The UCSC Genome Browser displays data gathered through the Encyclopedia of DNA Elements (ENCODE) project of the National Human Genome Research Institute (NHGRI), which aims to build a comprehensive parts list of the functional elements throughout the human genome. The project is driven by a highly interactive public research consortium. The University of California Santa Cruz (UCSC) is the official data coordination center for the ENCODE project, supporting data submission, organization, storage, retrieval, and visualization. Ensembl, a joint project of EBI and the Wellcome Trust Sanger Institute, coordinates much of the analysis effort.

To access the ENCODE data in the Genome Browser, go to your region of interest in the human genome and turn on the ENCODE-related tracks. See the Genome Browser User's Guide for information about displaying tracks and navigating in the Genome Browser. If you would like to submit your ENCODE data to the Genome Browser, click the Submission link for more information.

To view data and information from the ENCODE project pilot phase, which targeted regions amounting to about 1% of the human genome, click the ENCODE Pilot Project link.

We thank NHGRI and those who have contributed 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. Click the Contributors link for a complete list of the ENCODE data contributors and the UCSC staff who develop and maintain this website.

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

The ENCODE browser for UCSC human genome assembly hg18 (NCBI Build 36) is now available. You can access the browser directly by clicking here or via the Regions (hg18) link on the ENCODE Pilot Project 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 Genome Browser wiki.

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).

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.