EATdb: a database of human enhancers and their putative targets

Abstract

As a class of distal cis-regulatory elements, enhancers are crucial to the regulatory system orchestrating gene transcription. Numerous enhancers have been identified by experiments or predicted by computational models. However, there is a lack of resources collecting these enhancers and their targets, and providing an easy-to-use tool for browsing and searching. Here we built a database named EATdb to help users analysing enhancers in various aspects, such as transcription regulation and SNP annotation. EATdb integrates 560,488 non-redundant human enhancers from three million reported enhancer sequences. Among them, 3584 experimentally validated enhancers are manually curated from 180 publications, which can serve as benchmarks. The rest are predicted by four types of widely used methods. Furthermore, we predict putative target genes for these enhancers by searching the closest transcription start sites by chromosome coordinates, or those in a small physical distance by chromatin interaction. With both methods, we find targets for 94% of the enhancers. Besides, we present function annotations for the enhancers by showing enriched transcription factor binding sites, and their target genes by showing enriched Gene Ontology terms and biological pathways on the website. EATdb is freely available at http://jjwanglab.org/EATdb.