FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
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,...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-05-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-018-1432-2 |
| _version_ | 1811322530300952576 |
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| author | Tom Aharon Hait David Amar Ron Shamir Ran Elkon |
| author_facet | Tom Aharon Hait David Amar Ron Shamir Ran Elkon |
| author_sort | Tom Aharon Hait |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T13:36:40Z |
| format | Article |
| id | doaj.art-35bdbcbd72d44ba386b2937bfb76819c |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-13T13:36:40Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-35bdbcbd72d44ba386b2937bfb76819c2022-12-22T02:44:45ZengBMCGenome Biology1474-760X2018-05-0119111410.1186/s13059-018-1432-2FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter mapTom Aharon Hait0David Amar1Ron Shamir2Ran Elkon3Blavatnik School of Computer Science, Tel Aviv UniversityBlavatnik School of Computer Science, Tel Aviv UniversityBlavatnik School of Computer Science, Tel Aviv UniversityDepartment of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv UniversityAbstract 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.http://link.springer.com/article/10.1186/s13059-018-1432-2EnhancersPromotersGene regulationENCODERoadmapFANTOM5 |
| spellingShingle | Tom Aharon Hait David Amar Ron Shamir Ran Elkon FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map Genome Biology Enhancers Promoters Gene regulation ENCODE Roadmap FANTOM5 |
| title | FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map |
| title_full | FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map |
| title_fullStr | FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map |
| title_full_unstemmed | FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map |
| title_short | FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map |
| title_sort | focs a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer promoter map |
| topic | Enhancers Promoters Gene regulation ENCODE Roadmap FANTOM5 |
| url | http://link.springer.com/article/10.1186/s13059-018-1432-2 |
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