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APA in the 3\u2032-untranslated region (3\u2032-UTR) of mRNA produces transcripts with shorter or longer 3\u2032-UTR. Often, 3\u2032-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3\u2032-UTR APA is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. Current bioinformatics pipelines have limited capability in profiling 3\u2032-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3\u2032-UTR APA only using RNA-seq read coverage, causing false positive identifications. To overcome these limitations, we developed APA-Scan, a robust program that identifies 3\u2032-UTR APA events and visualizes the RNA-seq short-read coverage with gene annotations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      APA-Scan utilizes either predicted or experimentally validated actionable polyadenylation signals as a reference for polyadenylation sites and calculates the quantity of long and short 3\u2032-UTR transcripts in the RNA-seq data. APA-Scan works in three major steps: (i) calculate the read coverage of the 3\u2032-UTR regions of genes; (ii) identify the potential APA sites and evaluate the significance of the events among two biological conditions; (iii) graphical representation of user specific event with 3\u2032-UTR annotation and read coverage on the 3\u2032-UTR regions. APA-Scan is implemented in Python3. Source code and a comprehensive user\u2019s manual are freely available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/compbiolabucf\/APA-Scan\">https:\/\/github.com\/compbiolabucf\/APA-Scan<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Result<\/jats:title>\n                    <jats:p>APA-Scan was applied to both simulated and real RNA-seq datasets and compared with two widely used baselines DaPars and APAtrap. In simulation APA-Scan significantly improved the accuracy of 3\u2032-UTR APA identification compared to the other baselines. The performance of APA-Scan was also validated by 3\u2032-end-seq data and qPCR on mouse embryonic fibroblast cells. The experiments confirm that APA-Scan can detect unannotated 3\u2032-UTR APA events and improve genome annotation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>APA-Scan is a comprehensive computational pipeline to detect transcriptome-wide 3\u2032-UTR APA events. The pipeline integrates both RNA-seq and 3\u2032-end-seq data information and can efficiently identify the significant events with a high-resolution short reads coverage plots.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-022-04939-w","type":"journal-article","created":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T09:04:28Z","timestamp":1664355868000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["APA-Scan: detection and visualization of 3\u2032-UTR alternative polyadenylation with RNA-seq and 3\u2032-end-seq data"],"prefix":"10.1186","volume":"23","author":[{"given":"Naima Ahmed","family":"Fahmi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khandakar Tanvir","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jae-Woong","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heba","family":"Nassereddeen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deliang","family":"Fan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeongsik","family":"Yong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3605-9373","authenticated-orcid":false,"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,9,28]]},"reference":[{"issue":"17","key":"4939_CR1","doi-asserted-by":"publisher","first-page":"1770","DOI":"10.1101\/gad.17268411","volume":"25","author":"NJ Proudfoot","year":"2011","unstructured":"Proudfoot NJ. 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