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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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 https://web.archive.org/web/20110222111721/http://starbase.sysu.edu.cn/ and displayed in our deepView genome browser.
starBase also provides protein-RNA interaction maps 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 https://web.archive.org/web/20110222111721/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.
We have constructed TF(transcription factor)->microRNA->targets regulatory networks by integrating ChIP-Seq and CLIP-Seq data from our starBase and ChIPBase http://rna.sysu.edu.cn/chipbase/.