{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T03:27:21Z","timestamp":1778642841338,"version":"3.51.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,10,16]],"date-time":"2019-10-16T00:00:00Z","timestamp":1571184000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31601080"],"award-info":[{"award-number":["31601080"]}],"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":["61873075"],"award-info":[{"award-number":["61873075"]}],"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":["81772780"],"award-info":[{"award-number":["81772780"]}],"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":["81902646"],"award-info":[{"award-number":["81902646"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004027","name":"Postdoctoral Foundation of Hei Long Jiang Province","doi-asserted-by":"publisher","award":["LBH-TZ18"],"award-info":[{"award-number":["LBH-TZ18"]}],"id":[{"id":"10.13039\/501100004027","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province","award":["UNPYSCT-2017071"],"award-info":[{"award-number":["UNPYSCT-2017071"]}]},{"DOI":"10.13039\/100010722","name":"Harbin Medical University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010722","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>LnCeVar (http:\/\/www.bio-bigdata.net\/LnCeVar\/) is a comprehensive database that aims to provide genomic variations that disturb lncRNA-associated competing endogenous RNA (ceRNA) network regulation curated from the published literature and high-throughput data sets. LnCeVar curated 119\u00a0501 variation\u2013ceRNA events from thousands of samples and cell lines, including: (i) more than 2000 experimentally supported circulating, drug-resistant and prognosis-related lncRNA biomarkers; (ii) 11\u00a0418 somatic mutation\u2013ceRNA events from TCGA and COSMIC; (iii) 112\u00a0674 CNV\u2013ceRNA events from TCGA; (iv) 67\u00a0066 SNP\u2013ceRNA events from the 1000 Genomes Project. LnCeVar provides a user-friendly searching and browsing interface. In addition, as an important supplement of the database, several flexible tools have been developed to aid retrieval and analysis of the data. The LnCeVar\u2013BLAST interface is a convenient way for users to search ceRNAs by interesting sequences. LnCeVar\u2013Function is a tool for performing functional enrichment analysis. LnCeVar\u2013Hallmark identifies dysregulated cancer hallmarks of variation\u2013ceRNA events. LnCeVar\u2013Survival performs COX regression analyses and produces survival curves for variation\u2013ceRNA events. LnCeVar\u2013Network identifies and creates a visualization of dysregulated variation\u2013ceRNA networks. Collectively, LnCeVar will serve as an important resource for investigating the functions and mechanisms of personalized genomic variations that disturb ceRNA network regulation in human diseases.<\/jats:p>","DOI":"10.1093\/nar\/gkz887","type":"journal-article","created":{"date-parts":[[2019,10,12]],"date-time":"2019-10-12T19:28:51Z","timestamp":1570908531000},"source":"Crossref","is-referenced-by-count":22,"title":["LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation"],"prefix":"10.1093","author":[{"given":"Peng","family":"Wang","sequence":"first","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Gao","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiuyan","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shangwei","family":"Ning","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunpeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"},{"name":"Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA"},{"name":"Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shipeng","family":"Shang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junwei","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanxia","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Zhi","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Fang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weitao","family":"Shen","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangmei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven Xi","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA"},{"name":"Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xia","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,16]]},"reference":[{"key":"2019101605085327600_B1","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/nature12986","article-title":"The multilayered complexity of ceRNA crosstalk and competition","volume":"505","author":"Tay","year":"2014","journal-title":"Nature"},{"key":"2019101605085327600_B2","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gky1144","article-title":"LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments","volume":"47","author":"Wang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B3","doi-asserted-by":"crossref","first-page":"5653","DOI":"10.1093\/nar\/gkx331","article-title":"Exploring genetic associations with ceRNA regulation in the human genome","volume":"45","author":"Li","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B4","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gkv1220","article-title":"SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions","volume":"44","author":"Bhattacharya","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B5","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1002\/mc.22261","article-title":"A functional lncRNA HOTAIR genetic variant contributes to gastric cancer susceptibility","volume":"55","author":"Pan","year":"2016","journal-title":"Mol. Carcinog."