DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

2018 | Dimitra Karagkouni, Maria D. Paraskevopoulou, Serafeim Chatzopoulou, Ioannis S. Vlachos, Spyros Tastsoglou, Ilias Kanellos, Dimitris Papadimitriou, Ioannis Kavakiotis, Sofia Maniou, Giorgos Skoufos, Thanasis Vergoulis, Theodore Dalamagas, Artemis G. Hatzigeorgiou
DIANA-TarBase v8 is a comprehensive database of experimentally supported microRNA (miRNA)-gene interactions. It contains over 670,000 unique miRNA-target pairs, derived from more than 33 experimental methodologies applied to approximately 600 cell types/tissues under 451 experimental conditions. The database includes information on cell-type specific miRNA-gene regulation and reports hundreds of thousands of miRNA-binding locations. It has been continuously updated for over a decade and now includes a new module for browsing interactions through various filtering combinations. This module allows users to easily retrieve positive and negative miRNA targets per species, methodology, cell type, and tissue. A ranking system is used to display interactions based on the robustness of their supporting methodologies. Statistics, pie-charts, and interactive barplots are available through a dedicated result page. An intuitive interface is introduced, providing a user-friendly application with flexible options for different queries. The database integrates information from various experimental methodologies, including reporter gene assays, quantitative PCR, western blot, enzyme-linked immunosorbent assay, microarrays, proteomics, RNA immunoprecipitation combined with sequencing (RIP-seq), Ribosome profiling sequencing (RPF-seq), and CLIP-seq. These methods have enabled the identification of novel experimentally supported miRNA-gene interactions in a transcriptome-wide scale. The database also includes information from high-throughput experiments, such as miRNA-specific transfection/knockdown microarray, RPF-seq, RIP-seq, and RNA-seq experiments. The database has been integrated with other available DIANA-tools, including microT-CDS, LncBase v2.0, and DIANA-miRPath v3.0, facilitating the investigation of miRNA regulation in physiological and pathological molecular pathways. DIANA-TarBase v8 is an important asset to the research community, empowering experimental investigations as well as in silico miRNA-related exploratory studies.DIANA-TarBase v8 is a comprehensive database of experimentally supported microRNA (miRNA)-gene interactions. It contains over 670,000 unique miRNA-target pairs, derived from more than 33 experimental methodologies applied to approximately 600 cell types/tissues under 451 experimental conditions. The database includes information on cell-type specific miRNA-gene regulation and reports hundreds of thousands of miRNA-binding locations. It has been continuously updated for over a decade and now includes a new module for browsing interactions through various filtering combinations. This module allows users to easily retrieve positive and negative miRNA targets per species, methodology, cell type, and tissue. A ranking system is used to display interactions based on the robustness of their supporting methodologies. Statistics, pie-charts, and interactive barplots are available through a dedicated result page. An intuitive interface is introduced, providing a user-friendly application with flexible options for different queries. The database integrates information from various experimental methodologies, including reporter gene assays, quantitative PCR, western blot, enzyme-linked immunosorbent assay, microarrays, proteomics, RNA immunoprecipitation combined with sequencing (RIP-seq), Ribosome profiling sequencing (RPF-seq), and CLIP-seq. These methods have enabled the identification of novel experimentally supported miRNA-gene interactions in a transcriptome-wide scale. The database also includes information from high-throughput experiments, such as miRNA-specific transfection/knockdown microarray, RPF-seq, RIP-seq, and RNA-seq experiments. The database has been integrated with other available DIANA-tools, including microT-CDS, LncBase v2.0, and DIANA-miRPath v3.0, facilitating the investigation of miRNA regulation in physiological and pathological molecular pathways. DIANA-TarBase v8 is an important asset to the research community, empowering experimental investigations as well as in silico miRNA-related exploratory studies.
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