TarBase

TarBase v9.0 is the reference database of experimentally supported microRNA (miRNA) targets on protein-coding transcripts. Developed and maintained by the DIANA Lab at the University of Thessaly, TarBase provides researchers with a comprehensive, curated collection of validated miRNA-gene interactions.

Overview

TarBase exclusively contains experimentally supported miRNA-gene interactions identified through both high-throughput and low-throughput methods. The database represents a critical resource for researchers studying post-transcriptional gene regulation mediated by microRNAs.

Database Content

Experimental Methods

TarBase integrates interactions from two main sources:

1. High-Throughput Interactome Mapping: Raw datasets from state-of-the-art methods including:
   • HITS-CLIP (High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation)
   • PAR-CLIP (Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation)
   • CLASH (Crosslinking, ligation and sequencing of hybrids)
   • microCLIP (with super learner framework scoring)
2. Low-Throughput Validation: miRNA targets verified through manual curation of published literature and traditional experimental methods

All datasets are uniformly analyzed to maintain consistently high-quality standards across the database.

Species Coverage

TarBase v9.0 provides interaction data for multiple species, organized into separate downloadable files:

• Homo sapiens (Human)
• Mus musculus (Mouse)
• Viral species (Including EBV and other virally-encoded miRNAs)
• Other species

Annotations and Standards

TarBase uses standardized nomenclatures for consistency:

• miRNA annotations: miRBase v22
• Gene annotations: Ensembl 109
• Genomic coordinates: Absolute coordinate system relative to the entire genome

Key Features

Advanced Query Interface

Users can perform sophisticated searches with:

• miRNA-to-target queries: Find all experimentally validated targets for specific miRNAs
• Gene-to-miRNA queries: Identify all miRNAs that target specific genes
• Autofill functionality: Reduces mistyped entries when entering miRNA names/IDs or gene symbols/IDs

Comprehensive Filtering Options

Refine searches based on:

• miRNA confidence level (according to miRBase annotation)
• DIANA-microT-CDS prediction scores
• Cell line, cell type, and tissue
• Experimental conditions and methods
• Species
• miRNA expression levels
• Binding site information
• microCLIP super learner framework scores

Rich Metadata

Each miRNA-gene interaction includes detailed information:

• Experimental context: Method, technique, cell line, cell type, tissue, treatment conditions
• Genomic details: Binding site coordinates, transcript region (3’UTR, CDS, etc.), chromosome, strand
• Validation details: Regulation type (up/down-regulation), validation type, phenotype
• Publication information: PubMed ID linking to source literature
• Confidence metrics: Biological replicate consistency, interaction group rankings
• Prediction scores: DIANA-microT-CDS 2023 scores for experimental interactions

Interactive Visualizations

TarBase provides network graph visualizations to explore:

• Combinatorial effects of multiple miRNAs on common targets
• Network structure requires genes interacting with at least two selected miRNAs
• Visual representation with miRNAs and target genes as distinct node types

Integration with External Resources

TarBase is interconnected with:

• PubMed: Direct links to supporting publications
• Ensembl: Gene and transcript coordinate links
• miRBase: miRNA sequence and annotation details
• DIANA-microT 2023: Over 86 million in-silico predicted miRNA targets for complementary analysis

Data Downloads

Complete interaction datasets are freely available in tab-delimited format (gzip-compressed) for:

• Homo sapiens
• Mus musculus
• Viral species
• Other species

Each download file includes 22 fields per interaction, providing comprehensive details about:

• Species, miRNA, and gene identifiers
• Binding site genomic coordinates
• Experimental methodology and conditions
• Regulation type and confidence metrics
• DIANA-microT-CDS prediction scores

Accessibility

TarBase v9.0 is completely free and open to all users without any registration or login requirements, supporting the principles of open science and data sharing.

Citation

If TarBase is helpful for your research, please cite:

Giorgos Skoufos, Panos Kakoulidis, Spyros Tastsoglou, Elissavet Zacharopoulou, Vasiliki Kotsira, Marios Miliotis, Galatea Mavromati, Dimitris Grigoriadis, Maria Zioga, Angeliki Velli, Ioanna Koutou, Dimitra Karagkouni, Steve Stavropoulos, Filippos S Kardaras, Anna Lifousi, Eustathia Vavalou, Armen Ovsepian, Anargyros Skoulakis, Sotiris K Tasoulis, Spiros V Georgakopoulos, Vassilis P Plagianakos, Artemis G Hatzigeorgiou (2023). “TarBase-v9.0 extends experimentally supported miRNA–gene interactions to cell-types and virally encoded miRNAs.” Nucleic Acids Research, DOI: 10.1093/nar/gkad1071

Funding

This research has been co-financed by the European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH – CREATE – INNOVATE (project code: T2EDK-00391).

Contact

TarBase is developed and maintained by the DIANA Lab at the University of Thessaly, Greece.