CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps

Tom Aharon Hait, Ran Elkon, Ron Shamir

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)e55
JournalNucleic Acids Research
Issue number10
StatePublished - 10 Jun 2022


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