The National Human Genome Research Institute (NHGRI) supports the public research consortium named ENCODE, the Encyclopedia Of DNA Elements, to identify all functional elements in the human and mouse genomes.
ENCODE has produced vast amounts of data that can be accessed through the project's freely accessible database, the ENCODE Portal. The ENCODE "Encyclopedia" organizes these data into two levels of annotations: 1) integrative-level annotations, including a registry of candidate cis-regulatory elements and 2) ground-level annotations derived directly from experimental data.
As a result of outreach and collaboration, ENCODE data are widely used. Lists of publications using ENCODE resources can be found on the ENCODE Portal. (See ENCODE-funded Publications and Community Publications.) The ENCODE Portal also hosts data from modENCODE as well as data from the RoadMap Epigenomics and Genomics of Gene Regulation projects. Additional information about data standards and guidelines and uniform data processing can also be found on the ENCODE Portal.
The ENCODE Project started in 2003 with a pilot phase focused on 1% of the human genome and subsequently completed two additional phases (ENCODE 2 and ENCODE 3) which conducted whole-genome analyses on the human and mouse genomes. A parallel effort was devoted to whole-genome analyses of the C. elegans and D. melanogaster genomes under the modENCODE Project. In recognition of the need for new approaches, methods and technologies to achieve the goals of ENCODE, NHGRI has also funded four rounds of technology development initiatives since 2003. A number of these efforts have been incorporated into subsequent phases of ENCODE data production and analysis.
With the success of these three phases of the ENCODE Project and the recognition that additional effort was needed to complete and understand the catalog of candidate regulatory elements compiled, NHGRI funded the fourth phase of ENCODE (ENCODE 4) in February 2017 to continue and expand on its work to understand the human and mouse genomes.
ENCODE 4 seeks to expand the catalog of candidate regulatory elements in the human and mouse genomes through the study of a broader diversity of biological samples including those associated with disease as well as by employing novel assays not used previously in ENCODE. To maximize access to ENCODE data by the research community, all data is shared in databases without controlled access. All newly obtained human biological samples are consented for unrestricted data sharing. To study the biological function of candidate regulatory elements already compiled by ENCODE, a new component, functional element characterization, has been added in ENCODE 4.
For more information, see: ENCODE 4 Participants and Projects.
Read about the ENCODE Pilot Project.
The ENCODE Consortium is composed primarily of scientists who were funded under RFAs released by NHGRI. Other participants have been identified and brought into the Consortium or Analysis Working Group (which leads the integrative analysis of ENCODE data) as appropriate. The Consortium and Analysis Working Group are open to any investigator willing to abide by the criteria for participation established for the ENCODE Project by NHGRI. The ENCODE External Consultants Panel oversees the activities of the Consortium and provides advice and feedback on the Consortium's goals, progress and membership.
Those interested in applying for membership to the ENCODE Consortium or to the ENCODE Analysis Working Group should review the criteria for participation and contact Elise Feingold, Ph.D., Dan Gilchrist, Ph.D. or Mike Pazin, Ph.D. (See: Program Staff).
NHGRI has designated the ENCODE Project as a community resource project to accelerate access to and use of the data by the entire scientific community. Accordingly, the data release policy is based on the principle of rapid data release to the scientific community.
The data produced by ENCODE Consortium members are deposited to public databases, including the ENCODE Portal and are available for all to use without restriction. Data users are asked to abide by the ENCODE Data Release Policy when using data produced by ENCODE Consortium members, acknowledging the ENCODE Consortium as specified in the policy.
As the ENCODE Project has increased its study of primary cells and tissues, it has begun working on human biological samples that have been explicitly consented for genomic research and unrestricted sharing of genomic data, in order to maximize the accessibility and utility of ENCODE data. This means that data can be deposited in freely accessible databases, e.g., GEO and the ENCODE Portal and shared without registration or prior approval.
The ENCODE Consortium has developed sample informed consent language that explicitly asks for 1) consent to genomic research and 2) consent to unrestricted sharing of genomic data. Below are links to this sample language as well as two examples of IRB-approved consents allowing for release of genomic data to unrestricted, public databases:
These examples provide the research community with information and examples to assist with the development of informed consent processes and consent forms for genomics-related research projects. They are not provided as guidance or as a template promoted by NHGRI, but as a reference to inform investigators and IRBs considering these issues. It is important to tailor consent documents for each individual study.
For general information from NHGRI about the informed consent process in genomics research, including additional sample consent forms, see: www.genome.gov/informedconsent.
A variety of tutorials are available on accessing and using ENCODE human and mouse data for studies on basic biology and human disease.
At this time, there are no current ENCODE RFAs.
NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031
Slides from Applicant Information Meeting - HG-07-030
NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031
Slides from Applicant Information Meeting - HG-07-031
Program Directors
Elise Feingold, Ph.D.
E-mail: feingole@exchange.nih.gov
Michael Pazin, Ph.D.
E-mail: pazinm@mail.nih.gov
Daniel Gilchrist, Ph.D.
E-mail: daniel.gilchrist@nih.gov
Program Analysts
Michael Pagan
E-mail: Michael.pagan@nih.gov
Eileen Cahill
E-mail: eileen.cahill@nih.gov
Address
National Human Genome Research Institute
National Institutes of Health
6700B Rockledge Drive
Suite 3100, MSC 6908
Bethesda, MD 20892-6908
Phone:(301) 496-7531
Fax:(301) 480-2770
Last Updated: February 4, 2019
Nature ENCODE explorer
Sept. 5, 2012
ENCODE Resources:
ENCODE Web Focus
Related articles on ENCODE from Nature
Special Issue on ENCODE from Genome Research
June 2007
Ensembl
Gene Expression Omnibus (GEO)
European Bioinformatics Institute (EBI)
encodeproject.org
