Correlation between copy number variations of arm-level result and molecular subtypes
Esophageal Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1FJ2F7W
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/C1FJ2F7W
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 6 molecular subtypes across 73 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.

  • 3q gain 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 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, one significant finding detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
3q gain 33 (45%) 40 3.62e-05
(0.0174) 		0.00164
(0.777) 		0.00479
(1.00) 		0.00687
(1.00) 		0.0517
(1.00) 		0.00687
(1.00)
1p gain 10 (14%) 63 0.905
(1.00) 		0.616
(1.00) 		0.365
(1.00) 		0.394
(1.00) 		0.00746
(1.00) 		0.394
(1.00)
1q gain 25 (34%) 48 0.668
(1.00) 		0.246
(1.00) 		0.0775
(1.00) 		0.0309
(1.00) 		0.0193
(1.00) 		0.0309
(1.00)
2p gain 29 (40%) 44 0.16
(1.00) 		0.389
(1.00) 		0.116
(1.00) 		0.689
(1.00) 		0.00928
(1.00) 		0.689
(1.00)
2q gain 18 (25%) 55 0.728
(1.00) 		0.557
(1.00) 		0.673
(1.00) 		0.688
(1.00) 		0.0647
(1.00) 		0.688
(1.00)
3p gain 11 (15%) 62 0.0639
(1.00) 		0.22
(1.00) 		0.101
(1.00) 		0.306
(1.00) 		0.0533
(1.00) 		0.306
(1.00)
4p gain 6 (8%) 67 0.854
(1.00) 		1
(1.00) 		0.735
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
4q gain 5 (7%) 68 0.101
(1.00) 		0.845
(1.00) 		0.412
(1.00) 		0.667
(1.00) 		0.791
(1.00) 		0.667
(1.00)
5p gain 33 (45%) 40 0.557
(1.00) 		0.732
(1.00) 		0.293
(1.00) 		0.375
(1.00) 		0.36
(1.00) 		0.375
(1.00)
5q gain 10 (14%) 63 0.822
(1.00) 		0.822
(1.00) 		0.749
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.57
(1.00)
6p gain 9 (12%) 64 0.811
(1.00) 		0.898
(1.00) 		0.904
(1.00) 		0.765
(1.00) 		0.679
(1.00) 		0.765
(1.00)
6q gain 8 (11%) 65 0.309
(1.00) 		0.389
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
7p gain 47 (64%) 26 0.628
(1.00) 		1
(1.00) 		0.883
(1.00) 		0.541
(1.00) 		0.717
(1.00) 		0.541
(1.00)
7q gain 34 (47%) 39 0.18
(1.00) 		0.612
(1.00) 		0.527
(1.00) 		0.375
(1.00) 		0.358
(1.00) 		0.375
(1.00)
8p gain 29 (40%) 44 0.156
(1.00) 		0.241
(1.00) 		0.932
(1.00) 		1
(1.00) 		0.968
(1.00) 		1
(1.00)
8q gain 41 (56%) 32 0.118
(1.00) 		0.259
(1.00) 		0.669
(1.00) 		0.321
(1.00) 		0.667
(1.00) 		0.321
(1.00)
9p gain 7 (10%) 66 0.0423
(1.00) 		0.519
(1.00) 		0.419
(1.00) 		0.443
(1.00) 		0.39
(1.00) 		0.443
(1.00)
9q gain 17 (23%) 56 0.0512
(1.00) 		0.52
