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The UCSC Genome Browser displays data produced by the
Encyclopedia of DNA Elements
(ENCODE) Consortium, an international
collaboration of research groups funded by the
National Human Genome Research Institute
(NHGRI).
The goal of ENCODE is to
build a comprehensive parts list of the
functional elements in the human genome
The initial phase of the ENCODE project (2003-2007) was a pilot
where experiments focused on a limited set of genomic regions comprising
roughly 1% of the human genome.
In September 2007, the project
was scaled up to production phase.
Key differences from the pilot project are:
-
Whole-genome data (with a few remaining pilot region
projects)
-
Identification of
common cell types to
facilitate integrative analysis
-
New experimental technologies based on high-throughput
sequencing
-
A data release policy restricting
use of data for nine months following release
The
Genome Bioinformatics
group at the University of California Santa Cruz
(UCSC)
was the official repository for
sequence-related data during the pilot project, and now
serves as the data coordination
center for the production phase of ENCODE, supporting data
submission,
organization, storage, retrieval, and visualization.
The DCC at UCSC works closely with the ENCODE Data Analysis
Center (DAC) at the European Bioinformatics Institute
(EBI).
ENCODE data is accessioned at the
NCBI Gene Expression Omnibus
(GEO) public data repository.
To access genome-wide ENCODE data in the
Genome Browser,
go to your region of interest and select
ENCODE tracks (marked with the NHGRI logo
 ).
Data from the pilot phase of
ENCODE, which is limited to the defined ENCODE regions,
is located in ENCODE-specific track groups in the
browser. The ENCODE Pilot
Project web pages provide
convenient browser access to these regions.
Click here to go to
the main UCSC Genome Browser site, which provides access to
sequence and annotation data for a large collection of
genome assemblies.
See the Genome Browser
User's
Guide for information about displaying tracks and
navigating in the Genome Browser.
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