RT Journal Article SR Electronic T1 CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps JF bioRxiv FD Cold Spring Harbor Laboratory SP 707158 DO 10.1101/707158 A1 Hait, Tom Aharon A1 Elkon, Ran A1 Shamir, Ron YR 2021 UL http://biorxiv.org/content/early/2021/09/14/707158.abstract AB 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, 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.Competing Interest StatementThe authors have declared no competing interest.