starBase

starBase provides a database of miRNA-target interactions derived from CLIP-Seq and Degradome-Seq data to identify Argonaute-binding sites and miRNA-mediated cleavage events.

Key Features:

• Datasets: Incorporates data from 21 CLIP-Seq and 10 Degradome-Seq experiments across six organisms.
• Read-level analysis: Analyzes millions of mapped reads to identify approximately 1,000,000 Ago-binding clusters and approximately 2,000,000 cleaved target clusters.
• miRNA-target interactions: Reports ~400,000 interactions identified from CLIP-Seq data and ~66,000 interactions from Degradome-Seq data.
• Prediction integration: Integrates predictions from six established miRNA target prediction programs.
• Computational discovery and query support: Provides computational discovery of novel miRNA target sites from CLIP-Seq and Degradome-Seq data and supports queries for common targets, gene ontology, and biological pathway associations.

Scientific Applications:

• Mapping miRNA-target networks: Elucidates miRNA-mediated regulatory relationships by combining CLIP-Seq and Degradome-Seq evidence.
• Argonaute-binding site identification: Identifies Argonaute (Ago)-binding clusters from CLIP-Seq data.
• miRNA cleavage detection: Detects cleaved target clusters indicative of miRNA-mediated cleavage from Degradome-Seq data.
• Target validation and discovery: Supports validation and discovery of miRNA targets through integration with prediction program outputs.
• Functional annotation: Links miRNA-target interactions to gene ontology terms and biological pathways for functional interpretation.

Methodology:

Analysis of mapped reads from CLIP-Seq and Degradome-Seq to identify Ago-binding clusters and cleaved target clusters, combined with integration of outputs from six miRNA target prediction programs.