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Updated: Jun 7, 2026
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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
Published on: August 21, 2019
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
Jian-Hua Yang1, Jun-Hao Li, Peng Shao
1Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China.
Nucleic Acids Research
|November 2, 2010
Summary
We developed starBase, a novel database for exploring microRNA (miRNA) target interactions using CLIP-Seq and Degradome-Seq data. It identifies millions of regulatory relationships, aiding gene expression research.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- MicroRNAs (miRNAs) are small non-coding RNAs regulating gene expression by targeting messenger RNAs.
- Identifying specific miRNA-target interactions is a significant technical challenge in molecular biology.
- High-throughput sequencing methods like CLIP-Seq and Degradome-Seq offer new avenues for target identification.
Purpose of the Study:
- To introduce starBase, a novel database for comprehensive exploration of miRNA-target interaction maps.
- To integrate and analyze data from CLIP-Seq and Degradome-Seq experiments.
- To provide web servers for discovering novel miRNA target sites.
Main Methods:
- Development of the starBase database integrating CLIP-Seq and Degradome-Seq data.
- Analysis of millions of mapped reads from 21 CLIP-Seq and 10 Degradome-Seq experiments across six organisms.
- Utilizing 6 miRNA target prediction programs alongside experimental data.
Main Results:
- Identification of approximately 1 million Argonaute-binding clusters and 2 million cleaved target clusters.
- Discovery of approximately 400,000 miRNA-target regulatory relationships from CLIP-Seq data.
- Identification of approximately 66,000 miRNA-target regulatory relationships from Degradome-Seq data.
- Implementation of web servers for querying and exploring miRNA-target interactions, common targets, gene ontologies, and pathways.
Conclusions:
- starBase provides a valuable resource for studying miRNA-mediated gene regulation.
- The database facilitates the comprehensive analysis of miRNA-target interactions derived from high-throughput sequencing data.
- Web servers enhance accessibility for researchers to discover and explore miRNA targets.
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