CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps. Issue 10 (31st January 2022)

• Record Type: Journal Article
• Authors: Hait, Tom Aharon; Elkon, Ran; Shamir, Ron
• Is Part Of: Nucleic acids research. Volume 50:Issue 10(2022)
• Page Start: e55
• Page End: e55
• Publication Date: 2022-01-31
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac048
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Spatiotemporal gene expression patterns are governed to a large extent by the activity of enhancer elements, which engage in physical contacts with their target genes. Identification of enhancer–promoter (EP) links that are functional only in a specific subset of cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS (cell type FOCS), a statistical inference method that uses linear mixed effect models to infer EP links that show marked activity only in a single or a small subset of cell types out of a large panel of probed cell types. Analyzing 808 samples from FANTOM5, covering 472 cell lines, primary cells and tissues, CT-FOCS inferred such EP links more accurately than recent state-of-the-art methods. Furthermore, we show that strictly cell type-specific EP links are very uncommon in the human genome.