151
(1.00) 		0.0585
(1.00)
del 10q23 31 41 (40%) 62 0.0325
(1.00) 		0.145
(1.00) 		0.528
(1.00) 		0.753
(1.00) 		0.794
(1.00) 		0.836
(1.00) 		0.886
(1.00) 		0.836
(1.00)
del 11p15 4 39 (38%) 64 0.361
(1.00) 		0.289
(1.00) 		0.0775
(1.00) 		0.107
(1.00) 		0.12
(1.00) 		0.0463
(1.00) 		0.0858
(1.00) 		0.0463
(1.00)
del 11q24 3 43 (42%) 60 0.00301
(1.00) 		0.47
(1.00) 		0.665
(1.00) 		0.462
(1.00) 		0.592
(1.00) 		0.287
(1.00) 		0.187
(1.00) 		0.287
(1.00)
del 12q23 1 27 (26%) 76 0.652
(1.00) 		0.497
(1.00) 		0.181
(1.00) 		0.108
(1.00) 		0.167
(1.00) 		0.208
(1.00) 		0.435
(1.00) 		0.208
(1.00)
del 13q14 2 46 (45%) 57 0.000485
(0.265) 		0.00681
(1.00) 		0.0261
(1.00) 		0.0182
(1.00) 		0.0162
(1.00) 		0.00371
(1.00) 		0.00415
(1.00) 		0.00371
(1.00)
del 13q21 2 42 (41%) 61 0.00142
(0.759) 		0.194
(1.00) 		0.322
(1.00) 		0.157
(1.00) 		0.12
(1.00) 		0.0463
(1.00) 		0.0204
(1.00) 		0.0463
(1.00)
del 15q11 2 33 (32%) 70 0.218
(1.00) 		0.404
(1.00) 		0.784
(1.00) 		0.535
(1.00) 		0.665
(1.00) 		0.68
(1.00) 		0.462
(1.00) 		0.68
(1.00)
del 17p11 2 45 (44%) 58 0.103
(1.00) 		0.0013
(0.699) 		0.00818
(1.00) 		0.00333
(1.00) 		0.00732
(1.00) 		0.00406
(1.00) 		0.0032
(1.00) 		0.00406
(1.00)
del 17q24 3 14 (14%) 89 0.616
(1.00) 		0.658
(1.00) 		0.823
(1.00) 		0.282
(1.00) 		0.794
(1.00) 		0.737
(1.00) 		0.34
(1.00) 		0.737
(1.00)
del 17q25 3 25 (24%) 78 0.24
(1.00) 		0.924
(1.00) 		0.171
(1.00) 		0.577
(1.00) 		0.535
(1.00) 		0.76
(1.00) 		0.266
(1.00) 		0.76
(1.00)
del 18q12 2 55 (53%) 48 0.307
(1.00) 		0.136
(1.00) 		0.111
(1.00) 		0.0667
(1.00) 		0.0873
(1.00) 		0.0743
(1.00) 		0.0472
(1.00) 		0.0743
(1.00)
del 18q21 2 61 (59%) 42 0.635
(1.00) 		0.0866
(1.00) 		0.289
(1.00) 		0.109
(1.00) 		0.358
(1.00) 		0.181
(1.00) 		0.135
(1.00) 		0.181
(1.00)
del 19p13 3 46 (45%) 57 0.0491
(1.00) 		0.927
(1.00) 		0.705
(1.00) 		0.815
(1.00) 		0.202
(1.00) 		0.79
(1.00) 		0.441
(1.00) 		0.79
(1.00)
del 19q13 31 28 (27%) 75 0.0572
(1.00) 		0.043
(1.00) 		0.327
(1.00) 		0.183
(1.00) 		0.0861
(1.00) 		0.137
(1.00) 		0.398
(1.00) 		0.137
(1.00)
del 20p12 1 19 (18%) 84 0.0746
(1.00) 		0.835
(1.00) 		0.579
(1.00) 		0.317
(1.00) 		0.158
(1.00) 		0.426
(1.00) 		0.214
(1.00) 		0.426
(1.00)
del 21q11 2 61 (59%) 42 0.676
(1.00) 		0.396
(1.00) 		0.308
(1.00) 		0.0172
(1.00) 		0.567
(1.00) 		0.228
(1.00) 		0.472
(1.00) 		0.228
(1.00)
del 21q22 12 57 (55%) 46 0.459
(1.00) 		0.0583
(1.00) 		0.0167
(1.00) 		0.00991
(1.00) 		0.129
(1.00) 		0.0516
(1.00) 		0.0735
(1.00) 		0.0516
(1.00)
del 22q12 3 38 (37%) 65 0.0133
(1.00) 		0.00361
(1.00) 		0.0346
(1.00) 		0.062
(1.00) 		0.123
(1.00) 		0.0656
(1.00) 		0.163
(1.00) 		0.0656
(1.00)
del xp21 1 40 (39%) 63 0.00522
(1.00) 		0.0371
(1.00) 		0.0469
(1.00) 		0.112
(1.00) 		0.684
(1.00) 		0.375
(1.00) 		0.769
(1.00) 		0.375
(1.00)
del xp11 3 42 (41%) 61 0.00181
(0.953) 		0.0267
(1.00) 		0.0611
(1.00) 		0.00833
(1.00) 		0.105
(1.00) 		0.0353
(1.00) 		0.213
(1.00) 		0.0353
(1.00)
del xq21 33 23 (22%) 80 0.591
(1.00) 		0.595
(1.00) 		0.516
(1.00) 		0.755
(1.00) 		0.794
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.724
(1.00)
'amp_3q26.2' versus 'CN_CNMF'

