Database, 2017, 1–17 doi: 10.1093/database/bax028 Original article Original article GeneHancer: genome-wide integration of enhancers and target genes in GeneCards Simon Fishilevich1,†, Ron Nudel1,†, Noa Rappaport1, Rotem Hadar1, Inbar Plaschkes1, Tsippi Iny Stein1, Naomi Rosen1, Asher Kohn2, Michal Twik1, Marilyn Safran1, Doron Lancet1,* and Dana Cohen1,* 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel and 2LifeMap Sciences Inc, Marshfield, MA 02050, USA *Corresponding author: Tel: +972-54-4682521; Fax: +972-8-9344487. Email:
[email protected] Correspondence may also be addressed to Dana Cohen. Email:
[email protected] †These authors contributed equally to this work. Citation details: Fishilevich,S., Nudel,R., Rappaport,N. et al. GeneHancer: genome-wide integration of enhancers and tar- get genes in GeneCards. Database (2017) Vol. 2017: article ID bax028; doi:10.1093/database/bax028 Received 15 November 2016; Revised 9 March 2017; Accepted 10 March 2017 Abstract A major challenge in understanding gene regulation is the unequivocal identification of enhancer elements and uncovering their connections to genes. We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards. First, we integrated a total of 434 000 reported enhancers from four different genome-wide databases: the Encyclopedia of DNA Elements (ENCODE), the Ensembl regulatory build, the functional annotation of the mammalian genome (FANTOM) project and the VISTA Enhancer Browser. Employing an integration algorithm that aims to re- move redundancy, GeneHancer portrays 285 000 integrated candidate enhancers (cover- ing 12.4% of the genome), 94 000 of which are derived from more than one source, and each assigned an annotation-derived confidence score.