{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:28:22Z","timestamp":1760956102101,"version":"3.37.3"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T00:00:00Z","timestamp":1620691200000},"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":["61873202","61473232","31671373"],"award-info":[{"award-number":["61873202","61473232","31671373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2020M683568"],"award-info":[{"award-number":["2020M683568"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>N 6-methyladenosine (m6A) is the most abundant mammalian mRNA methylation with versatile functions. To date, although a number of bioinformatics tools have been developed for location discovery of m6A modification, functional understanding is still quite limited. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, there is an urgent need for user-friendly tools to identify and explore the functional relevance of context-specific m6A methylation to gain insights into the epitranscriptome layer of gene expression regulation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduced here Funm6AViewer, a novel platform to identify, prioritize and visualize the functional gene interaction networks mediated by dynamic m6A RNA methylation unveiled from a case control study. By taking the differential RNA methylation data and differential gene expression data, both of which can be inferred from the widely used MeRIP-seq data, as the inputs, Funm6AViewer enables a series of analysis, including: (i) examining the distribution of differential m6A sites, (ii) prioritizing the genes mediated by dynamic m6A methylation and (iii) characterizing functionally the gene regulatory networks mediated by condition-specific m6A RNA methylation. Funm6AViewer should effectively facilitate the understanding of the epitranscriptome circuitry mediated by this reversible RNA modification.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Funm6AViewer is available both as a convenient web server (https:\/\/www.xjtlu.edu.cn\/biologicalsciences\/funm6aviewer) with graphical interface and as an independent R package (https:\/\/github.com\/NWPU-903PR\/Funm6AViewer) for local usage.<\/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\/btab362","type":"journal-article","created":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T13:09:04Z","timestamp":1620652144000},"page":"4277-4279","source":"Crossref","is-referenced-by-count":4,"title":["Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation"],"prefix":"10.1093","volume":"37","author":[{"given":"Song-Yao","family":"Zhang","sequence":"first","affiliation":[{"name":"Key Laboratory of Information Fusion Technology of Ministry of Education, Department of Intelligent Science and Technology, School of Automation, Northwestern Polytechnical University , X\u0131\u2019an 710072, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1305-7447","authenticated-orcid":false,"given":"Shao-Wu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Information Fusion Technology of Ministry of Education, Department of Intelligent Science and Technology, School of Automation, Northwestern Polytechnical University , X\u0131\u2019an 710072, China"}]},{"given":"Yujiao","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Integrative Biology, University of Liverpool , Liverpool L7 8TX, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3308-2201","authenticated-orcid":false,"given":"Xiao-Nan","family":"Fan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Information Fusion Technology of Ministry of Education, Department of Intelligent Science and Technology, School of Automation, Northwestern Polytechnical University , X\u0131\u2019an 710072, China"}]},{"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":"Institute of Integrative Biology, University of Liverpool , Liverpool L7 8TX, UK"},{"name":"AI University Center, Xi\u2019an Jiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}]}],"member":"286","published-online":{"date-parts":[[2021,5,11]]},"reference":[{"key":"2023051607085581900_btab362-B1","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1016\/j.stem.2014.09.019","article-title":"m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells","volume":"15","author":"Batista","year":"2014","journal-title":"Cell Stem Cell"},{"key":"2023051607085581900_btab362-B2","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/nature25784","article-title":"The SMAD2\/3 interactome reveals that TGF beta controls m(6)A mRNA methylation in pluripotency","volume":"555","author":"Bertero","year":"2018","journal-title":"Nature"},{"key":"2023051607085581900_btab362-B3","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1109\/TCBB.2015.2403355","article-title":"MeTDiff: a novel differential RNA methylation analysis for MeRIP-Seq data","volume":"15","author":"Cui","year":"2018","journal-title":"IEEE ACM Trans. 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