A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The Encyclopedia of DNA Elements (ENCODE) Project was created to enable the scientific and medical communities to interpret the human genome sequence and to use it to understand human biology and improve health. The ENCODE Consortium, a large group of scientists from around the world, uses a variety of experimental methods to identify and describe the regions of the 3 billion base-pair human genome that are important for function. Using experimental, computational, and statistical analyses, we aimed to discover and describe genes, transcripts, and transcriptional regulatory regions, as well as DNA binding proteins that interact with regulatory regions in the genome, including transcription factors, different versions of histones and other markers, and DNA methylation patterns that define states of the genome in various cell types. The ENCODE Project has developed standards for each experiment type to ensure high-quality, reproducible data and novel algorithms to facilitate analysis. All data and derived results are made available through a freely accessible database. This article provides an overview of the complete project and the resources it is generating, as well as examples to illustrate the application of ENCODE data as a user's guide to facilitate the interpretation of the human genome.