ENCODE Project at NHGRI    Encyclopedia of DNA Elements

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  About ENCODE Data

The Encyclopedia of DNA Elements (ENCODE) 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.

Click to enlarge ENCODE data are now available for the entire human genome. All ENCODE data are free and available for immediate use via :

To search for ENCODE data related to your area of interest and set up a browser view, use the UCSC Experiment Matrix or Track Search tool (Advanced features). The Experiment List (Human) and Experiment List (Mouse) links provide comprehensive listings of ENCODE data that is released or in preparation.

All ENCODE data is freely available for download and analysis. However, before publishing research that uses ENCODE data, please read the ENCODE Data Release Policy, which places some restrictions on publication use of data for nine months following data release.    Read more about ENCODE data at UCSC.


17 April 2014 - New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE

The latest Transcription Factor ChIP-seq track has been enhanced with the display of Factorbook motifs. Within a cluster, a green highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the corresponding factor. Along with the ability to suppress motif highlights and cell abbreviations, the track configuration page now also enables the filtering of factors.

The newly added Genome Segmentations from ENCODE tracks display multivariate genome-segmentation performed on six human cell types (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data. In total, twenty-five states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. These Genome Segmentations are the same data as found in the Analysis Working Group Hub, but now hosted natively in the Browser with enhanced filtering capability where desired segmented states can be selected using the 'Filter by Segment Type' control on the track configuration page.

12 Sept 2013 - New UDR ENCODE Download Method Available

The UCSC Genome Browser is pleased to offer a new download protocol to use when downloading large sets of files from our download servers: UDR (UDT Enabled Rsync). UDR utilizes rsync as the transport mechanism, but sends the data over the UDT protocol, which enables huge amounts of data to be downloaded more efficiently over long distances. Read more.

25 July 2013 - BLUEPRINT Epigenome Data Hub and Quick Reference PDF Now Available

We are pleased to announce the addition of the BLUEPRINT Epigenomics Data Hub on the UCSC Genome Browser through our Public Hubs function. Also the ENCODE Quick Reference Card is now available in PDF courtesy of OpenHelix on the ENCODE Education and Outreach page. Read more.

28 May 2013 - ENCODE portal changes: New Link to NHGRI Tutorials, New External Software Tools Page, Updates to Publications including New 2013 Consortium Papers Section

The ENCODE portal was updated to include informative new and expanded pages. Read more.

  Conditions of Use

The sequence and annotation data displayed in the Genome Browser are freely available for academic, nonprofit, and personal use with the following conditions: