starBase: explore microRNA–mRNA interaction maps from CLIP-Seq and Degradome-Seq data

[yjhua2110]

Dear All,

Here, we introduce a public platform, starBase (sRNA target Base), for exploring microRNA-target interaction maps from Argonaute (Ago) CLIP-Seq (HITS-CLIP,PAR-CLIP) and degradome sequencing (Degradome-Seq, PARE) data.

CLIP-Seq (HITS-CLIP,PAR-CLIP) and Degradome-Seq (PARE) are the newest high-throughput technology for the transcriptome-wide identification of miRNA target sites in animals and plants. Currently, starBase contains high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms: human, mouse, C.elegans, Arabidopsis thaliana, Rice, Grapevine.

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

Please visit http://starbase.sysu.edu.cn/ or read our starBase paper (Nucleic Acids Res. 2011;39: D202-D209. 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!
JianHua

[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.

[yjhua2110]

integrating mirSVR microRNA targets into 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) . mirSVR was developed by Leslie's group at Memorial Sloan-Kettering Cancer Center.

We have integrated microRNA targets predicted by mirSVR into our starBase. You can browse the mirSVR microRNA targets using our deepView Genome Browser.

[yjhua2110]

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 our starBase 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]

Mouse embryonic stem cells(ESC) Ago2 CLIP-Seq clusters

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

[yjhua2110]

Human and Mouse TDP-43 CLIP-Seq(iCLIP) clusters

Binding sites (clusters) for Human and Mouse TDP-43 (Tollervey et al. Nat Neurosci. 2011 Apr;14(4):452-8; Polymenidou et al. Nat Neurosci. 2011 Apr;14(4):459-68.) obtained from from Ule and Yeo labs were added in our starBase.

[yjhua2110]

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.

[rnaNGS]

microRNA regulatory networks

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.