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bioRxiv · 10.1101/707158

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

Hait, T. A.·Elkon, R.·Shamir, R.
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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, 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.

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Hait, T. A., Elkon, R., Shamir, R.. 2019-07-18. CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps. https://doi.org/10.1101/707158

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