Abstract
The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome. This phase of the project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements. To date, results for almost 5000 experiments have been released for use by the scientific community. These data are available for searching, visualization and download at the new ENCODE Portal (www.encodeproject.org). The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance. In addition, it is a flexible platform that allows integration of genomic data from multiple projects. The portal experience was designed to improve access to ENCODE data by relying on metadata that allow reusability and reproducibility of the experiments.
Highlights
The Encyclopedia of DNA Elements (ENCODE) Project began as a Pilot Project on 1% of the human genome [1,2]
The ENCODE Project continues to create a comprehensive catalog of gene elements and functional elements in the human and mouse genomes by measuring RNA expression levels, identifying proteins that interact with RNA and DNA, measuring the levels of DNA methylation and identifying regions of DNA hypersensitivity
These data generated by ENCODE Consortium members are submitted to the ENCODE Data Coordination Center (DCC) whose primary task is to curate, process and validate the data in preparation for release to the scientific community
Summary
The Encyclopedia of DNA Elements (ENCODE) Project began as a Pilot Project on 1% of the human genome [1,2]. These data are made available at the ENCODE Portal (www.encodeproject.org), created by the DCC, and are distributed through the UCSC genome browser, GEO and Ensembl and used extensively as a community resource [6,7,8,9,10,11].
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