{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T04:06:41Z","timestamp":1773806801909,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,4,22]],"date-time":"2020-04-22T00:00:00Z","timestamp":1587513600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM084089"],"award-info":[{"award-number":["GM084089"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM129069"],"award-info":[{"award-number":["GM129069"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Most eukaryotic genes produce alternative polyadenylation (APA) isoforms. APA is dynamically regulated under different growth and differentiation conditions. Here, we present a bioinformatics package, named APAlyzer, for examining 3\u2032UTR APA, intronic APA and gene expression changes using RNA-seq data and annotated polyadenylation sites in the PolyA_DB database. Using APAlyzer and data from the GTEx database, we present APA profiles across human tissues.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>APAlyzer is freely available at https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/APAlyzer.html as an R\/Bioconductor package.<\/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\/btaa266","type":"journal-article","created":{"date-parts":[[2020,4,16]],"date-time":"2020-04-16T11:10:23Z","timestamp":1587035423000},"page":"3907-3909","source":"Crossref","is-referenced-by-count":69,"title":["APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms"],"prefix":"10.1093","volume":"36","author":[{"given":"Ruijia","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Microbiology , Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA"},{"name":"QIAGEN Digital Insights , Concord, MA 01742, USA"}]},{"given":"Bin","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Microbiology , Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA"},{"name":"Program in Gene Expression and Regulation, and Center for Systems and Computational Biology, Wistar Institute , Philadelphia, PA 19104, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,4,22]]},"reference":[{"key":"2023063011474366500_btaa266-B1","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/1471-2164-7-189","article-title":"Conservation of alternative polyadenylation patterns in mammalian genes","volume":"7","author":"Ara","year":"2006","journal-title":"BMC Genomics"},{"key":"2023063011474366500_btaa266-B2","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.cels.2019.07.011","article-title":"mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-seq","volume":"9","author":"Cass","year":"2019","journal-title":"Cell Syst"},{"key":"2023063011474366500_btaa266-B1494470","doi-asserted-by":"crossref","first-page":"6758","DOI":"10.1073\/pnas.0701266104","article-title":"Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus","volume":"104","author":"Graham","year":"2007","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2023063011474366500_btaa266-B4","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/s41576-019-0145-z","article-title":"Alternative cleavage and polyadenylation in health and disease","volume":"20","author":"Gruber","year":"2019","journal-title":"Nat. Rev. Genet"},{"key":"2023063011474366500_btaa266-B5","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","year":"2017","journal-title":"Nature"},{"key":"2023063011474366500_btaa266-B6","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s40484-018-0148-3","article-title":"Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data","volume":"6","author":"Guvenek","year":"2018","journal-title":"Quant. Biol"},{"key":"2023063011474366500_btaa266-B7","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13059-018-1414-4","article-title":"QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data","volume":"19","author":"Ha","year":"2018","journal-title":"Genome Biol"},{"key":"2023063011474366500_btaa266-B9","doi-asserted-by":"crossref","first-page":"7028","DOI":"10.1073\/pnas.0900028106","article-title":"Progressive lengthening of 3\u2032 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development","volume":"106","author":"Ji","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023063011474366500_btaa266-B10","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nmeth.1528","article-title":"Analysis and design of RNA sequencing experiments for identifying isoform regulation","volume":"7","author":"Katz","year":"2010","journal-title":"Nat. Methods"},{"key":"2023063011474366500_btaa266-B11","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1126\/science.1155390","article-title":"Proliferating cells express mRNAs with shortened 3\u2032 untranslated regions and fewer microRNA target sites","volume":"320","author":"Sandberg","year":"2008","journal-title":"Science (New York, N.Y.)"},{"key":"2023063011474366500_btaa266-B12","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1261\/rna.2581711","article-title":"Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq","volume":"17","author":"Shepard","year":"2011","journal-title":"RNA (New York, N.Y.)"},{"key":"2023063011474366500_btaa266-B13","doi-asserted-by":"crossref","first-page":"1716","DOI":"10.1038\/s41467-018-04112-z","article-title":"Widespread intronic polyadenylation diversifies immune cell transcriptomes","volume":"9","author":"Singh","year":"2018","journal-title":"Nat. Commun"},{"key":"2023063011474366500_btaa266-B15","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/nrm.2016.116","article-title":"Alternative polyadenylation of mRNA precursors","volume":"18","author":"Tian","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol"},{"key":"2023063011474366500_btaa266-B16","doi-asserted-by":"crossref","first-page":"D315","DOI":"10.1093\/nar\/gkx1000","article-title":"PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes","volume":"46","author":"Wang","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023063011474366500_btaa266-B17","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1101\/gr.237826.118","article-title":"A compendium of conserved cleavage and polyadenylation events in mammalian genes","volume":"28","author":"Wang","year":"2018","journal-title":"Genome Res"},{"key":"2023063011474366500_btaa266-B18","doi-asserted-by":"crossref","first-page":"5274","DOI":"10.1038\/ncomms6274","article-title":"Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3\u2032-UTR landscape across seven tumour types","volume":"5","author":"Xia","year":"2014","journal-title":"Nat. Commun"},{"key":"2023063011474366500_btaa266-B19","doi-asserted-by":"crossref","first-page":"R100","DOI":"10.1186\/gb-2005-6-12-r100","article-title":"Biased alternative polyadenylation in human tissues","volume":"6","author":"Zhang","year":"2005","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa266\/33183709\/btaa266.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/12\/3907\/50748332\/bioinformatics_36_12_3907.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/12\/3907\/50748332\/bioinformatics_36_12_3907.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T11:48:36Z","timestamp":1688125716000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/12\/3907\/5823886"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,4,22]]},"references-count":17,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2020,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa266","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,6,15]]},"published":{"date-parts":[[2020,4,22]]}}}