(1.00) 		0.439
(1.00) 		0.58
(1.00) 		0.649
(1.00) 		0.58
(1.00)
10p gain 14 (19%) 59 0.46
(1.00) 		0.385
(1.00) 		0.0902
(1.00) 		0.764
(1.00) 		0.217
(1.00) 		0.764
(1.00)
10q gain 9 (12%) 64 0.335
(1.00) 		0.523
(1.00) 		0.132
(1.00) 		0.525
(1.00) 		0.094
(1.00) 		0.525
(1.00)
11p gain 15 (21%) 58 0.285
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.48
(1.00) 		0.518
(1.00) 		0.48
(1.00)
11q gain 13 (18%) 60 0.723
(1.00) 		0.619
(1.00) 		0.206
(1.00) 		0.198
(1.00) 		0.451
(1.00) 		0.198
(1.00)
12p gain 31 (42%) 42 0.00761
(1.00) 		0.0137
(1.00) 		0.0123
(1.00) 		0.00479
(1.00) 		0.0656
(1.00) 		0.00479
(1.00)
12q gain 18 (25%) 55 0.131
(1.00) 		0.0516
(1.00) 		0.239
(1.00) 		0.336
(1.00) 		0.51
(1.00) 		0.336
(1.00)
13q gain 15 (21%) 58 0.000531
(0.254) 		0.00413
(1.00) 		0.00139
(0.661) 		0.000595
(0.284) 		0.00204
(0.96) 		0.000595
(0.284)
14q gain 22 (30%) 51 0.437
(1.00) 		0.388
(1.00) 		0.469
(1.00) 		0.457
(1.00) 		0.238
(1.00) 		0.457
(1.00)
15q gain 12 (16%) 61 0.778
(1.00) 		0.091
(1.00) 		0.188
(1.00) 		0.601
(1.00) 		0.768
(1.00) 		0.601
(1.00)
16p gain 16 (22%) 57 0.903
(1.00) 		0.134
(1.00) 		0.158
(1.00) 		0.105
(1.00) 		0.111
(1.00) 		0.105
(1.00)
16q gain 13 (18%) 60 0.247
(1.00) 		0.0837
(1.00) 		0.0749
(1.00) 		0.104
(1.00) 		0.0297
(1.00) 		0.104
(1.00)
17p gain 15 (21%) 58 0.0882
(1.00) 		0.198
(1.00) 		0.759
(1.00) 		1
(1.00) 		0.853
(1.00) 		1
(1.00)
17q gain 21 (29%) 52 0.898
(1.00) 		0.677
(1.00) 		0.352
(1.00) 		0.46
(1.00) 		0.749
(1.00) 		0.46
(1.00)
18p gain 24 (33%) 49 0.0442
(1.00) 		0.268
(1.00) 		0.447
(1.00) 		0.517
(1.00) 		0.405
(1.00) 		0.517
(1.00)
18q gain 9 (12%) 64 0.335
(1.00) 		0.652
(1.00) 		0.812
(1.00) 		0.765
(1.00) 		0.956
(1.00) 		0.765
(1.00)
19p gain 11 (15%) 62 0.00598
(1.00) 		0.913
(1.00) 		0.749
(1.00) 		0.57
(1.00) 		0.341
(1.00) 		0.57
(1.00)
19q gain 15 (21%) 58 0.00174
(0.82) 		0.2
(1.00) 		0.0536
(1.00) 		0.0301
(1.00) 		0.0266
(1.00) 		0.0301
(1.00)
20p gain 39 (53%) 34 0.852
(1.00) 		0.746
(1.00) 		0.658
(1.00) 		0.615
(1.00) 		0.7
(1.00) 		0.615
(1.00)
20q gain 42 (58%) 31 0.246
(1.00) 		0.1
(1.00) 		0.12
(1.00) 		0.0516
(1.00) 		0.335
(1.00) 		0.0516
(1.00)
21q gain 8 (11%) 65 0.795
(1.00) 		0.701
(1.00) 		0.775
(1.00) 		0.726
(1.00) 		0.108
(1.00) 		0.726
(1.00)
22q gain 17 (23%) 56 0.0108
(1.00) 		0.00246
(1.00) 		0.00202
(0.954) 		0.0011
(0.521) 		0.00966
(1.00) 		0.0011
(0.521)
xq gain 17 (23%) 56 0.26
(1.00) 		0.323
