{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:54Z","timestamp":1772138034866,"version":"3.50.1"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,1,13]],"date-time":"2020-01-13T00:00:00Z","timestamp":1578873600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BBSRC Norwich Research Park Biosciences Doctoral Training Partnership","award":["BB\/J014524\/1"],"award-info":[{"award-number":["BB\/J014524\/1"]}]},{"name":"University of East Anglia high-performance computing"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>MicroRNA (miRNA) target prediction algorithms do not generally consider biological context and therefore generic target prediction based on seed binding can lead to a high level of false-positive predictions. Here, we present FilTar, a method that incorporates RNA-Seq data to make miRNA target prediction specific to a given cell type or tissue of interest.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We demonstrate that FilTar can be used to: (i) provide sample specific 3\u2032-UTR reannotation; extending or truncating default annotations based on RNA-Seq read evidence and (ii) filter putative miRNA target predictions by transcript expression level, thus removing putative interactions where the target transcript is not expressed in the tissue or cell line of interest. We test the method on a variety of miRNA transfection datasets and demonstrate increased accuracy versus generic miRNA target prediction methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>FilTar is freely available and can be downloaded from https:\/\/github.com\/TBradley27\/FilTar. The tool is implemented using the Python and R programming languages, and is supported on GNU\/Linux operating systems.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa007","type":"journal-article","created":{"date-parts":[[2020,1,9]],"date-time":"2020-01-09T15:10:08Z","timestamp":1578582608000},"page":"2410-2416","source":"Crossref","is-referenced-by-count":4,"title":["FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0218-5021","authenticated-orcid":false,"given":"Thomas","family":"Bradley","sequence":"first","affiliation":[{"name":"School of Biological Sciences, University of East Anglia , Norwich NR4 7TJ, UK"},{"name":"Earlham Institute, Norwich Research Park , Norwich NR4 7UZ, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4644-1816","authenticated-orcid":false,"given":"Simon","family":"Moxon","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of East Anglia , Norwich NR4 7TJ, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,1,13]]},"reference":[{"key":"2023013110251906700_btaa007-B1","doi-asserted-by":"crossref","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":"2023013110251906700_btaa007-B2","doi-asserted-by":"crossref","first-page":"baw093","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system","volume":"2016","author":"Aken","year":"2016","journal-title":"Database"},{"key":"2023013110251906700_btaa007-B3","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cell.2018.03.006","article-title":"Metazoan microRNAs","volume":"173","author":"Bartel","year":"2018","journal-title":"Cell"},{"key":"2023013110251906700_btaa007-B4","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1101\/gr.1860604","article-title":"An overview of Ensembl","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"key":"2023013110251906700_btaa007-B5","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res"},{"key":"2023013110251906700_btaa007-B6","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. 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