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DIANA-LncBase v3: Indexing experimentally supported miRNA targets on non-coding transcripts

dc.creatorKaragkouni D., Paraskevopoulou M.D., Tastsoglou S., Skoufos G., Karavangeli A., Pierros V., Zacharopoulou E., Hatzigeorgiou A.G.en
dc.date.accessioned2023-01-31T08:30:50Z
dc.date.available2023-01-31T08:30:50Z
dc.date.issued2020
dc.identifier10.1093/nar/gkz1036
dc.identifier.issn03051048
dc.identifier.urihttp://hdl.handle.net/11615/74358
dc.description.abstractDIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts. Its third version provides approximately half a million entries, corresponding to ∼240 000 unique tissue and cell type specific miRNA-lncRNA pairs. This compilation of interactions is derived from the manual curation of publications and the analysis of >300 high-throughput datasets. miRNA targets are supported by 14 experimental methodologies, applied to 243 distinct cell types and tissues in human and mouse. The largest part of the database is highly confident, AGO-CLIP-derived miRNA-binding events. LncBase v3.0 is the first relevant database to employ a robust CLIP-Seq-guided algorithm, microCLIP framework, to analyze 236 AGO-CLIP-Seq libraries and catalogue ∼370 000 miRNA binding events. The database was redesigned from the ground up, providing new functionalities. Known short variant information, on >67,000 experimentally supported target sites and lncRNA expression profiles in different cellular compartments are catered to users. Interactive visualization plots, portraying correlations of miRNA-lncRNA pairs, as well as lncRNA expression profiles in a wide range of cell types and tissues, are presented for the first time through a dedicated page. LncBase v3.0 constitutes a valuable asset for ncRNA research, providing new insights to the understanding of the still widely unexplored lncRNA functions. © 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.en
dc.language.isoenen
dc.sourceNucleic Acids Researchen
dc.source.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85077667860&doi=10.1093%2fnar%2fgkz1036&partnerID=40&md5=323c6ed0a60cb1d19847a7bfa9d9b5c7
dc.subjectlong untranslated RNAen
dc.subjectmicroRNAen
dc.subjectmicroRNAen
dc.subjectuntranslated RNAen
dc.subjectalgorithmen
dc.subjectanimal cellen
dc.subjectanimal tissueen
dc.subjectArticleen
dc.subjectcell compartmentalizationen
dc.subjectcellular distributionen
dc.subjectcontrolled studyen
dc.subjectgene locationen
dc.subjecthigh throughput sequencingen
dc.subjecthumanen
dc.subjecthuman cellen
dc.subjecthuman tissueen
dc.subjectmolecular libraryen
dc.subjectmolecular recognitionen
dc.subjectmouseen
dc.subjectnonhumanen
dc.subjectnucleic acid databaseen
dc.subjectpriority journalen
dc.subjectRNA bindingen
dc.subjectRNA sequenceen
dc.subjectRNA transcriptionen
dc.subjectsequence analysisen
dc.subjectbiologyen
dc.subjectgene expression regulationen
dc.subjectgeneticsen
dc.subjectmolecular geneticsen
dc.subjectproceduresen
dc.subjectRNA interferenceen
dc.subjectsoftwareen
dc.subjectComputational Biologyen
dc.subjectDatabases, Nucleic Aciden
dc.subjectGene Expression Regulationen
dc.subjectHigh-Throughput Nucleotide Sequencingen
dc.subjectMicroRNAsen
dc.subjectMolecular Sequence Annotationen
dc.subjectRNA Interferenceen
dc.subjectRNA, Untranslateden
dc.subjectSequence Analysis, RNAen
dc.subjectSoftwareen
dc.subjectOxford University Pressen
dc.titleDIANA-LncBase v3: Indexing experimentally supported miRNA targets on non-coding transcriptsen
dc.typejournalArticleen


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