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Old 10-30-2010, 02:18 AM   #1
yjhua2110
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Default starBase: explore microRNA–mRNA interaction maps from CLIP-Seq and Degradome-Seq data

Abstract

MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq (HITS-CLIP,PAR-CLIP) and degradome sequencing (Degradome-Seq, PARE) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively. In this study, we introduce a novel database, starBase (sRNA target Base), which we have developed 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, we 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 our identification of approximately 400 000 and approximately 66 000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively. Furthermore, two web servers were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our 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/.

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
Nucleic Acids Res. 2011;39: D202-D209.
doi: 10.1093/nar/gkq1056

First published online: October 30, 2010
http://nar.oxfordjournals.org/conten...pl_1/D202.full

Last edited by yjhua2110; 03-04-2011 at 11:24 PM.
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Old 02-02-2011, 08:50 AM   #2
rnaNGS
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Default integrate Binding site dataset for other RNA-binding proteins (RBPs) into starBase

Binding sites (clusters) for other RNA-binding proteins (RBPs)(PUM2, QKI, IGF2BP1, IGF2BP2 and IGF2BP3) obtained from Tuschl lab (Hafner et al. Cell. 2010 Apr 2;141(1):129-41.) were added in starBase and displayed in deepView genome browser.
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