miRTarBas

miRTarBas provides a curated database of experimentally validated microRNA–target interactions (MTIs) to support analysis of miRNA regulatory networks.

Key Features:

• Database size: Contains over 360,000 experimentally validated microRNA–target interactions (MTIs).
• Experimental validation: Includes MTIs supported by reporter assays, western blotting, microarray analysis, and next-generation sequencing experiments.
• Literature curation: Aggregates interactions through manual review of publications combined with natural language processing (NLP)–based article filtering.
• Regular updates: Maintains up-to-date content by comparing and integrating data with other related databases.

Scientific Applications:

• ceRNA network construction in cancer: Supports building competitive endogenous RNA (ceRNA) networks, exemplified by studies of hepatocellular carcinoma (HCC).
• Differential expression analysis integration: Facilitates linking differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) to validated miRNA targets.
• Target retrieval for predictive pipelines: Provides validated target mRNAs for miRNAs predicted from resources such as miRcode, miRDB, and TargetScan.
• Functional interpretation and prognosis: Enables functional annotation, pathway enrichment, protein–protein interaction analysis, and identification of hub genes and lncRNAs (e.g., KPNA2, MCM7, SNHG1, SNHG3) associated with patient prognosis in HCC.

Methodology:

Interactions are collected by manual literature curation combined with NLP-based filtering; microarray datasets were analyzed using the limma R package; miRNA targets were identified using resources such as miRDB, TargetScan, and miRTarBas; protein–protein interaction networks were constructed with STRING and hub genes identified with Cytoscape; functional annotation, pathway enrichment analyses, and survival analysis were performed as described in the input study.