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The Encyclopedia of DNA Elements (ENCODE)

ENCODE is a public research consortium aimed at identifying all functional elements in the human and mouse genomes.

Overview

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 the ENCODE Pilot Project, which 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

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.

Read about the ENCODE Pilot Project.

Participants and Projects

Phase 4 (Current)
Grantees Institutions Title Grant Number
Mapping Awards
Bradley Bernstein
Chad Nusbaum		 Broad Institute of Harvard and MIT A Catalog of Cell Types and Genomic Elements in Tissues, Organoids and Disease UM1 HG009390
Erez Lieberman Aiden Baylor College of Medicine Genome-Wide Mapping of Loops Using In Situ Hi-C UM1 HG009375
Mats Ljungman University of Michigan Mapping of Novel Candidate Functional Elements with Bru-Seq Technology UM1 HG009382
Richard Myers
Eric Mendenhall		 HudsonAlpha Institute for Biotechnology
University of Alabama in Huntsville		 An ENCODE ChIP-seq pipeline using endogenously tagged human DNA-associated proteins UM1 HG009411
Yijun Ruan The Jackson Laboratory Comprehensive Mapping of Long-Range Chromatin Interactions in Human and Mouse Genomes UM1 HG009409
Michael Snyder Stanford University Production Center for Mapping Regulatory Regions of the Human Genome UM1 HG009442
John Stamatoyannopoulos Altius Institute for Biomedical Sciences ENCODE Mapping Center - A Comprehensive Catalog of Dnase I Hypersensitive Sites UM1 HG009444
Barbara Wold
Ali Mortazavi		 California Institute of Technology
University of California, Irvine		 High Precision Human and Mouse Transcriptomes UM1 HG009443
Functional Characterization Awards
Nadav Ahituv
Jay Shendure		 University of California, San Francisco
University of Washington		 Massively parallel reporter assays and genome editing of ENCODE predicted regulatory elements UM1 HG009408
William Greenleaf
Michael Bassik		 Stanford University High-throughput systematic characterization of regulatory element function UM1 HG009436
John Lis
Haiyuan Yu		 Cornell University High-throughput functional characterization of human enhancers UM1 HG009393
Len Pennacchio
Axel Visel		 Lawrence Berkeley National Laboratory In Vivo Characterization of Major ENCODE-Predicted Classes of Noncoding Variants UM1 HG009421
Tim Reddy
Maria Ciofani
Gregory Crawford
Charles Gersbach		 Duke University Regulatory Mechanisms Of CD4+ T Cell Differentiation UM1 HG009428
Pardis Sabeti Broad Institute Comprehensive Functional Characterisation And Dissection of Noncoding Regulatory Elements And Human Genetic Variation UM1 HG009435
Yin Shen|
Bing Ren		 University of California, San Francisco
University of California, San Diego
Ludwig Institute for Cancer Research		 High-throughput CRISPR-mediated functional validation of regulatory elements UM1 HG009402
Kevin White University of Chicago Center For Functional Validation and Evaluation Of ENCODE Enhancer Regions UM1 HG009426
Computational Analysis Awards
Michael Beer Johns Hopkins University Systematic Identification of Core Regulatory Circuitry from ENCODE Data U01 HG009380
Christina Leslie Memorial Sloan Kettering Cancer Center Encoding genomic architecture in the encyclopedia: linking DNA elements, chromatin state, and gene expression in 3D U01 HG009395
Alkes Price
Soumya Raychaudhuri		 Harvard University
Brigham and Women's Hopsital		 Functionally specialized components of disease heritability in ENCODE data U01 HG009379
Jonathan Pritchard Stanford University Decoding the regulatory architecture of the human genome across cell types, indviduals and disease U01 HG009431
Ting Wang
Barak Cohen
Cedric Feschotte		 Washington University
University of Utah		 Connecting transposable elements and regulatory innovation using ENCODE data U01 HG009391
Xinshu Grace Xiao University of California, Los Angeles Analysis of functional genetic variants in RNA processing and expression U01 HG009417
Data Coordination Center
J. Michael Cherry Stanford University A Data Coordinating Center for ENCODE U24 HG009397
Data Analysis Center
Zhiping Weng
Mark Gerstein		 University of Massachusetts Medical School
Yale University		 EDAC: ENCODE Data Analysis Center U24 HG009446
Affiliate Members

Brenton Graveley, Gene Yeo
University of Connecticut Health Center

Guo-Cheng Yuan
Dana-Farber Cancer Institute

Alexander Dobin
Cold Spring Harbor Laboratory

Melissa Fulwood
Nanyang Technological University and Cancer Science Institute

Nir Yosef
University of California, Berkeley

Jesse Engreitz
Broad Institute and Harvard University

Adam Siepel
Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory

Douglas Phanstiel
University of North Carolina at Chapel Hill

Feng Yue
Northwestern University

Max Libbrecht
Simon Fraser University

Jian Ma
Carnegie Mellon University

Katie Pollard
University of California, San Francisco

Past Participants and Projects

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).

