starBase: deciphering miRNA-target interactions from CLIP-Seq and Degradome-Seq data

[rnaNGS]

Dear All,

Here, we introduce a public platform, starBase, for decoding microRNA-target and protein-RNA interaction maps from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP) and degradome sequencing (Degradome-Seq, PARE) data. starBase currently includes tens of thousands of miRNA-target interactions among 6 species. starBase also integrates thousands of binding sites of other RNA-binding proteins (RBPs), such as Agos, PTB, PUM2, QKI, IGF2BP1, IGF2BP2 and IGF2BP3.

the distinctive features in our starBase are as follows:

(i) our improved deepView Genome Browser was developed to provide an integrated view of multidimensional data, including predicted targets (targetScan (V5.1), miRanda, picTar, RNA22, PITA and CleaveLand), known targets, known ncRNAs, genes, clusters....

(ii) Target site intersections : Search for intersections among targets predicted by different target prediction programs[targetScan, miRanda, picTar, RNA22 and PITA].

(iii)MiRNA-target interactions: animal miRNA-target and plant miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively.

(iv) microRNA Pathways, KEGG Pathway Analysis for miRNA target genes overlapping with CLIP-Seq data.

(v) microRNA Gene Ontology, GO Analysis for miRNA target genes overlapping with CLIP-Seq data.

(vi) Two web servers, ClipSearch and DegradomeSearch, were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data.

(vii)RNA-binding proteins, Binding peaks for RBPs: PTB, PUM2, QKI, IGF2BP1-3, FOX2, AGOs/ALG1.

Please visit http://starbase.sysu.edu.cn/ or read our starBase paper (Nucleic Acids Res. doi: 10.1093/nar/gkq1056, First published online: October 30, 2010) for details.

This is the first version of starBase database. We look forward to your feedback.

Thanks!

[yjhua2110]

deepView genome browser to browse microRNA targets

You can use our improved deepView Genome browser to browse and simultaneously compare the microRNA targets predicted by TargetScan (V5.1), PicTar, miRanda, PITA(top), RNA22 and CleaveLand (for plant) target prediction softwares.

Recently, we also have integrated microRNA targets predicted by mirSVR into our starBase. mirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score (Betel et al. Genome Biology 2010, 11:R90) .

[rnaNGS]

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 ourstarBase and displayed in our deepView genome browser.

[rnaNGS]

CLIP-Seq clusters (peaks) for polypyrimidine tract-binding protein (PTB) (Xue et al. Mol. Cell 2009;36:996-1006.) were added in our starBase and displayed in our deepView genome browser.

[rnaNGS]

the release of starBase v2.0, miRNA-target and protein-RNA interaction maps

We are pleased to announce the release of starBase v2.0. In this release, we provided protein-RNA interaction maps from other RNA Binding Proteins, including FOX2, IGF2BP1, IGF2BP2, IGF2BP3, PTB, PUM2, QKI, TDP-43, TNRC6, AGOs/ALG1 and Nova. In addition, we provided many filter steps to guide user to select high-confidence microRNA targets, such as microRNA expression abundance, biology complex, etc.

[yjhua2110]

starBase provides two new tools, miRPathway and miRGO, to explore microRNA regulatory networks by combining Gene Ontology (GO) categories, KEGG biological pathways and high-confidence microRNA targets overlapping with CLIP-Seq data.

[rnaNGS]

combinatorial effects of Ago and other RNA Binding Proteins(RBPs)

starBase provides a new tool, AGO-RBPs interactions : decoding combinatorial effects of Ago and other RNA Binding Proteins(RBPs), such as FOX2, IGF2BP1, IGF2BP2, IGF2BP3, PTB, PUM2, QKI, TDP-43, HuR, and Nova.

Example: Combinatorial effects between Ago and Pum2. Pum2 binding cluster overlaps with the known miR-221/222 target site (Kedde et al. Nat Cell Biol 12:1014-1020.).

[rnaNGS]

starBase Tutorial Paper

a book chapter for describing how to identify miRNA-target interactions and miRNA regulatory networks from high-throughput deep sequencing, CLIP-Seq (HITS-CLIP, PAR-CLIP) and degradome sequencing data using starBase platforms has been published in Adv Exp Med Biol..

Yang JH, Qu LH.
Discovery of microRNA Regulatory Networks by Integrating Multidimensional High-Throughput Data.
Adv Exp Med Biol. 2013;774:251-66.
PMID: 23377977