Text Mining miRNA-gene Interactions for the mx-plore Platform

Abstract

miRNAs are post-transcriptional regulators which bind to the specific mRNA of expressed genes and induce increased mRNA degradation, thereby reducing the gene expression of their target genes. miRNAs perform their regulatory functions in a context-specific manner. Several databases contain collections of miRNA-target interactions, which are either experimentally validated, derived from high-throughput experiments, or computationally predicted or captured from existing literature. For most databases, the specific context of the miRNA-target interaction is unknown or missing in these databases. mx-plore is not only a database of text-dervied miRNA-gene interactions, but it enhances the found interactions including detailed context information from scientific publications. To derive the entries in the mx-plore database, a newly developed text mining strategy combining dependency graph analysis and rule-based systems has been used. The mx-plore platform makes miRNA-gene interactions accessible and searchable on various levels, such as by cell type, disease or involved processes. The platform is available at https://rest.bio.ifi.lmu.de/mxplore and corresponding source code is deposited on GitHub. Author summaryO_LIThe mx-plore platform is a comprehensive database of miRNA:target interactions as described in the scientific literature. C_LIO_LImx-plore is a new text-mining approach to extract context-dependent miRNA interactions from Pubmed abstracts and PMC full texts. C_LIO_LImx-plore allows to query the comprehensive database in a context-specific manner, both on- and off-line. C_LI