Welcome to the UCSC ENCODE Project portal. This site contains information related to the ENCODE project at NHGRI. The University of California Santa Cruz (UCSC) manages the official repository of sequence-related data for the ENCODE Consortium and supports the coordination of data submission, storage, retrieval, and visualization. Ensembl, a joint project of EBI and the Wellcome Trust Sanger Institute, coordinates much of the analysis effort.

To view the ENCODE data on the NCBI Build 36 human assembly (March 2006), click the Regions (hg18) link in the left sidebar menu. To view data on the previous ENCODE reference assembly (May 2004, hg17, Build 35) that was used as the basis of the June 2007 Nature and Genome Research publications, click the Regions (hg17) link.

The data from ENCODE contributors that has been released by UCSC is listed on the release log page. Primary data for ENCODE is available from the NCBI GEO and EBI ArrayExpress public array data repositories. Ensembl provides an ENCODE resource page, and NHGRI provides the ENCODEdb portal.

We'd like to thank NHGRI and the contributors of annotations and analyses to this project. This portal is maintained by the UCSC Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering (CBSE) at UCSC. The individuals who develop and maintain this website include Kate Rosenbloom, Rachel Harte, Ting Wang, Jim Kent, and the UCSC Genome Bioinformatics staff, with input from Daryl Thomas.

To go to the main UCSC Genome Browser site that provides access to sequence and annotation data for a large collection of genome assemblies, click here.

4 Oct. 2007 - ENCODE Genome Browser Released for hg18 Assembly

The ENCODE browser for UCSC human genome assembly hg18 (NCBI Build 36) is now available. You can access the browser directly at http://genome.ucsc.edu/ENCODE/encode.hg18.html or by clicking the ENCODE link on the Genome Browser home page, then selecting the Regions (hg18) item in the sidebar menu on the ENCODE portal page.

The hg18 ENCODE browser includes 540 data tables in 59 browser tracks that were migrated from the hg17 browser. The hg17 data coordinates were converted to hg18 coordinates using the UCSC liftOver process.

To improve the accessibility of the data, related ENCODE tracks have been gathered into new configuration groupings ("super-tracks") that can be displayed or hidden using a single visiblity control. We have also reduced the number of track groups and have modified some of the group names for clarity.

The following table summarizes the data currently present in the hg18 ENCODE browser:

Group	Super-tracks	Tracks	Tables
Regions and Genes	2	12	73
Transcription	2	11	67
Chromatin Immunoprecipitation	8	28	349
Chromatin Structure	2	8	51

Note that the Variation and Comparative Genomics data were not lifted during this migration; instead, they will be replaced by new data. The first ENCODE MSA alignment for hg18 (TBA) is currently in progress on the UCSC development server.

During the migration, ENCODE tracks with whole-genome data were moved into the standard browser track groups. These include the GIS PET and UCSD/LI TAF1 tracks. Future submissions of whole-genome ENCODE data will be loaded directly into the standard track groups.

We have expanded the ENCODE downloads site to include original data for all "wiggle" datasets. These data files now have filename extensions indicating the wiggle input format (fixed step, variable step, or bedGraph).

You can find a description of the migration project and full details of the tables, tracks, and super-tracks available at the UCSC ENCODE portal on the UCSC genomeWiki.

The UCSC team members who contributed to this effort were: Andy Pohl (data conversion and database loading), Ting Wang and Donna Karolchik (super-track documentation), Bob Kuhn (portal updates), Brooke Rhead, Kayla Smith, and Ann Zweig (quality assurance), and Kate Rosenbloom (super-track development, project management).

12 Jun. 2007 - Spring 2007 ENCODE News: Between January and May of 2007, several new or upgraded data tracks were released by UCSC. Read more.

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

• The general Conditions of Use for the UCSC Genome Browser apply.
• The ENCODE-specific conditions of use are still being developed and will be displayed here in the future. Until then, please contact us for the conditions on the use of this data.