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, 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.

Figure 1.

Overview of the updated miRNA target prediction algorithm, MirTarget. Training data were derived from both miRNA binding and target expression data. MirTarget was trained under an SVM machine learning framework.

Figure 2.

miRDB target expression analysis. miRDB hosts the expression profiles of over 1000 cell lines. (A) A screenshot for selection of specific cell models. (B) A screenshot for integrative presentation of both target prediction and expression data for the selected cell model.

Figure 3.

A screenshot for miRDB target ontology analysis. miRNA target prediction data and GO data were integratively analyzed to predict miRNA functions.