{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T21:35:36Z","timestamp":1768772136403,"version":"3.49.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,29]],"date-time":"2021-05-29T00:00:00Z","timestamp":1622246400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"CAMS Innovation Fund for Medical Sciences","award":["2019-I2M-2-002"],"award-info":[{"award-number":["2019-I2M-2-002"]}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["2017-I2M-1-006"],"award-info":[{"award-number":["2017-I2M-1-006"]}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LY21C060002"],"award-info":[{"award-number":["LY21C060002"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fundamental Research Funds for the Provincial Universities of Zhejian","award":["SJLZ2021001"],"award-info":[{"award-number":["SJLZ2021001"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970630"],"award-info":[{"award-number":["31970630"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017553","name":"Zhejiang Key Laboratory of Pathophysiology","doi-asserted-by":"publisher","award":["201812"],"award-info":[{"award-number":["201812"]}],"id":[{"id":"10.13039\/501100017553","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Zhejiang Provincial Research Center for Cancer Intelligent Diagnosis and Molecular Technology","award":["JBZX-202003"],"award-info":[{"award-number":["JBZX-202003"]}]},{"DOI":"10.13039\/501100020738","name":"K. C. Wong Magna Fund in Ningbo University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100020738","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Increasing evidence proves the essential regulatory roles of non-coding RNAs (ncRNAs) in biological processes. However, characterizing the specific functions of ncRNAs remains a challenging task, owing to the intensive consumption of the experimental approaches. Here, we present an online platform ncFANs v2.0 that is a significantly enhanced version of our previous ncFANs to provide multiple computational methods for ncRNA functional annotation. Specifically, ncFANs v2.0 was updated to embed three functional modules, including ncFANs-NET, ncFANs-eLnc and ncFANs-CHIP. ncFANs-NET is a new module designed for data-free functional annotation based on four kinds of pre-built networks, including the co-expression network, co-methylation network, long non-coding RNA (lncRNA)-centric regulatory network and random forest-based network. ncFANs-eLnc enables the one-stop identification of enhancer-derived\u00a0lncRNAs from the de novo assembled transcriptome based on the user-defined or our pre-annotated enhancers. Moreover, ncFANs-CHIP inherits the original functions for microarray data-based functional annotation and supports more chip types. We believe that our ncFANs v2.0 carries sufficient convenience and practicability for biological researchers and facilitates unraveling the regulatory mechanisms of ncRNAs. The ncFANs v2.0 server is freely available at http:\/\/bioinfo.org\/ncfans or http:\/\/ncfans.gene.ac.<\/jats:p>","DOI":"10.1093\/nar\/gkab435","type":"journal-article","created":{"date-parts":[[2021,5,5]],"date-time":"2021-05-05T21:36:17Z","timestamp":1620250577000},"page":"W459-W468","source":"Crossref","is-referenced-by-count":26,"title":["ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8395-3020","authenticated-orcid":false,"given":"Yuwei","family":"Zhang","sequence":"first","affiliation":[{"name":"The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China"},{"name":"Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315000, China"}]},{"given":"Dechao","family":"Bu","sequence":"additional","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of\u00a0Sciences, Beijing,\u00a0100190,\u00a0China"}]},{"given":"Peipei","family":"Huo","sequence":"additional","affiliation":[{"name":"Luoyang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Henan, 471000, China"}]},{"given":"Zhihao","family":"Wang","sequence":"additional","affiliation":[{"name":"Luoyang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Henan, 471000, China"}]},{"given":"Hao","family":"Rong","sequence":"additional","affiliation":[{"name":"The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China"},{"name":"Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315000, China"}]},{"given":"Yanguo","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315000,\u00a0China"}]},{"given":"Jingjia","family":"Liu","sequence":"additional","affiliation":[{"name":"Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 315000, China"}]},{"given":"Meng","family":"Ye","sequence":"additional","affiliation":[{"name":"The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China"}]},{"given":"Yang","family":"Wu","sequence":"additional","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of\u00a0Sciences, Beijing,\u00a0100190,\u00a0China"}]},{"given":"Zheng","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Colorectal Surgery, National Cancer Center\/National Clinical Research Center for Cancer\/Cancer Hospital, Chinese Academy of Medical Sciences\u00a0and Peking Union Medical College, Beijing, 100021, China"}]},{"given":"Qi","family":"Liao","sequence":"additional","affiliation":[{"name":"The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China"},{"name":"Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315000, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6046-8420","authenticated-orcid":false,"given":"Yi","family":"Zhao","sequence":"additional","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of\u00a0Sciences, Beijing,\u00a0100190,\u00a0China"}]}],"member":"286","published-online":{"date-parts":[[2021,5,29]]},"reference":[{"key":"2021070812130268200_B1","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1101\/gr.247239.118","article-title":"Decrypting noncoding RNA interactions, structures, and functional networks","volume":"29","author":"Fabbri","year":"2019","journal-title":"Genome Res."},{"key":"2021070812130268200_B2","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1038\/s41588-018-0139-3","article-title":"MiCEE is a ncRNA-protein complex that mediates epigenetic silencing and nucleolar organization","volume":"50","author":"Singh","year":"2018","journal-title":"Nat. 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