miRDB

miRDB predicts microRNA (miRNA) targets and provides transcriptome-wide functional annotations to support analysis of miRNA regulatory roles.

Key Features:

• Improved prediction algorithm: Employs an improved algorithm for miRNA target prediction.
• Transcriptome-wide predictions: Provides over 3.5 million predicted targets regulated by approximately 7,000 miRNAs across human, mouse, rat, dog, and chicken.
• Custom sequence-based prediction: Supports custom target prediction using user-provided sequences.
• Cell-specific predictions: Generates cell-specific miRNA target predictions by incorporating expression profiles from over 1,000 cell lines.
• Functional annotations: Associates predicted targets with functional annotations, including Gene Ontology (GO) data.

Scientific Applications:

• miRNA target discovery: Identify putative miRNA–mRNA interactions across transcriptomes of human, mouse, rat, dog, and chicken.
• Functional annotation and pathway analysis: Infer biological processes and pathways affected by miRNAs by integrating predictions with Gene Ontology (GO) annotations.
• Cell-type specific regulatory inference: Obtain cell-specific target sets using expression profiles from over 1,000 cell lines to study context-dependent regulation.
• Custom sequence analysis: Predict targets for user-provided sequences to tailor experimental hypotheses and designs.
• Comparative cross-species analysis: Enable comparative studies of miRNA regulation across the five supported species.

Methodology:

Uses an improved miRNA target prediction algorithm to generate transcriptome-wide predictions across human, mouse, rat, dog, and chicken; incorporates expression profiles from over 1,000 cell lines for cell-specific predictions; supports custom predictions on user-provided sequences; and integrates predictions with Gene Ontology (GO) annotations.