PT  - JOURNAL ARTICLE
AU  - Hait, Tom Aharon
AU  - Elkon, Ran
AU  - Shamir, Ron
TI  - CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps
AID  - 10.1101/707158
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 707158
4099  - http://biorxiv.org/content/early/2021/09/14/707158.short
4100  - http://biorxiv.org/content/early/2021/09/14/707158.full
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.