miRWalk – Database: Prediction of possible miRNA binding sites by “walking” the genes of three genomes

MicroRNAs are small, non-coding RNA molecules that can complementarily bind to the mRNA 3′-UTR region to regulate the gene expression by transcriptional repression or induction of mRNA degradation. Increasing evidence suggests a new mechanism by which miRNAs may regulate target gene expression by binding in promoter and amino acid coding regions. Most of the existing databases on miRNAs are restricted to mRNA 3′-UTR region. To address this issue, we present miRWalk, a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat.All mRNAs, mitochondrial genes and 10 kb upstream flanking regions of all known genes of human, mouse and rat were analyzed by using a newly developed algorithm named ‘miRWalk’ as well as with eight already established programs for putative miRNA binding sites. An automated and extensive text-mining search was performed on PubMed database to extract validated information on miRNAs. Combined information was put into a MySQL database.miRWalk presents predicted and validated information on miRNA-target interaction. Such a resource enables researchers to validate new targets of miRNA not only on 3′-UTR, but also on the other regions of all known genes. The ‘Validated Target module’ is updated every month and the ‘Predicted Target module’ is updated every 6 months. miRWalk is freely available at http://mirwalk.uni-hd.de/.

Graphical abstractmiRWalk (http://mirwalk.uni-hd.de/), a comprehensive database that provides predicted as well as validated miRNA binding site information on miRNAs for human, mouse and rat. miRWalk gathers all the information on predicted as well as validated miRNA targets, this database has the potential of becoming an important resource for scientists engaged with miRNA research.Figure optionsDownload full-size imageDownload as PowerPoint slideHighlights► A newly developed algorithm is used to predict all the possible miRNA binding sites. ► miRWalk are presented together with the results obtained from eight already established miRNA-target prediction programs. ► Holistic view of genetic networks of miRNA-gene-pathways and miRNA-gene-OMIM disorder interactions. ► miRWalk hosts new and unique features on experimentally validated miRNAs. ► Information on proteins known to be involved in miRNA processing.