Informed Consent

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.

Data 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.

External data users may freely download, analyze and publish results based on any ENCODE data without restrictions as soon as they are released. This applies to all datasets, regardless of type or size, and includes no grace period for ENCODE data producers, either as individual members or as part of the Consortium. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Consortium will continue to publish the results of its own analysis efforts in independent publications. ?We request that researchers who use ENCODE datasets (published or unpublished) in publications and talks cite the ENCODE Consortium in all of the following ways:

  1. Cite the Consortium's most recent integrative publication (PMID: 22955616; PMC: PMC3439153);
  2. Reference the ENCODE Data Coordination Center (DCC) or GEO accession numbers of the datasets; and
  3. Acknowledge the ENCODE Consortium and the ENCODE production laboratory(s) generating the particular dataset(s).

Data Release Policies

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.

Tutorials

These tutorials were prepared for biologists using human and/or mouse genetic data to study disease, gene regulation, and basic biology. They explain what data are available, what they mean, how they can be displayed and downloaded and how they can be used in genetic research on human disease.

News and Events

Meetings and Workshops

Publications

Features

Press Releases

Meetings and Workshops

Funding Opportunities

Current ENCODE RFAs

At this time, there are no current ENCODE RFAs.

Recently Expired RFAs
  • ENCODE FOA Webinar Information   

    NOT-HG-16-007 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 Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Mouse (UM1) 
       
    • RFA-HG-16-003 Characterizing the Functional Elements in the Encyclopedia of DNA Elements (ENCODE) Catalog (UM1)
       
    • RFA-HG-16-004 Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01)
       
    • RFA-HG-16-005 ENCODE Data Coordinating Center (U24)
       
    • RFA-HG-16-006 ENCODE Data Analysis Center (U24)
       
    • NOT-HG-15-034 Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Mapping Centers (UM1)
       
  • NOT-HG-15-035 Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Characterization Centers (UM1)
     
  • NOT-HG-15-036 Notice of Intent to Publish a Funding Opportunity Announcement for Computational Analysis Research Projects (U01)
     
  • NOT-HG-15-037 Notice of Intent to Publish a Funding Opportunity Announcement for ENCODE Data Coordination and Analysis Center (U24) 
Past ENCODE RFAs
  • NOT-HG-12-002 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 Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) (Expired)
     
  • RFA-HG-11-025 Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01) (Expired)
     
  • RFA-HG-11-026 Data Analysis and Coordination Center for the Encyclopedia of DNA Elements (ENCODE) (U41) (Expired)
     
  • RFA-HG-11-013 Technology Development for High-Throughput Functional Genomics (R01) (Expired)
     
  • RFA-HG-11-014 Technology Development for High-Throughput Functional Genomics (R21) (Expired)
     
  • RFA-HG-11-015 Technology Development for High-Throughput Functional Genomics (R43/44) (Expired)
     
  • RFA-HG-07-030 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 
  • RFA-HG-07-031 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
     
  • RFA-HG-07-010: A Data Analysis Center for the Encyclopedia of DNA Elements (ENCODE) Project (U01) (Expired)
     
  • RFA HG-03-003 Determination of All Functional Elements in Human DNA (Expired)
     
  • RFA HG-03-004 Technologies to Find Functional Elements in Genomic DNA (Expired)
     
  • RFA-HG-04-001 Technologies to Find Functional Elements in Genomic DNA. (Expired)
     
  • RFA-HG-07-028 Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R21) (Expired)
     
  • RFA HG-07-029 Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R01) (Expired)

Program Staff

Elise Feingold, Ph.D.
Elise Feingold, Ph.D.
  • Program Director Genome Analysis
  • Division of Genome Sciences
Mike Pazin, Ph.D.
Mike Pazin, Ph.D.
  • Program Director, Functional Genomics
  • Division of Genome Sciences
Daniel A. Gilchrist, Ph.D.
Daniel A. Gilchrist, Ph.D.
  • Program Director Computational Genomics and Data Science
  • Division of Genome Sciences
Michael R. Pagan
Michael R. Pagan
  • Scientific Program Analyst
  • Division of Genome Sciences
Eileen W. Cahill
Eileen W. Cahill
  • Scientific Program Analyst
  • Division of Genome Sciences

Last updated: August 14, 2019