ArticleGenome biology2018
FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance.Genome medicine · 2021Pooled it
- Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies.Genome biology · 2026Article
- Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data.Bioinformatics (Oxford, England) · 2026Article
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Network Analysis of Enhancer-Promoter Interactions Highlights Cell-Type-Specific Mechanisms of Transcriptional Regulation Variation.International journal of molecular sciences · 2024Article
- Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.Nucleic acids research · 2024Article
- O-GlcNAcylation controls pro-fibrotic transcriptional regulatory signaling in myofibroblasts.Cell death & disease · 2024Article
- CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms.Genome biology · 2023Article
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
- Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning.Nature biomedical engineering · 2023Article
- A unifying statistical framework to discover disease genes from GWASs.Cell genomics · 2023Article
- Enhancer/gene relationships: Need for more reliable genome-wide reference sets.Frontiers in bioinformatics · 2023Review
- Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis.Nature communications · 2022Article
- CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps.Nucleic acids research · 2022Article
- DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data.Science advances · 2022Article
- Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.Genome biology · 2022Article
- Classification of non-coding variants with high pathogenic impact.PLoS genetics · 2022Article
- A framework to score the effects of structural variants in health and disease.Genome research · 2022Article
- GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data.Nucleic acids research · 2022Article
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Authors and funding
4 authors.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.