P value = 1.49e-10 (Fisher's exact test), Q value = 8.5e-08

Table S1.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 26
AMP PEAK 4(3Q26.2) MUTATED 13 39 18
AMP PEAK 4(3Q26.2) WILD-TYPE 25 0 8

Figure S1.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.024

Table S2.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 43 20
AMP PEAK 4(3Q26.2) MUTATED 19 39 12
AMP PEAK 4(3Q26.2) WILD-TYPE 21 4 8

Figure S2.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.57e-06 (Fisher's exact test), Q value = 0.0048

Table S3.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 4 39
AMP PEAK 4(3Q26.2) MUTATED 12 3 37
AMP PEAK 4(3Q26.2) WILD-TYPE 15 1 2

Figure S3.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 7.2e-06 (Fisher's exact test), Q value = 0.0041

Table S4.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 14 28
AMP PEAK 4(3Q26.2) MUTATED 29 12 12
AMP PEAK 4(3Q26.2) WILD-TYPE 1 2 16

Figure S4.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00018

Table S5.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 28 43
AMP PEAK 4(3Q26.2) MUTATED 0 12 41
AMP PEAK 4(3Q26.2) WILD-TYPE 1 16 2

Figure S5.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.63e-05 (Fisher's exact test), Q value = 0.042

Table S6.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 9 25 26
AMP PEAK 4(3Q26.2) MUTATED 11 7 24 11
AMP PEAK 4(3Q26.2) WILD-TYPE 1 2 1 15

Figure S6.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00018

Table S7.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 28 43
AMP PEAK 4(3Q26.2) MUTATED 0 12 41
AMP PEAK 4(3Q26.2) WILD-TYPE 1 16 2

Figure S7.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0085

Table S8.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 26
AMP PEAK 16(12P13.33) MUTATED 5 25 12
AMP PEAK 16(12P13.33) WILD-TYPE 33 14 14

Figure S8.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 2.08e-05 (Fisher's exact test), Q value = 0.012

Table S9.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 26
AMP PEAK 17(12P12.1) MUTATED 7 27 14
AMP PEAK 17(12P12.1) WILD-TYPE 31 12 12

Figure S9.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.3' versus 'CN_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.078

Table S10.  Gene #30: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 26
DEL PEAK 6(3P14.3) MUTATED 21 36 14
DEL PEAK 6(3P14.3) WILD-TYPE 17 3 12

Figure S10.  Get High-res Image Gene #30: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.078

Table S11.  Gene #30: 'del_3p14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 4 39
DEL PEAK 6(3P14.3) MUTATED 15 2 37
DEL PEAK 6(3P14.3) WILD-TYPE 12 2 2

Figure S11.  Get High-res Image Gene #30: 'del_3p14.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.12

Table S12.  Gene #30: 'del_3p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 14 28
DEL PEAK 6(3P14.3) MUTATED 29 12 15
DEL PEAK 6(3P14.3) WILD-TYPE 1 2 13

Figure S12.  Get High-res Image Gene #30: 'del_3p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0069

Table S13.  Gene #30: 'del_3p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 28 43
DEL PEAK 6(3P14.3) MUTATED 0 15 41
DEL PEAK 6(3P14.3) WILD-TYPE 1 13 2

Figure S13.  Get High-res Image Gene #30: 'del_3p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0069

Table S14.  Gene #30: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 28 43
DEL PEAK 6(3P14.3) MUTATED 0 15 41
DEL PEAK 6(3P14.3) WILD-TYPE 1 13 2

Figure S14.  Get High-res Image Gene #30: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 2.04e-06 (Fisher's exact test), Q value = 0.0012

Table S15.  Gene #45: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 26
DEL PEAK 21(9P21.3) MUTATED 22 39 17
DEL PEAK 21(9P21.3) WILD-TYPE 16 0 9

Figure S15.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S16.  Gene #45: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 28 43
DEL PEAK 21(9P21.3) MUTATED 0 19 42
DEL PEAK 21(9P21.3) WILD-TYPE 1 9 1

Figure S16.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S17.  Gene #45: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 28 43
DEL PEAK 21(9P21.3) MUTATED 0 19 42
DEL PEAK 21(9P21.3) WILD-TYPE 1 9 1

Figure S17.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.075

Table S18.  Gene #56: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 26
DEL PEAK 32(16P13.3) MUTATED 13 3 14
DEL PEAK 32(16P13.3) WILD-TYPE 25 36 12

Figure S18.  Get High-res Image Gene #56: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 2.5e-06 (Fisher's exact test), Q value = 0.0014

Table S19.  Gene #57: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 26
DEL PEAK 33(16Q23.1) MUTATED 14 9 22
DEL PEAK 33(16Q23.1) WILD-TYPE 24 30 4

Figure S19.  Get High-res Image Gene #57: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.21

Table S20.  Gene #57: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 43 20
DEL PEAK 33(16Q23.1) MUTATED 27 11 7
DEL PEAK 33(16Q23.1) WILD-TYPE 13 32 13

Figure S20.  Get High-res Image Gene #57: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

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

  • Molecular subtype file = ESCA-TP.transferedmergedcluster.txt

  • Number of patients = 103

  • Number of significantly focal cnvs = 71

  • Number of molecular subtypes = 8

  • Exclude genes that fewer than K tumors have alterations, 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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