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!
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!
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