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The Encyclopedia of
DNA Elements (ENCODE) Consortium is an international collaboration
of research groups funded by the National Human Genome Research
Institute (NHGRI).
The goal of the consortium is to build a comprehensive parts list of
the functional elements of the human genome, including elements that
act at the protein level (coding genes) and RNA level (non-coding
genes), and regulatory elements that control the cells and
circumstances in which a gene is active. The discovery and annotation
of gene elements is accomplished primarily by sequencing RNA from a
diverse range of sources, comparative genomics, integrative
bioinformatic methods, and human curation. Regulatory elements are
typically investigated through DNA hypersensitivity assays, assays of
DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins
that interact with DNA, including modified histones and transcription
factors, followed by sequencing (ChIP-Seq). The results of ENCODE
experiments, collected in the ENCODE DCC database, are displayed on the
UCSC Genome Browser. The data can also be downloaded from the ENCODE
DCC website in text format.
ENCODE data is now available for the
entire human genome. Mouse ENCODE experiments are currently
underway, and data on the mouse genome from such experiments will be
made available as soon as possible. To access the human ENCODE data, open the
Genome Browser, select the
March 2006 assembly of the human genome, and go to your region of
interest. ENCODE tracks will be marked with the NHGRI logo  . The bulk of
the ENCODE data can be found in the Expression and Regulation
track groups, with a few in the Mapping, Genes, and
Variation groups. Although most
participating research groups have provided several tracks, generally
only selected data from each research group are displayed by default.
Click the hyperlinked name of a particular track to display a page
containing configuration options and details about the methods used to
generate the data. See the Genome Browser User's Guide for
further information about displaying tracks and navigating in the
Genome Browser. To receive notifications of ENCODE data releases and
related news by email, subscribe to the encode-announce mailing list.
Data from the earlier ENCODE project
pilot phase, which covered approximately 1% of the genome, are
available on the May 2004 and March 2006 human
assemblies. The ENCODE Pilot Project web
pages provide convenient browser access to these regions.
Before publishing research that uses
ENCODE data, please read the data release policy,
which
places
some
restrictions on publication use of data for nine
months following the data release.
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