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The accurate miRNA promoter identification in multiple cell types is a fundamental endeavor towards understanding and characterizing the underlying mechanisms of both physiological as well as pathological conditions. DIANA-miRGen v4 (www.microrna.gr\/mirgenv4) provides cell type specific miRNA transcription start sites (TSSs) for over 1500 miRNAs retrieved from the analysis of &amp;gt;1000 cap analysis of gene expression (CAGE) samples corresponding to 133 tissues, cell lines and primary cells available in FANTOM repository. MiRNA TSS locations were associated with transcription factor binding site (TFBSs) annotation, for &amp;gt;280 TFs, derived from analyzing the majority of ENCODE ChIP-Seq datasets. For the first time, clusters of cell types having common miRNA TSSs are characterized and provided through a user friendly interface with multiple layers of customization. DIANA-miRGen v4 significantly improves our understanding of miRNA biogenesis regulation at the transcriptional level by providing a unique integration of high-quality annotations for hundreds of cell specific miRNA promoters with experimentally derived TFBSs.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1060","type":"journal-article","created":{"date-parts":[[2020,11,26]],"date-time":"2020-11-26T20:11:26Z","timestamp":1606421486000},"page":"D151-D159","source":"Crossref","is-referenced-by-count":28,"title":["DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8763-3382","authenticated-orcid":false,"given":"Nikos","family":"Perdikopanis","sequence":"first","affiliation":[{"name":"Hellenic Pasteur Institute, Athens\u00a011521, Greece"},{"name":"Department of Electrical and Computer Engineering, University of Thessaly, Volos\u00a038221, Greece"},{"name":"Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens\u00a015784, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georgios K","family":"Georgakilas","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology, Masaryk University, Kamenice 735\/5, 62500 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dimitris","family":"Grigoriadis","sequence":"additional","affiliation":[{"name":"Hellenic Pasteur Institute, Athens\u00a011521, Greece"},{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vasilis","family":"Pierros","sequence":"additional","affiliation":[{"name":"Hellenic Pasteur Institute, Athens\u00a011521, Greece"},{"name":"Department of Electrical and Computer Engineering, University of Thessaly, Volos\u00a038221, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ioannis","family":"Kavakiotis","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3437-7482","authenticated-orcid":false,"given":"Panagiotis","family":"Alexiou","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology, Masaryk University, Kamenice 735\/5, 62500 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1414-5668","authenticated-orcid":false,"given":"Artemis","family":"Hatzigeorgiou","sequence":"additional","affiliation":[{"name":"Hellenic Pasteur Institute, Athens\u00a011521, Greece"},{"name":"Department of Electrical and Computer Engineering, University of Thessaly, Volos\u00a038221, Greece"},{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,27]]},"reference":[{"key":"2021010313115701100_B1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/S0092-8674(01)00616-X","article-title":"microRNAs: tiny regulators with great potential","volume":"107","author":"Ambros","year":"2001","journal-title":"Cell"},{"key":"2021010313115701100_B2","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"Elife"},{"key":"2021010313115701100_B3","doi-asserted-by":"crossref","first-page":"W169","DOI":"10.1093\/nar\/gkt393","article-title":"DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows","volume":"41","author":"Paraskevopoulou","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2021010313115701100_B4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1146\/annurev.arplant.57.032905.105218","article-title":"MicroRNAs and their regulatory roles in plants","volume":"57","author":"Jones-Rhoades","year":"2006","journal-title":"Annu. 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