starBase: microRNA targets, CLIP-Seq,degradome sequencing

[rnaworld2110]

Dear All,

We introduce a novel platform, starBase, which we have developed to explore microRNA-target interactions from Argonaute (Ago) CLIP-Seq (HITS-CLIP) and degradome sequencing (Degradome-Seq, PARE) data.

Ago, PUM2, QKI and IGF2BP1-3 CLIP-Seq data, degradome sequencing data, animal and plant microRNA targets [ targetScan (V51), picTar, miRanda, RNA22, PITA(top), mirSVR and CleaveLand] had been integrated into starBase database.

Please visit or read starBase paper (Nucleic Acids Res. doi:10.1093/nar/gkq1056, 2010, October 30) for details.

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

Thanks!

[rnaworld2110]

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 [COLOR="Red"]deepView genome browser[/COLOR].

[rnaworld2110]

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 [COLOR="Red]FOX2, IGF2BP1, IGF2BP2, IGF2BP3, PTB, PUM2, QKI, TDP-43, TNRC6, AGOs/ALG1 and Nova[/COLOR]. In addition, we provided many filter steps to guide user to select high-confidence microRNA targets, such as microRNA expression abundance, biology complex, etc.