7 replies to this topic

[yjhua2110]

Dear All,

Here, we introduce a public platform, starBase (sRNA target Base), which we have developed to explore miRNA-target interactions from Argonaute (Ago) CLIP-Seq (HITS-CLIP) and degradome sequencing (Degradome-Seq, PARE) data.

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 of starBase as follows:
(1) 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....

(2) Target site intersections: Search for intersections among targets predicted by different target prediction programs.

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

(4) Two web servers, ClipSearchand 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. doi: 10.1093/nar/gkq1056, First published online: October 30, 2010) for details.

This is the first version of starBase , we are looking forward to hearing your feedback.

Thanks!

Edited by yjhua2110, 09 November 2010 - 08:26 AM.

[yjhua2110]

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.

Edited by yjhua2110, 10 November 2010 - 07:22 PM.

[yjhua2110]

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]

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.

[yjhua2110]

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.

Edited by yjhua2110, 09 May 2011 - 06:45 AM.

[yjhua2110]

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.

[yjhua2110]

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.).