Skip to main content
NIH

The ENCODE Project: ENCyclopedia Of DNA Elements

ENCODE logo

Follow the ENCODE Project on:


ENCODE Overview

The National Human Genome Research Institute (NHGRI) supports the public research consortium named ENCODE, the Encyclopedia ODNA 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.

ENCODE 4 includes the following components:
  • Functional Element Mapping Centers
    • Conduct high-throughput experiments that map biochemical activities to identify candidate functional elements in the human and mouse genomes.
  • Functional Element Characterization Centers
    • Develop and apply generalizable approaches to characterize the role of candidate functional elements in specific biological contexts.
  • Computational Analysis Groups
    • Pilot new applications of ENCODE data
  • Data Coordination Center (DCC)
    • Processes and shares ENCODE metadata and data, and provide a portal for the community to visualize and download data.
  • Data Analysis Center (DAC)
    • Specifies data processing pipelines and quality metrics for major data types, design and perform integrative analysis of ENCODE data to update and refine the Encyclopedia.

For more information, see: ENCODE 4 Participants and Projects.

Read about the ENCODE Pilot Project.

Meetings and Workshops

ENCODE Publications, Features and Press Releases

Publications
Features
Press Releases

ENCODE Consortium Membership

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).

ENCODE Data Release Policy

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.

Accessing ENCODE Data

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.

Informed Consent for ENCODE Samples

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.

ENCODE Tutorials

A variety of tutorials are available on accessing and using ENCODE human and mouse data for studies on basic biology and human disease.

Top of page

ENCODE Project Requests For Application (RFAs)

Current ENCODE RFAs

At this time, there are no current ENCODE RFAs.

Recently Expired RFAs
  • ENCODE FOA Webinar Information   

    NOT-HG-16-007 [grants1.nih.gov]: Notice of Applicant Information Webinar for NHGRI ENCODE RFAs: RFA-HG-16-002, RFA-HG-16-003, RFA-HG-16-004, RFA-HG-16-005, and RFA-HG-16-006
    This notice applies to the following ENCODE RFAs:
    • RFA-HG-16-002 [grants.nih.gv]: Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Mouse (UM1)
       
    • RFA-HG-16-003 [grants.nih.gov]: Characterizing the Functional Elements in the Encyclopedia of DNA Elements (ENCODE) Catalog (UM1)
       
    • RFA-HG-16-004 [grants.nih.gov]: Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01)
       
    • RFA-HG-16-005 [grants.nih.gov]: ENCODE Data Coordinating Center (U24)
       
    • RFA-HG-16-006 [grants.nih.gov]: ENCODE Data Analysis Center (U24)
    • NOT-HG-15-034 [grants.nih.gov]: Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Mapping Centers (UM1)
  • NOT-HG-15-035 [grants.nih.gov]: Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Characterization Centers (UM1)
     
  • NOT-HG-15-036 [grants.nih.gov]: Notice of Intent to Publish a Funding Opportunity Announcement for Computational Analysis Research Projects (U01)
     
  • NOT-HG-15-037 [grants.nih.gov]: Notice of Intent to Publish a Funding Opportunity Announcement for ENCODE Data Coordination and Analysis Center (U24) 
Past ENCODE RFAs
  • NOT-HG-12-002 [grants.nih.gov]: Notice of Change in the Receipt Date: RFA-HG-11-024, Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) and RFA-HG-11-025, Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01) (Expired)
     
  • RFA-HG-11-024 [grants.nih.gov]: Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) (Expired)
     
  • RFA-HG-11-025 [grants.nih.gov]: Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01) (Expired)
     
  • RFA-HG-11-026 [grants.nih.gov]: Data Analysis and Coordination Center for the Encyclopedia of DNA Elements (ENCODE) (U41)(Expired)
     
  • RFA-HG-11-013 [grants.nih.gov]: Technology Development for High-Throughput Functional Genomics (R01) (Expired)
     
  • RFA-HG-11-014 [grants.nih.gov]: Technology Development for High-Throughput Functional Genomics (R21) (Expired)
     
  • RFA-HG-11-015 [grants.nih.gov]: Technology Development for High-Throughput Functional Genomics (R43/44) (Expired)
     
  • RFA-HG-07-030 [grants.nih.gov]: Creating the Encyclopedia of DNA Elements (ENCODE) in the Human Genome (U01 and U54) (Expired)

    NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031

    Slides from Applicant Information Meeting - HG-07-030 PDF Icon

  • RFA-HG-07-031 [grants.nih.gov]: A Data Coordination Center for the Encyclopedia of DNA Elements (ENCODE) Project (U41) (Expired)

    NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031

    Slides from Applicant Information Meeting - HG-07-031 PDF Icon

  • RFA-HG-07-010: [grants1.nih.gov] A Data Analysis Center for the Encyclopedia of DNA Elements (ENCODE) Project (U01) (Expired)
     
  • RFA HG-03-003 [grants.nih.gov]: Determination of All Functional Elements in Human DNA (Expired)
     
  • RFA HG-03-004 [grants.nih.gov]: Technologies to Find Functional Elements in Genomic DNA (Expired)
     
  • RFA-HG-04-001 [grants1.nih.gov]: Technologies to Find Functional Elements in Genomic DNA. (Expired)
     
  • RFA-HG-07-028 [grants.nih.gov]: Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R21) (Expired)
     
  • RFA HG-07-029 [grants.nih.gov]: Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R01) (Expired)

 

ENCODE Program Staff

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

Top of page

Last Updated: September 17, 2018

See Also:

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project PDF Icon
Nature, June 13, 2007

Major Findings from The ENCODE Pilot Project
June 2007

The modENCODE Project

Grants Home

On Other Sites:

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