{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T06:36:33Z","timestamp":1770964593002,"version":"3.50.1"},"reference-count":100,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,7,3]],"date-time":"2023-07-03T00:00:00Z","timestamp":1688342400000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LR21H300001"],"award-info":[{"award-number":["LR21H300001"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22220102001"],"award-info":[{"award-number":["22220102001"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U1909208"],"award-info":[{"award-number":["U1909208"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>With the rapid advances of RNA sequencing and microarray technologies in non-coding RNA (ncRNA) research, functional tools that perform enrichment analysis for ncRNAs are needed. On the one hand, because of the rapidly growing interest in circRNAs, snoRNAs, and piRNAs, it is essential to develop tools for enrichment analysis for these newly emerged ncRNAs. On the other hand, due to the key role of ncRNAs\u2019 interacting target in the determination of their function, the interactions between ncRNA and its corresponding target should be fully considered in functional enrichment. Based on the ncRNA\u2013mRNA\/protein-function strategy, some tools have been developed to functionally analyze a single type of ncRNA (the majority focuses on miRNA); in addition, some tools adopt predicted target data and lead to only low-confidence results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Herein, an online tool named RNAenrich was developed to enable the comprehensive and accurate enrichment analysis of ncRNAs. It is unique in (i) realizing the enrichment analysis for various RNA types in humans and mice, such as miRNA, lncRNA, circRNA, snoRNA, piRNA, and mRNA; (ii) extending the analysis by introducing millions of experimentally validated data of RNA\u2013target interactions as a built-in database; and (iii) providing a comprehensive interacting network among various ncRNAs and targets to facilitate the mechanistic study of ncRNA function. Importantly, RNAenrich led to a more comprehensive and accurate enrichment analysis in a COVID-19-related miRNA case, which was largely attributed to its coverage of comprehensive ncRNA\u2013target interactions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>RNAenrich is now freely accessible at https:\/\/idrblab.org\/rnaenr\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad421","type":"journal-article","created":{"date-parts":[[2023,7,3]],"date-time":"2023-07-03T15:56:37Z","timestamp":1688399797000},"source":"Crossref","is-referenced-by-count":16,"title":["RNAenrich: a web server for non-coding RNA enrichment"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1263-6693","authenticated-orcid":false,"given":"Song","family":"Zhang","sequence":"first","affiliation":[{"name":"Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People\u2019s Hospital, Affiliated People's Hospital, Hangzhou Medical College , Hangzhou, Zhejiang 310014, China"},{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"}]},{"given":"Kuerbannisha","family":"Amahong","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"}]},{"given":"Yintao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"}]},{"given":"Xiaoping","family":"Hu","sequence":"additional","affiliation":[{"name":"Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People\u2019s Hospital, Affiliated People's Hospital, Hangzhou Medical College , Hangzhou, Zhejiang 310014, China"}]},{"given":"Shijie","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"}]},{"given":"Mingkun","family":"Lu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"}]},{"given":"Zhenyu","family":"Zeng","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou, Zhejiang 330110, China"}]},{"given":"Zhaorong","family":"Li","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou, Zhejiang 330110, China"}]},{"given":"Bing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou, Zhejiang 330110, China"}]},{"given":"Yunqing","family":"Qiu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University , Hangzhou, Zhejiang 310000, China"}]},{"given":"Haibin","family":"Dai","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"}]},{"given":"Jianqing","family":"Gao","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"},{"name":"Westlake Laboratory of Life Sciences and Biomedicine , Hangzhou, Zhejiang 310030, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8069-0053","authenticated-orcid":false,"given":"Feng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People\u2019s Hospital, Affiliated People's Hospital, Hangzhou Medical College , Hangzhou, Zhejiang 310014, China"},{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou, Zhejiang 310058, China"}]}],"member":"286","published-online":{"date-parts":[[2023,7,3]]},"reference":[{"key":"2023072002433129000_btad421-B1","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/nrc.2017.99","article-title":"Non-coding RNA networks in cancer","volume":"18","author":"Anastasiadou","year":"2018","journal-title":"Nat Rev Cancer"},{"key":"2023072002433129000_btad421-B2","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1152\/physrev.00041.2015","article-title":"Non-coding RNAs in development and disease: background, mechanisms, and therapeutic approaches","volume":"96","author":"Beermann","year":"2016","journal-title":"Physiol Rev"},{"key":"2023072002433129000_btad421-B3","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1016\/j.cell.2020.04.026","article-title":"Imbalanced host response to SARS-CoV-2 drives 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