{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T09:17:48Z","timestamp":1770455868941,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T00:00:00Z","timestamp":1572998400000},"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\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["Y201900029"],"award-info":[{"award-number":["Y201900029"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018522","name":"Jiangsu Collaborative Innovation Center for Modern Crop Production","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100018522","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>A critical aspect for exploring the biological function of a microRNA (miRNA) lies on exact detection and validation of its target mRNAs. However, no convenient and efficient web-based server is available for plant biologists to identify the experimentally verified target mRNAs of miRNAs. In this work, we built a comprehensive web-based platform for miRNA\u2013target analysis, named as Whole-degradome-based Plant MiRNA\u2013target Interaction Analysis Server (WPMIAS), for validation of predicted interactions of miRNAs and their target mRNAs (MTIs) by user-submitted data or all available pre-loaded degradome data. Besides, the server can construct degradome-based miRNA regulatory networks (MRNs) based on the validated MTIs to help study the functions and relations among miRNAs and target mRNAs. WPMIAS is also suitable for other small RNAs (sRNAs), such as 21-nt phased siRNAs and natural antisense siRNAs, which direct cleavage of target mRNAs. Currently, WPMIAS supports 68 plant species with 189 cDNA and 271 pre-loaded plant degradome datasets. The user can identify all validated MTIs by analyzing all degradome data at a time and understand when and where MTIs take place and their cleavage levels. With the data obtained from WPMIAS, the user can build a plant miRNA\u2013target map, where it is convenient to find interesting research ideas on miRNAs. In summary, WPMIAS is able to support a comprehensive web-based plant miRNA\u2013target analysis and expected to greatly promote future research on plant miRNAs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>It can be freely accessed at https:\/\/cbi.njau.edu.cn\/WPMIAS\/.<\/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\/btz820","type":"journal-article","created":{"date-parts":[[2019,10,31]],"date-time":"2019-10-31T12:22:45Z","timestamp":1572524565000},"page":"1937-1939","source":"Crossref","is-referenced-by-count":11,"title":["WPMIAS: Whole-degradome-based Plant MicroRNA\u2013target Interaction Analysis Server"],"prefix":"10.1093","volume":"36","author":[{"given":"Yuhan","family":"Fei","sequence":"first","affiliation":[{"name":"State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University , Nanjing 210095, China"},{"name":"Department of Genetics, Harvard Medical School , Boston, MA 02115, USA"}]},{"given":"Yiyang","family":"Mao","sequence":"additional","affiliation":[{"name":"College of Information Science and Technology, Nanjing Agricultural University , Nanjing 210095, China"}]},{"given":"Chengji","family":"Shen","sequence":"additional","affiliation":[{"name":"College of Information Science and Technology, Nanjing Agricultural University , Nanjing 210095, China"}]},{"given":"Rui","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University , Nanjing 210095, China"}]},{"given":"Hongsheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University , Nanjing 210095, China"}]},{"given":"Ji","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University , Nanjing 210095, China"}]}],"member":"286","published-online":{"date-parts":[[2019,11,6]]},"reference":[{"key":"2023060912005131200_btz820-B1","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1016\/j.cub.2008.04.042","article-title":"Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome","volume":"18","author":"Addo-Quaye","year":"2008","journal-title":"Curr. 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