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How to correctly identify the gene TSS and the core promoter is essential for our understanding of the transcriptional regulation of genes. As a complement to conventional experimental methods, computational techniques with easy-to-use platforms as essential bioinformatics tools can be effectively applied to annotate the functions and physiological roles of promoters. In this work, we propose a deep learning-based method termed Depicter (Deep learning for predicting promoter), for identifying three specific types of promoters, i.e. promoter sequences with the TATA-box (TATA model), promoter sequences without the TATA-box (non-TATA model), and indistinguishable promoters (TATA and non-TATA model). Depicter is developed based on an up-to-date, species-specific dataset which includes Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana promoters. A convolutional neural network coupled with capsule layers is proposed to train and optimize the prediction model of Depicter. Extensive benchmarking and independent tests demonstrate that Depicter achieves an improved predictive performance compared with several state-of-the-art methods. The webserver of Depicter is implemented and freely accessible at https:\/\/depicter.erc.monash.edu\/.<\/jats:p>","DOI":"10.1093\/bib\/bbaa299","type":"journal-article","created":{"date-parts":[[2020,10,8]],"date-time":"2020-10-08T19:09:39Z","timestamp":1602184179000},"source":"Crossref","is-referenced-by-count":52,"title":["Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks"],"prefix":"10.1093","volume":"22","author":[{"given":"Yan","family":"Zhu","sequence":"first","affiliation":[{"name":"School of Science, Dalian Maritime University, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5216-3213","authenticated-orcid":false,"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongxu","family":"Xiang","sequence":"additional","affiliation":[{"name":"Northwest A&F University, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8031-9086","authenticated-orcid":false,"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cangzhi","family":"Jia","sequence":"additional","affiliation":[{"name":"College of Science, Dalian Maritime University"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,11,24]]},"reference":[{"key":"2021101812514421800_ref1","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1101\/gad.303149.117","article-title":"The punctilious RNA polymerase II core promoter","volume":"31","author":"Ngoc","year":"2017","journal-title":"Gene Dev"},{"key":"2021101812514421800_ref2","doi-asserted-by":"crossref","first-page":"4378","DOI":"10.1093\/nar\/gki753","article-title":"Human POL II promoter prediction: time series descriptors and machine learning (vol 33, pg 1332, 2005)","volume":"33","author":"Gangal","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2021101812514421800_ref3","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.ygeno.2009.08.011","article-title":"Structural differentiation of the three eukaryotic RNA polymerases","volume":"94","author":"Carter","year":"2009","journal-title":"Genomics"},{"key":"2021101812514421800_ref4","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.omtn.2018.05.001","article-title":"RNA polymerase II activity of type 3 pol III promoters","volume":"12","author":"Gao","year":"2018","journal-title":"Mol Ther-Nucl Acids"},{"key":"2021101812514421800_ref5","doi-asserted-by":"crossref","first-page":"100","DOI":"10.2174\/1574893614666181119121916","article-title":"Dysfunctional mechanism of liver cancer mediated by transcription factor and non-coding RNA","volume":"14","author":"Zeng","year":"2019","journal-title":"Curr Bioinform"},{"key":"2021101812514421800_ref6","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbl003","article-title":"Advances in the exon-intron database (EID)","volume":"7","author":"Shepelev","year":"2006","journal-title":"Brief Bioinform"},{"key":"2021101812514421800_ref7","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/emm.2002.36","article-title":"The DPE, a core promoter element for transcription by RNA polymerase II","volume":"34","author":"Kadonaga","year":"2002","journal-title":"Exp Mol Med"},{"key":"2021101812514421800_ref8","doi-asserted-by":"crossref","first-page":"5943","DOI":"10.1093\/nar\/gkl608","article-title":"Identification of core promoter modules in drosophila and their application in accurate transcription start site prediction","volume":"34","author":"Ohler","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2021101812514421800_ref9","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/nmeth937","article-title":"Rational design of a super core promoter that enhances gene expression","volume":"3","author":"Juven-Gershon","year":"2006","journal-title":"Nat Methods"},{"key":"2021101812514421800_ref10","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1002\/2211-5463.12166","article-title":"DNA structural features of eukaryotic TATA-containing and TATA-less promoters","volume":"7","author":"Yella","year":"2017","journal-title":"Febs Open Bio"},{"key":"2021101812514421800_ref11","doi-asserted-by":"crossref","first-page":"2418","DOI":"10.1101\/gad.342405","article-title":"Roberts SGE. 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