{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T21:54:00Z","timestamp":1758405240530,"version":"3.41.2"},"reference-count":60,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T00:00:00Z","timestamp":1572393600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007046","name":"Wuhan University","doi-asserted-by":"publisher","award":["2042017kf0233"],"award-info":[{"award-number":["2042017kf0233"]}],"id":[{"id":"10.13039\/501100007046","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91640115","31670827","31690090","31770310"],"award-info":[{"award-number":["91640115","31670827","31690090","31770310"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2017YFA0504400"],"award-info":[{"award-number":["2017YFA0504400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Malvaceae is a family of flowering plants containing many economically important plant species including cotton, cacao and durian. Recently, the genomes of several Malvaceae species have been decoded, and many omics data were generated for individual species. However, no integrative database of multiple species, enabling users to jointly compare and analyse relevant data, is available for Malvaceae. Thus, we developed a user-friendly database named MaGenDB (http:\/\/magen.whu.edu.cn) as a functional genomics hub for the plant community. We collected the genomes of 13 Malvaceae species, and comprehensively annotated genes from different perspectives including functional RNA\/protein element, gene ontology, KEGG orthology, and gene family. We processed 374 sets of diverse omics data with the ENCODE pipelines and integrated them into a customised genome browser, and designed multiple dynamic charts to present gene\/RNA\/protein-level knowledge such as dynamic expression profiles and functional elements. We also implemented a smart search system for efficiently mining genes. In addition, we constructed a functional comparison system to help comparative analysis between genes on multiple features in one species or across closely related species. This database and associated tools will allow users to quickly retrieve large-scale functional information for biological discovery.<\/jats:p>","DOI":"10.1093\/nar\/gkz953","type":"journal-article","created":{"date-parts":[[2019,10,10]],"date-time":"2019-10-10T15:51:12Z","timestamp":1570722672000},"source":"Crossref","is-referenced-by-count":15,"title":["MaGenDB: a functional genomics hub for Malvaceae plants"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9465-0957","authenticated-orcid":false,"given":"Dehe","family":"Wang","sequence":"first","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"},{"name":"State Key Laboratory of Virology, Wuhan University, Wuhan\u00a0430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weiliang","family":"Fan","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaolong","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"},{"name":"State Key Laboratory of Virology, Wuhan University, Wuhan\u00a0430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"},{"name":"State Key Laboratory of Virology, Wuhan University, Wuhan\u00a0430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyu","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Information Science and Engineering, Hunan University, Changsha 410082, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zonggui","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute for Advanced Studies, Wuhan University, Wuhan 430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danyang","family":"Li","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5910-1568","authenticated-orcid":false,"given":"Kun","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2371-5933","authenticated-orcid":false,"given":"Yuxian","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"},{"name":"Institute for Advanced Studies, Wuhan University, Wuhan 430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2102-9377","authenticated-orcid":false,"given":"Yu","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Wuhan University, Wuhan\u00a0430072, China"},{"name":"State Key Laboratory of Virology, Wuhan University, Wuhan\u00a0430072, China"},{"name":"Institute for Advanced Studies, Wuhan University, Wuhan 430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,30]]},"reference":[{"key":"2019103013395138100_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/boj.12385","article-title":"An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV","volume":"181","author":"Group","year":"2016","journal-title":"Bot. 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