miRTarBase

miRTarBase catalogs experimentally validated microRNA (miRNA)-target interactions (MTIs) to support research on miRNA regulation, disease associations, variant effects, and biomarker discovery.

Key Features:

• Scale and curation: Contains over 2,200,449 verified MTIs curated from more than 13,389 manually curated articles.
• Experimental evidence types: Includes interactions supported by CLIP-seq experiments and other validation assays.
• Optimized scoring: Implements an optimized scoring system to prioritize MTI-related literature and associated disease information.
• Variant integration: Integrates single-nucleotide polymorphisms (SNPs) and disease-related variants that affect miRNA binding efficiency in 3' untranslated regions (3' UTRs).
• Expression profiles: Provides comprehensive miRNA expression profiles across extracellular vesicles, blood, and different tissues, including exosomal and tissue-specific miRNAs.
• Seed sequence analysis: Utilizes seed sequence information to evaluate and annotate miRNA binding sites.
• Validation annotations: Classifies attributes of validation experiments, including RNA expression, interaction details, protein expression, and biological function.

Scientific Applications:

• miRNA functional studies: Support investigation of miRNA regulatory roles through experimentally validated MTIs and expression context.
• Disease association analysis: Enable exploration of MTIs and integrated variant data for linking miRNAs to disease mechanisms.
• Biomarker discovery: Facilitate identification of exosomal and tissue-specific miRNAs as potential biomarkers in blood and tissues.
• Variant impact assessment: Allow analysis of how SNPs and disease-related variants in 3' UTRs alter miRNA binding and gene regulation.
• Interpretation of CLIP-seq data: Provide reference MTIs to corroborate and interpret CLIP-seq-derived miRNA–mRNA interactions.

Methodology:

Manual literature curation, incorporation of CLIP-seq-derived interactions, use of seed sequence information to evaluate binding sites, and an optimized scoring system for literature and disease annotation.