Dataset Information

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.

ABSTRACT: BACKGROUND:Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. RESULTS:To facilitate the development of computational methods for predicting target genes, we develop a Benchmark of candidate Enhancer-Gene Interactions (BENGI) by integrating the recently developed Registry of cCREs with experimentally derived genomic interactions. We use BENGI to test several published computational methods for linking enhancers with genes, including signal correlation and the TargetFinder and PEP supervised learning methods. We find that while TargetFinder is the best-performing method, it is only modestly better than a baseline distance method for most benchmark datasets when trained and tested with the same cell type and that TargetFinder often does not outperform the distance method when applied across cell types. CONCLUSIONS:Our results suggest that current computational methods need to be improved and that BENGI presents a useful framework for method development and testing.

SUBMITTER: Moore JE

PROVIDER: S-EPMC6977301 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.

Moore Jill E JE Pratt Henry E HE Purcaro Michael J MJ Weng Zhiping Z

Genome biology 20200122 1

<h4>Background</h4>Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes.<h4>Results</h4>To facilitate the development of computational methods for predicting target genes, we develop a Benchmark of candidate Enhancer-Gene Interactions (BENGI) by integrating the recently developed Registry of cCREs with experimentally derived genomic interactio ...[more]

PMID: 31969180

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Dataset Information

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.

Publications

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.

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