(1.00) 		0.445
(1.00) 		0.37
(1.00) 		0.623
(1.00) 		0.37
(1.00)
1p loss 13 (18%) 60 0.529
(1.00) 		0.619
(1.00) 		0.362
(1.00) 		0.374
(1.00) 		0.916
(1.00) 		0.374
(1.00)
1q loss 11 (15%) 62 0.013
(1.00) 		0.579
(1.00) 		0.158
(1.00) 		0.426
(1.00) 		0.963
(1.00) 		0.426
(1.00)
2p loss 3 (4%) 70 1
(1.00) 		0.138
(1.00) 		0.796
(1.00) 		1
(1.00) 		0.864
(1.00) 		1
(1.00)
2q loss 9 (12%) 64 0.728
(1.00) 		0.0187
(1.00) 		0.131
(1.00) 		0.194
(1.00) 		0.218
(1.00) 		0.194
(1.00)
3p loss 43 (59%) 30 0.141
(1.00) 		0.295
(1.00) 		0.184
(1.00) 		0.04
(1.00) 		0.181
(1.00) 		0.04
(1.00)
3q loss 13 (18%) 60 0.785
(1.00) 		0.723
(1.00) 		0.179
(1.00) 		0.34
(1.00) 		0.676
(1.00) 		0.34
(1.00)
4p loss 42 (58%) 31 0.14
(1.00) 		0.665
(1.00) 		0.446
(1.00) 		0.164
(1.00) 		0.698
(1.00) 		0.164
(1.00)
4q loss 35 (48%) 38 0.00244
(1.00) 		0.677
(1.00) 		0.794
(1.00) 		0.836
(1.00) 		0.969
(1.00) 		0.836
(1.00)
5p loss 18 (25%) 55 0.217
(1.00) 		0.382
(1.00) 		0.106
(1.00) 		0.117
(1.00) 		0.00908
(1.00) 		0.117
(1.00)
5q loss 32 (44%) 41 1
(1.00) 		0.581
(1.00) 		0.669
(1.00) 		0.719
(1.00) 		0.294
(1.00) 		0.719
(1.00)
6p loss 18 (25%) 55 0.101
(1.00) 		0.519
(1.00) 		0.401
(1.00) 		0.439
(1.00) 		0.391
(1.00) 		0.439
(1.00)
6q loss 16 (22%) 57 0.196
(1.00) 		0.407
(1.00) 		0.445
(1.00) 		0.37
(1.00) 		0.607
(1.00) 		0.37
(1.00)
7p loss 6 (8%) 67 0.397
(1.00) 		0.283
(1.00) 		0.554
(1.00) 		0.443
(1.00) 		0.0618
(1.00) 		0.443
(1.00)
7q loss 10 (14%) 63 0.0146
(1.00) 		0.449
(1.00) 		1
(1.00) 		1
(1.00) 		0.801
(1.00) 		1
(1.00)
8p loss 27 (37%) 46 0.258
(1.00) 		0.605
(1.00) 		0.717
(1.00) 		0.634
(1.00) 		0.69
(1.00) 		0.634
(1.00)
8q loss 10 (14%) 63 0.245
(1.00) 		0.905
(1.00) 		0.679
(1.00) 		0.57
(1.00) 		0.304
(1.00) 		0.57
(1.00)
9p loss 42 (58%) 31 0.0694
(1.00) 		0.414
(1.00) 		0.675
(1.00) 		0.534
(1.00) 		0.911
(1.00) 		0.534
(1.00)
9q loss 23 (32%) 50 0.0147
(1.00) 		0.252
(1.00) 		0.447
(1.00) 		0.517
(1.00) 		0.165
(1.00) 		0.517
(1.00)
10p loss 22 (30%) 51 0.339
(1.00) 		0.374
(1.00) 		0.618
(1.00) 		0.575
(1.00) 		0.841
(1.00) 		0.575
(1.00)
10q loss 26 (36%) 47 0.0123
(1.00) 		0.0172
(1.00) 		0.0976
(1.00) 		0.0438
(1.00) 		0.124
(1.00) 		0.0438
(1.00)
11p loss 22 (30%) 51 0.0131
(1.00) 		0.374
(1.00) 		0.322
(1.00) 		0.293
(1.00) 		0.418
(1.00) 		0.293
(1.00)
11q loss 27 (37%) 46 0.014
(1.00) 		0.335
(1.00) 		0.24
(1.00) 		0.146
(1.00) 		0.245
(1.00) 		0.146
(1.00)
12p loss 15 (21%) 58 0.0217
