starBase: a database for exploring microRNA–mRNA interaction maps

by Chris on December 9, 2010

in Web Based Tools

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

UPDATE: starBase v2.0 released

Assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively.

Researchers at Sun Yat-sen University, China have developed a novel database, starBase (sRNA target Base), to facilitate the comprehensive exploration of miRNA–target interaction maps from CLIP-Seq and Degradome-Seq data. The current version includes high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms. By analyzing millions of mapped CLIP-Seq and Degradome-Seq reads, the authors identified ∼1 million Ago-binding clusters and ∼2 million cleaved target clusters in animals and plants, respectively. Analyses of these clusters, and of target sites predicted by 6 miRNA target prediction programs, resulted in identification of approximately 400 000 and approximately 66 000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively.

Two web servers are provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. The web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways.

The starBase is available at http://starbase.sysu.edu.cn/.

Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. (2010) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res [Epub ahead of print]. [article]

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{ 4 comments… read them below or add one }

yjhua2110 May 16, 2011 at 10:28 am

Mouse embryonic stem cells(ESC) Ago2 CLIP-Seq clusters (Leung et al. Nat Struct Mol Biol. 2011 Feb;18(2):237-44.) obtained from Phillip A Sharp lab were added in our starBase (http://starbase.sysu.edu.cn/) and displayed in our deepView genome browser.

jianhua September 27, 2011 at 9:08 pm

Currently, starBase provides several new tools for exploring microRNA regulatory networks from CLIP-Seq(HITS-CLIP, PAR-CLIP, iCLIP) data.
1. miRPathway (http://starbase.sysu.edu.cn/miRPathway.php): KEGG Pathway Analysis for miRNA target genes overlapping with CLIP-Seq data.
2. miRGO (http://starbase.sysu.edu.cn/miRGO.php): Gene Ontology (GO) Analysis for miRNA target genes overlapping with CLIP-Seq data.
3. AGO-RBPs interactions (http://starbase.sysu.edu.cn/AgoRBPs.php): decoding combinatorial effects of Ago and other RNA Binding Proteins(RBPs).

yjhua2110 December 13, 2011 at 7:05 am

starBase also provides protein-RNA interaction maps (http://starbase.sysu.edu.cn/proteinRNA.php) from other RNA Binding Proteins (RBPs), including FOX2, IGF2BP1, IGF2BP2, IGF2BP3, PTB, PUM2, QKI, TDP-43, TNRC6, AGOs/ALG1 , HuR, and Nova. User can explore the combinatorial effects between Ago and other RBPs.

StarBase provides the in-house developed deepView Genome Browser (http://starbase.sysu.edu.cn/browser.php), which enables access to mapped reads, predicted targets (TargetScan (V5.1), PicTar, miRanda, PITA(top), RNA22 and CleaveLand (for plant)) and known miRNA targets (miRecords), ncRNAs, protein coding genes, target clusters, target peaks and target plots.

yjhua2110 November 19, 2012 at 4:58 am

We have constructed TF(transcription factor)->microRNA->targets regulatory networks (http://deepbase.sysu.edu.cn/chipbase/tfmiRtargetNetworks.php) by integrating ChIP-Seq and CLIP-Seq data from our starBase and ChIPBase (http://deepbase.sysu.edu.cn/chipbase/).

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