ENCODE: Encyclopedia of DNA Elements



The ENCODE (Encyclopedia of DNA Elements) Consortium is 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 functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

Image credits: Darryl Leja (NHGRI), Ian Dunham (EBI), Michael Pazin (NHGRI)




Quick Start

To find and download ENCODE Consortium data:

Additional help using the ENCODE Portal:

ENCODE investigators employ a variety of assays and methods to identify functional elements. The discovery and annotation of gene elements is accomplished primarily by sequencing a diverse range of RNA sources, comparative genomics, integrative bioinformatic methods, and human curation. Regulatory elements are typically investigated through DNA hypersensitivity assays, assays of DNA methylation, and immunoprecipitation (IP) of proteins that interact with DNA and RNA, i.e., modified histones, transcription factors, chromatin regulators, and RNA-binding proteins, followed by sequencing.

All ENCODE data is freely available for download and analysis. Please refer to the ENCODE Data Release Policy


August 25th, 2016: 111 Annotation File Sets of promoter-like and enhancer-like regions have been released! [read more]

August 3rd, 2016: With collaborations from the DAC (Data Analysis Center), a total of 336 Annotation File Sets of promoter-like and enhancer-like regions have been released! [read more]

August 1st, 2016: 191 new ENCODE experiments released in July - check them all out here.

July 21st, 2016: Check out the latest GGR release from the Reddy lab, here on the portal, 84 ChIP-seq expts in A549 +/- dex treatment.

July 20th, 2016: Mouse e10.5 histone ChIP-seq dataset from from the Ren lab available on the portal here.

July 6th, 2016: 367 modERN experiments released today! [read more]

June 29th, 2016: 182 new experiments were released in June 2016! [read more]

June 13th, 2016: ENCODE's own Gene Yeo will be chairing “Computational Methods for RNA Data Analysis” and running a workshop with Yoseph Barash at RNA 2016 (http://www2.convention.co.jp/rna2016/ )

See our news archive for additional news and updates.