starBase: microRNA targets, high-throughput CLIP-Seq and degradome sequencing data

[rnaworld2110]

Dear All,

We introduce a novel platform, [Only registered users see links. ], which we have developed to explore microRNA-target interactions from Argonaute (Ago) CLIP-Seq (HITS-CLIP, PAR-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 [Only registered users see links. ] or read [Only registered users see links. ] (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]

You can use our improved [Only registered users see links. ] 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.

[Only registered users see links. ]

[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 [Only registered users see links. ].

[rnaworld2110]

Binding sites (peaks) of polypyrimidine tract-binding protein (PTB) obtained from Fu lab (Xue et al. Mol. Cell 2009;36:996-1006.) were added in our starBase and displayed in our [Only registered users see links. ].

[rnaworld2110]

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 [Only registered users see links. ].

[rnaworld2110]

We are pleased to announce the release of [Only registered users see links. ]. In this release, we provided [Only registered users see links. ] 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.

[rnaworld2110]

[Only registered users see links. ]provides two new tools, [Only registered users see links. ]and [Only registered users see links. ], to explore microRNA regulatory networks by combining Gene Ontology (GO) categories, KEGG biological pathways and high-confidence microRNA targets overlapping with CLIP-Seq data.

[rnaworld2110]

[Only registered users see links. ] provides a new tool, [Only registered users see links. ]: 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 ([Only registered users see links. ]).