{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T01:51:27Z","timestamp":1767923487046,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T00:00:00Z","timestamp":1731974400000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FCT\u2014Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia I.P"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>APAtizer is a tool designed to analyze alternative polyadenylation events on RNA-sequencing data. The tool handles different file formats, including BAM, htseq, and DaPars bedGraph files. It provides a user-friendly interface that allows users to generate informative visualizations, including Volcano plots, heatmaps, and gene lists. These outputs allow the user to retrieve useful biological insights such as the occurrence of polyadenylation events when comparing two biological conditions. In addition, it can perform differential gene expression, gene ontology analysis, visualization of Venn diagram intersections, and correlation analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and example case studies for APAtizer are available at https:\/\/github.com\/GeneRegulationi3S\/APAtizer\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae689","type":"journal-article","created":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T06:34:53Z","timestamp":1731998093000},"source":"Crossref","is-referenced-by-count":1,"title":["APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data"],"prefix":"10.1093","volume":"40","author":[{"given":"Bruno","family":"Sousa","sequence":"first","affiliation":[{"name":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]},{"name":"FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto, 4169-007,","place":["Portugal"]}]},{"given":"Maria","family":"Bessa","sequence":"additional","affiliation":[{"name":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]}]},{"given":"Filipa L","family":"de Mendon\u00e7a","sequence":"additional","affiliation":[{"name":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]}]},{"given":"Pedro G","family":"Ferreira","sequence":"additional","affiliation":[{"name":"FCUP\u2014Faculdade de Ci\u00eancias, Universidade do Porto , Porto, 4169-007,","place":["Portugal"]},{"name":"Laboratory of Artificial Intelligence and Decision Support, Institute for Systems and Computer Engineering Technology and Science , Porto, 4200-465,","place":["Portugal"]}]},{"given":"Alexandra","family":"Moreira","sequence":"additional","affiliation":[{"name":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]},{"name":"ICBAS\u2014Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar, Universidade do Porto , Porto, 4050-313,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4149-4310","authenticated-orcid":false,"given":"Isabel","family":"Pereira-Castro","sequence":"additional","affiliation":[{"name":"Gene Regulation Group, i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto, 4200-135,","place":["Portugal"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,18]]},"reference":[{"key":"2024112717335122700_btae689-B1","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1261\/rna.078886.121","article-title":"Shortening of 3\u02b9 UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism","volume":"27","author":"Burri","year":"2021","journal-title":"RNA"},{"key":"2024112717335122700_btae689-B2","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1471-2105-12-35","article-title":"VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R","volume":"12","author":"Chen","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2024112717335122700_btae689-B3","doi-asserted-by":"crossref","first-page":"D1027","DOI":"10.1093\/nar\/gkx892","article-title":"TC3A: the cancer 3\u02b9 UTR Atlas","volume":"46","author":"Feng","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024112717335122700_btae689-B4","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/nmeth.2288","article-title":"Analysis of alternative cleavage and polyadenylation by 3\u2032 region extraction and deep sequencing","volume":"10","author":"Hoque","year":"2013","journal-title":"Nat Methods"},{"key":"2024112717335122700_btae689-B5","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/s41586-018-0465-8","article-title":"Widespread intronic polyadenylation inactivates tumor suppressor in leukemia","volume":"561","author":"Lee","year":"2018","journal-title":"Nature"},{"key":"2024112717335122700_btae689-B6","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1038\/s41588-021-00864-5","article-title":"An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability","volume":"53","author":"Li","year":"2021","journal-title":"Nat Genet"},{"key":"2024112717335122700_btae689-B7","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2024112717335122700_btae689-B8","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1146\/annurev-genet-120116-024704","article-title":"Regulation by 3\u02b9-untranslated regions","volume":"51","author":"Mayr","year":"2017","journal-title":"Annu Rev Genet"},{"key":"2024112717335122700_btae689-B9","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1016\/j.cell.2009.06.016","article-title":"Widespread shortening of 3\u02b9UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells","volume":"138","author":"Mayr","year":"2009","journal-title":"Cell"},{"key":"2024112717335122700_btae689-B10","doi-asserted-by":"crossref","first-page":"e1653","DOI":"10.1002\/wrna.1653","article-title":"On the function and relevance of alternative 3\u02b9-UTRs in gene expression regulation","volume":"12","author":"Pereira-Castro","year":"2021","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2024112717335122700_btae689-B11","doi-asserted-by":"crossref","first-page":"3907","DOI":"10.1093\/bioinformatics\/btaa266","article-title":"APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms","volume":"36","author":"Wang","year":"2020","journal-title":"Bioinformatics"},{"key":"2024112717335122700_btae689-B12","doi-asserted-by":"crossref","first-page":"1182525","DOI":"10.3389\/fimmu.2023.1182525","article-title":"Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages","volume":"14","author":"Wilton","year":"2023","journal-title":"Front Immunol"},{"key":"2024112717335122700_btae689-B13","first-page":"100141","article-title":"ClusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"2024112717335122700_btae689-B15","doi-asserted-by":"crossref","first-page":"D116","DOI":"10.1093\/nar\/gki055","article-title":"PolyA_DB: a database for mammalian MRNA polyadenylation","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae689\/60744093\/btae689.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae689\/60833202\/btae689.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae689\/60833202\/btae689.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T17:34:02Z","timestamp":1732728842000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae689\/7903284"}},"subtitle":[],"editor":[{"given":"Macha","family":"Nikolski","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,11,1]]},"references-count":14,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2024,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae689","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,11]]},"published":{"date-parts":[[2024,11,1]]},"article-number":"btae689"}}