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OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

Perspectives on ENCODE

Journal Article · · Nature (London)
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The Encyclopedia 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. The project has been extended to model organisms, particularly the mouse. Finally, 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.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Contributing Organization:
ENCODE Project Consortium
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1906809
Journal Information:
Nature (London), Journal Name: Nature (London) Journal Issue: 7818 Vol. 583; ISSN 0028-0836
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

References (38)

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PacBio Sequencing and Its Applications journal October 2015
Resources for the Comprehensive Discovery of Functional RNA Elements journal March 2016
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Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF journal January 2001
Initial sequencing and comparative analysis of the mouse genome journal January 2002
A high-resolution map of human evolutionary constraint using 29 mammals journal October 2011
An integrated encyclopedia of DNA elements in the human genome journal September 2012
Principles of regulatory information conservation between mouse and human journal November 2014
A comparative encyclopedia of DNA elements in the mouse genome journal November 2014
Single-cell chromatin accessibility reveals principles of regulatory variation journal June 2015
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Development and applications of single-cell transcriptome analysis journal March 2011
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RNA-Seq: a revolutionary tool for transcriptomics journal January 2009
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program journal January 2019
Occupancy maps of 208 chromatin-associated proteins in one human cell type journal July 2020
A large-scale binding and functional map of human RNA-binding proteins journal July 2020
An atlas of dynamic chromatin landscapes in mouse fetal development journal July 2020
Spatiotemporal DNA methylome dynamics of the developing mouse fetus journal July 2020
Landscape of cohesin-mediated chromatin loops in the human genome journal July 2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes journal July 2020
Global reference mapping of human transcription factor footprints journal July 2020
Defining functional DNA elements in the human genome journal April 2014
GENCODE: The reference human genome annotation for The ENCODE Project journal September 2012
Linking disease associations with regulatory information in the human genome journal September 2012
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia journal September 2012
Genome-Wide Mapping of in Vivo Protein-DNA Interactions journal June 2007
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project journal December 2010
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE journal December 2010
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA journal September 2012
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq journal January 2013
Genome-Wide Location and Function of DNA Binding Proteins journal December 2000
The novel mouse mutant, chuzhoi, has disruption of Ptk7 protein and exhibits defects in neural tube, heart and lung development and abnormal planar cell polarity in the ear journal August 2010
Accurate prediction of cell type-specific transcription factor binding journal January 2019
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) journal April 2011
The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors journal March 2018
The Human Cell Atlas journal December 2017

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
epigenetics
epigenomics
genome
transcriptomics