},{"key":"2019101605085327600_B6","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.devcel.2013.03.002","article-title":"Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal","volume":"25","author":"Wang","year":"2013","journal-title":"Dev. Cell"},{"key":"2019101605085327600_B7","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.cell.2011.07.014","article-title":"A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?","volume":"146","author":"Salmena","year":"2011","journal-title":"Cell"},{"key":"2019101605085327600_B8","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nature09144","article-title":"A coding-independent function of gene and pseudogene mRNAs regulates tumour biology","volume":"465","author":"Poliseno","year":"2010","journal-title":"Nature"},{"key":"2019101605085327600_B9","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.celrep.2018.03.064","article-title":"Pan-Cancer analysis of lncRNA regulation supports their targeting of cancer genes in each tumor context","volume":"23","author":"Chiu","year":"2018","journal-title":"Cell Rep."},{"key":"2019101605085327600_B10","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng.3547","article-title":"Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer","volume":"48","author":"Fujimoto","year":"2016","journal-title":"Nat. Genet."},{"key":"2019101605085327600_B11","doi-asserted-by":"crossref","first-page":"D276","DOI":"10.1093\/nar\/gkx1004","article-title":"lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs","volume":"46","author":"Miao","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B12","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1093\/bioinformatics\/btw581","article-title":"LncVar: a database of genetic variation associated with long non-coding genes","volume":"33","author":"Chen","year":"2017","journal-title":"Bioinformatics"},{"key":"2019101605085327600_B13","doi-asserted-by":"crossref","first-page":"D1028","DOI":"10.1093\/nar\/gky1096","article-title":"Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers","volume":"47","author":"Gao","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B14","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nature12531","article-title":"Transcriptome and genome sequencing uncovers functional variation in humans","volume":"501","author":"Lappalainen","year":"2013","journal-title":"Nature"},{"key":"2019101605085327600_B15","doi-asserted-by":"crossref","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the Catalogue Of Somatic Mutations In Cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B16","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.cels.2019.06.006","article-title":"Before and after: Comparison of legacy and harmonized TCGA genomic data commons' data","volume":"9","author":"Gao","year":"2019","journal-title":"Cell Syst."},{"key":"2019101605085327600_B17","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2011-12-4-r41","article-title":"GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers","volume":"12","author":"Mermel","year":"2011","journal-title":"Genome Biol."},{"key":"2019101605085327600_B18","doi-asserted-by":"crossref","first-page":"D149","DOI":"10.1093\/nar\/gkm995","article-title":"The microRNA.org resource: targets and expression","volume":"36","author":"Betel","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B19","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1101\/gr.082701.108","article-title":"Most mammalian mRNAs are conserved targets of microRNAs","volume":"19","author":"Friedman","year":"2009","journal-title":"Genome Res."},{"key":"2019101605085327600_B20","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1261\/rna.5248604","article-title":"Fast and effective prediction of microRNA\/target duplexes","volume":"10","author":"Rehmsmeier","year":"2004","journal-title":"RNA"},{"key":"2019101605085327600_B21","doi-asserted-by":"crossref","first-page":"D239","DOI":"10.1093\/nar\/gkx1141","article-title":"DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions","volume":"46","author":"Karagkouni","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B22","doi-asserted-by":"crossref","first-page":"D296","DOI":"10.1093\/nar\/gkx1067","article-title":"miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions","volume":"46","author":"Chou","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B23","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The Gene Ontology Resource: 20 years and still GOing strong","volume":"47","author":"The Gene Ontology, C.","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B24","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gky962","article-title":"New approach for understanding genome variations in KEGG","volume":"47","author":"Kanehisa","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B25","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The reactome pathway knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B26","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst."},{"key":"2019101605085327600_B27","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"2019101605085327600_B28","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1101\/gr.133991.111","article-title":"A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers","volume":"22","author":"Plaisier","year":"2012","journal-title":"Genome Res."},{"key":"2019101605085327600_B29","doi-asserted-by":"crossref","first-page":"3478","DOI":"10.1093\/nar\/gkv233","article-title":"Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B30","doi-asserted-by":"crossref","first-page":"D1038","DOI":"10.1093\/nar\/gky1151","article-title":"OMIM.org: leveraging knowledge across phenotype-gene relationships","volume":"47","author":"Amberger","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019101605085327600_B31","doi-asserted-by":"crossref","first-page":"D181","DOI":"10.1093\/nar\/gkx1035","article-title":"MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases","volume":"46","author":"Yue","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz887\/30155521\/gkz887.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz887\/30155521\/gkz887.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,16]],"date-time":"2019-10-16T09:29:47Z","timestamp":1571218187000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkz887\/5588344"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,16]]},"references-count":31,"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz887","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,10,16]]},"article-number":"gkz887"}}