The Encyclopedia of DNA Elements (ENCODE) project entails identifying all the functional elements in the human and mouse genome. It is a public research consortium that has produced and stored large amount of gene study data on a freely accessible database called the ENCODE Portal. The ENCODE Portal also holds data from modENCODE and collectively from the RoadMap Epigenomics and Genomics of Gene Regulation projects.

The ENCODE Project started in 2003, with the ENCODE Pilot Project focusing on 1% of the human genome. Following the pilot project were 2 additional phases (ENCODE 2 and ENCODE 3), that laid emphasis on whole genome analysis of human and mouse genomes. Under the modENCODE project, whole genome analysis  in roundworms and fruitflies was carried out.