FOCS: A novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map

Tom Aharon Hait, David Amar, Ron Shamir*, Ran Elkon

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer-promoter links. We show that current enhancer-promoter inference methods produce a high rate of false positive links. We introduce FOCS, a new inference method, and by benchmarking against ChIA-PET, HiChIP, and eQTL data show that it results in lower false discovery rates and at the same time higher inference power. By applying FOCS to 2630 samples taken from ENCODE, Roadmap Epigenomics, FANTOM5, and a new compendium of GRO-seq samples, we provide extensive enhancer-promotor maps (http://acgt.cs.tau.ac.il/focs ). We illustrate the usability of our maps for deriving biological hypotheses.

Original languageEnglish
Article number56
JournalGenome Biology
Volume19
Issue number1
DOIs
StatePublished - 1 May 2018

Keywords

  • ChIA-PET
  • ENCODE
  • EQTL
  • ERNA
  • Enhancers
  • FANTOM5
  • GRO-seq
  • Gene regulation
  • Promoters
  • Roadmap

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