GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

2017 | Simon Fishilevich, Ron Nudel, Noa Rappaport, Rotem Hadar, Inbar Plaschkes, Tsippi Iny Stein, Naomi Rosen, Asher Kohn, Michal Twik, Marilyn Safran, Doron Lancet and Dana Cohen
GeneHancer is a novel database that integrates human enhancers and their inferred target genes within the GeneCards framework. The database combines data from four different genome-wide databases: ENCODE, Ensembl regulatory build, FANTOM project, and VISTA Enhancer Browser. It integrates 434,000 reported enhancers into 285,000 candidate enhancers, with 94,000 derived from multiple sources. Each enhancer is assigned a confidence score based on the number of supporting data sources, the presence of transcription factor binding sites, and overlap with ultra-conserved non-coding elements. GeneHancer links enhancers to genes using five methods: eQTLs, eRNA co-expression, TF co-expression, capture Hi-C, and gene-target distance. The database defines 'elite' enhancer-gene relations, which are supported by two or more methods. GeneHancer is integrated into the GeneCards Suite, providing a comprehensive resource for understanding gene regulation and variant interpretation in health and disease. The database is updated regularly and is freely available for educational and research purposes.GeneHancer is a novel database that integrates human enhancers and their inferred target genes within the GeneCards framework. The database combines data from four different genome-wide databases: ENCODE, Ensembl regulatory build, FANTOM project, and VISTA Enhancer Browser. It integrates 434,000 reported enhancers into 285,000 candidate enhancers, with 94,000 derived from multiple sources. Each enhancer is assigned a confidence score based on the number of supporting data sources, the presence of transcription factor binding sites, and overlap with ultra-conserved non-coding elements. GeneHancer links enhancers to genes using five methods: eQTLs, eRNA co-expression, TF co-expression, capture Hi-C, and gene-target distance. The database defines 'elite' enhancer-gene relations, which are supported by two or more methods. GeneHancer is integrated into the GeneCards Suite, providing a comprehensive resource for understanding gene regulation and variant interpretation in health and disease. The database is updated regularly and is freely available for educational and research purposes.
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