TarBase v9.0: Expanding Experimentally Validated miRNA– Gene Interactions to Virally Encoded miRNAs and Cell-Type Specific Contexts

Introduction TarBase v9.0 is a major update to the well-established database of experimentally validated microRNA (miRNA)–gene interactions. This latest version incorporates over 6 million interactions, including new data on virally encoded miRNAs and target-directed miRNA degradation (TDMD) events. TarBase v9.0 is designed to support researchers in exploring miRNA interactions across various cell types, tissues, and experimental conditions. Methods TarBase v9.0 integrates data from 37 experimental protocols across 172 tissues and cell types, providing a comprehensive view of miRNA–gene interactions. The platform includes interactions obtained from both high- and low-throughput experiments, annotated with rich metadata, including gene, transcript, miRNA, and experimental context information. A new interface offers advanced search options with filtering criteria for miRNA expression levels, cell lines, and experimental conditions. Results TarBase v9.0 represents the largest collection of experimentally supported miRNA–gene interactions, with over 2 million unique miRNA–gene pairs. New features such as cell-type resolution of miRNA binding sites and interactions with virally encoded miRNAs enhance the database’s utility for diverse biological and clinical research applications. The redesigned platform facilitates efficient data retrieval and analysis, empowering researchers to perform complex queries. Conclusions TarBase v9.0 offers an unparalleled resource for the study of miRNA–gene interactions, with expanded content and enhanced functionality. Its integration of vast experimental data, combined with advanced search capabilities, provides researchers with a powerful tool to explore miRNA regulation in various biological systems and diseases.