miRDB: an online database for prediction of functional microRNA targets

Abstract MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end,...

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Vydáno v:Nucleic acids research Ročník 48; číslo D1; s. D127 - D131
Hlavní autoři: Chen, Yuhao, Wang, Xiaowei
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 08.01.2020
Témata:
Algorithms
Computational Biology - methods
Database Issue
Databases, Nucleic Acid
Gene Expression Regulation
Gene Ontology
MicroRNAs - genetics
RNA Interference
RNA, Messenger - genetics
User-Computer Interface
Web Browser
ISSN:0305-1048, 1362-4962, 1362-4962
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Shrnutí:Abstract MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online database, miRDB, for miRNA target prediction and functional annotations. Recently, we have performed major updates for miRDB. Specifically, by employing an improved algorithm for miRNA target prediction, we now present updated transcriptome-wide target prediction data in miRDB, including 3.5 million predicted targets regulated by 7000 miRNAs in five species. Further, we have implemented the new prediction algorithm into a web server, allowing custom target prediction with user-provided sequences. Another new database feature is the prediction of cell-specific miRNA targets. miRDB now hosts the expression profiles of over 1000 cell lines and presents target prediction data that are tailored for specific cell models. At last, a new web query interface has been added to miRDB for prediction of miRNA functions by integrative analysis of target prediction and Gene Ontology data. All data in miRDB are freely accessible at http://mirdb.org.
Bibliografie:ObjectType-Article-1
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkz757