Perspectives on ENCODE

Snyder, M. P., Gingeras, T. R., Moore, J. E., Weng, Z., Gerstein, M. B., Ren, B., Hardison, R. C., Stamatoyannopoulos, J. A., Graveley, B. R., Feingold, E. A., Pazin, M. J., Pagan, M., Gilchrist, D. A., Hitz, B. C., Cherry, J. M., Bernstein, B. E., Mendenhall, E. M., Zerbino, D. R., Frankish, A., Flicek, P., Myers, R. M. (July 2020) Perspectives on ENCODE. Nature, 583 (7818). pp. 693-698. ISSN 0028-0836 (Print)0028-0836

Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression(1). The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Item Type:	Paper
Additional Information:	1476-4687 ENCODE Project Consortium Snyder, Michael P Orcid: 0000-0003-0784-7987 Gingeras, Thomas R Moore, Jill E Orcid: 0000-0002-3023-0806 Weng, Zhiping Gerstein, Mark B Ren, Bing Orcid: 0000-0002-5435-1127 Hardison, Ross C Orcid: 0000-0003-4084-7516 Stamatoyannopoulos, John A Graveley, Brenton R Feingold, Elise A Pazin, Michael J Pagan, Michael Gilchrist, Daniel A Hitz, Benjamin C Cherry, J Michael Orcid: 0000-0001-9163-5180 Bernstein, Bradley E Orcid: 0000-0002-5726-6278 Mendenhall, Eric M Orcid: 0000-0002-7395-6295 Zerbino, Daniel R Frankish, Adam Flicek, Paul Orcid: 0000-0002-3897-7955 Myers, Richard M R01 DK050107/DK/NIDDK NIH HHS/United States R01 DK068634/DK/NIDDK NIH HHS/United States R37 DK050107/DK/NIDDK NIH HHS/United States U24 HG009397/HG/NHGRI NIH HHS/United States Journal Article Review Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29.
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification organism description > animal bioinformatics > computational biology bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein methylation > histone methylation organism description > animal > mammal > primates > hominids > human organism description > animal > mammal organism description > animal > mammal > rodent > mouse bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein methylation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types organism description > animal > mammal > rodent bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:	Gingeras, Thomas R.
Communities:	CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL labs > Gingeras lab
Depositing User:	Matthew Dunn
Date:	July 2020
Date Deposited:	14 Dec 2020 21:30
Last Modified:	01 Feb 2024 18:40
PMCID:	PMC7410827
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/39633

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