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Though these elements are known to be able to induce either positive or negative transcriptional control, the community has been mostly studying enhancers which amplify transcription initiation, with less emphasis given to silencers which repress gene expression. To facilitate the study of silencers and the investigation of their potential roles in transcriptional control, we developed SilencerDB (http:\/\/health.tsinghua.edu.cn\/silencerdb\/), a comprehensive database of silencers by manually curating silencers from 2300 published articles. The current version, SilencerDB 1.0, contains (1) 33 060 validated silencers from experimental methods, and (ii) 5 045 547 predicted silencers from state-of-the-art machine learning methods. The functionality of SilencerDB includes (a) standardized categorization of silencers in a tree-structured class hierarchy based on species, organ, tissue and cell line and (b) comprehensive annotations of silencers with the nearest gene and potential regulatory genes. SilencerDB, to the best of our knowledge, is the first comprehensive database at this scale dedicated to silencers, with reliable annotations and user-friendly interactive database features. We believe this database has the potential to enable advanced understanding of silencers in regulatory mechanisms and to empower researchers to devise diverse applications of silencers in disease development.<\/jats:p>","DOI":"10.1093\/nar\/gkaa839","type":"journal-article","created":{"date-parts":[[2020,9,18]],"date-time":"2020-09-18T11:35:39Z","timestamp":1600428939000},"page":"D221-D228","source":"Crossref","is-referenced-by-count":58,"title":["SilencerDB: a comprehensive database of silencers"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3426-0890","authenticated-orcid":false,"given":"Wanwen","family":"Zeng","sequence":"first","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China"},{"name":"College of Software, Nankai University, Tianjin 300071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengquan","family":"Chen","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuejian","family":"Cui","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyang","family":"Chen","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zijing","family":"Gao","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Jiang","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,10,12]]},"reference":[{"key":"2021010313125055200_B1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.biosystems.2015.10.002","article-title":"The identification of cis-regulatory elements: A review from a machine learning perspective","volume":"138","author":"Li","year":"2015","journal-title":"Biosystems"},{"key":"2021010313125055200_B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1146\/annurev-genom-091416-035537","article-title":"Gene regulatory elements, major drivers of human disease","volume":"18","author":"Chatterjee","year":"2017","journal-title":"Annu. 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