Title |
FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
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Published in |
Genome Biology, May 2018
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DOI | 10.1186/s13059-018-1432-2 |
Pubmed ID | |
Authors |
Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon |
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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United States | 17 | 40% |
United Kingdom | 5 | 12% |
Israel | 2 | 5% |
Norway | 1 | 2% |
France | 1 | 2% |
Germany | 1 | 2% |
Australia | 1 | 2% |
Japan | 1 | 2% |
Unknown | 13 | 31% |
Demographic breakdown
Type | Count | As % |
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Scientists | 23 | 55% |
Members of the public | 18 | 43% |
Science communicators (journalists, bloggers, editors) | 1 | 2% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 129 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 30 | 23% |
Researcher | 26 | 20% |
Student > Master | 19 | 15% |
Student > Bachelor | 10 | 8% |
Student > Postgraduate | 6 | 5% |
Other | 17 | 13% |
Unknown | 21 | 16% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 42 | 33% |
Agricultural and Biological Sciences | 32 | 25% |
Medicine and Dentistry | 9 | 7% |
Computer Science | 6 | 5% |
Engineering | 4 | 3% |
Other | 9 | 7% |
Unknown | 27 | 21% |