{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T02:15:19Z","timestamp":1783649719965,"version":"3.55.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,12,11]],"date-time":"2020-12-11T00:00:00Z","timestamp":1607644800000},"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671373"],"award-info":[{"award-number":["31671373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-T-01"],"award-info":[{"award-number":["KSF-T-01"]}]},{"name":"AI University Research Centre through XJTLU Key Programme Special Fund","award":["KSF-P-02"],"award-info":[{"award-number":["KSF-P-02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>The distribution of biological features strongly indicates their functional relevance. Compared to DNA-related features, deciphering the distribution of mRNA-related features is non-trivial due to the existence of isoform ambiguity and compositional diversity of mRNAs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose here a rigorous statistical framework, MetaTX, for deciphering the distribution of mRNA-related features. Through a standardized mRNA model, MetaTX firstly unifies various mRNA transcripts of diverse compositions, and then corrects the isoform ambiguity by incorporating the overall distribution pattern of the features through an EM algorithm. MetaTX was tested on both simulated and real data. Results suggested that MetaTX substantially outperformed existing direct methods on simulated datasets, and that a more informative distribution pattern was produced for all the three datasets tested, which contain N6-Methyladenosine sites generated by different technologies. MetaTX should make a useful tool for studying the distribution and functions of mRNA-related biological features, especially for mRNA modifications such as N6-Methyladenosine.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The MetaTX R package is freely available at GitHub: https:\/\/github.com\/yue-wang-biomath\/MetaTX.1.0.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa938","type":"journal-article","created":{"date-parts":[[2020,10,24]],"date-time":"2020-10-24T19:09:38Z","timestamp":1603566578000},"page":"1285-1291","source":"Crossref","is-referenced-by-count":19,"title":["MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6271-6547","authenticated-orcid":false,"given":"Yue","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Mathematical Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Department of Computer Science, University of Liverpool , Liverpool L69 7ZB, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunqi","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Ageing & Chronic Disease, University of Liverpool , Liverpool L69 7ZB, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Ageing & Chronic Disease, University of Liverpool , Liverpool L69 7ZB, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frans","family":"Coenen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Liverpool , Liverpool L69 7ZB, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jionglong","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3455-205X","authenticated-orcid":false,"given":"Jia","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"AI University Research Centre, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,11]]},"reference":[{"key":"2023051706055167000_btaa938-B1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2023051706055167000_btaa938-B2","doi-asserted-by":"crossref","first-page":"e1004751","DOI":"10.1371\/journal.pcbi.1004751","article-title":"Metagene profiles analyses reveal regulatory element\u2019s factor-specific recruitment patterns","volume":"12","author":"Beauparlant","year":"2016","journal-title":"PLoS Comput. 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