(1.00) 		0.054
(1.00) 		0.00538
(1.00) 		0.00504
(1.00) 		0.0769
(1.00) 		0.00504
(1.00)
12q loss 15 (21%) 58 0.157
(1.00) 		0.054
(1.00) 		0.0536
(1.00) 		0.0301
(1.00) 		0.171
(1.00) 		0.0301
(1.00)
13q loss 31 (42%) 42 0.0445
(1.00) 		0.0946
(1.00) 		0.0407
(1.00) 		0.0123
(1.00) 		0.00806
(1.00) 		0.0123
(1.00)
14q loss 18 (25%) 55 0.378
(1.00) 		0.134
(1.00) 		0.0395
(1.00) 		0.21
(1.00) 		0.0283
(1.00) 		0.21
(1.00)
15q loss 20 (27%) 53 0.923
(1.00) 		0.35
(1.00) 		0.529
(1.00) 		0.46
(1.00) 		0.655
(1.00) 		0.46
(1.00)
16p loss 18 (25%) 55 0.378
(1.00) 		0.218
(1.00) 		0.127
(1.00) 		0.117
(1.00) 		0.138
(1.00) 		0.117
(1.00)
16q loss 19 (26%) 54 0.0326
(1.00) 		0.299
(1.00) 		0.0621
(1.00) 		0.0534
(1.00) 		0.133
(1.00) 		0.0534
(1.00)
17p loss 26 (36%) 47 0.0544
(1.00) 		0.0123
(1.00) 		0.0526
(1.00) 		0.0239
(1.00) 		0.0334
(1.00) 		0.0239
(1.00)
17q loss 8 (11%) 65 0.615
(1.00) 		0.488
(1.00) 		0.152
(1.00) 		0.232
(1.00) 		0.094
(1.00) 		0.232
(1.00)
18p loss 25 (34%) 48 0.271
(1.00) 		0.122
(1.00) 		0.0717
(1.00) 		0.526
(1.00) 		0.0893
(1.00) 		0.526
(1.00)
18q loss 40 (55%) 33 0.455
(1.00) 		0.35
(1.00) 		0.216
(1.00) 		0.238
(1.00) 		0.117
(1.00) 		0.238
(1.00)
19p loss 26 (36%) 47 0.0123
(1.00) 		0.154
(1.00) 		0.0257
(1.00) 		0.426
(1.00) 		0.0469
(1.00) 		0.426
(1.00)
19q loss 21 (29%) 52 0.0241
(1.00) 		0.029
(1.00) 		0.0258
(1.00) 		0.137
(1.00) 		0.198
(1.00) 		0.137
(1.00)
20p loss 9 (12%) 64 0.811
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.391
(1.00) 		0.398
(1.00) 		0.391
(1.00)
20q loss 3 (4%) 70 0.436
(1.00) 		0.138
(1.00) 		0.599
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.576
(1.00)
21q loss 44 (60%) 29 0.472
(1.00) 		0.0724
(1.00) 		0.15
(1.00) 		0.0524
(1.00) 		0.0857
(1.00) 		0.0524
(1.00)
22q loss 26 (36%) 47 0.422
(1.00) 		0.0394
(1.00) 		0.287
(1.00) 		0.244
(1.00) 		0.375
(1.00) 		0.244
(1.00)
xq loss 19 (26%) 54 0.413
(1.00) 		0.048
(1.00) 		0.334
(1.00) 		0.389
(1.00) 		0.398
(1.00) 		0.389
(1.00)
'3q gain' versus 'CN_CNMF'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.017

Table S1.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 34 24
3Q GAIN MUTATED 10 6 17
3Q GAIN WILD-TYPE 5 28 7

Figure S1.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 73

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 6

  • 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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