About the starBase Site

Welcome to starBase

   starBase, a public platform for decoding microRNA-target and protein-RNA interaction maps from CLIP-Seq (HITS-CLIP, PAR-CLIP) 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) to decode combinatorial effects of Ago and other RBPs. In addition, starBase provides several web-based softwares (miRPathway, miRGO, ClipSearch, DegradomeSearch) to explore microRNA regulatory networks.    (Release 2.1: 27 Sept. 2011)   (starBase Tutorial Paper)

We have constructed a novel database, ChIPBase, to decode lncRNA (long noncoding RNA) and miRNA regulatory networks(Transcription factors,miRNAs and miRNA targets) by integrating ChIP-Seq data, CLIP-Seq data and miRNA targets from starBase.


How to cite:

    If you make use of the data and web-server presented here, please cite the following article in addition to the primary data sources:
   Yang JH, Li JH, Shao P, Zhou H, Chen YQ, and Qu LH.
   starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.
   Nucleic Acids Res. 2011;39:D202-D209. First published online: October 30, 2010
   [Full Text]   [Print PDF]   [Screen PDF]   [Supplementary Data]

   The current release of starBase contains

  • microRNA Pathways, KEGG Pathway Analysis for miRNA target genes overlapping with CLIP-Seq data.

  • microRNA Gene Ontology, GO Analysis for miRNA target genes overlapping with CLIP-Seq data.

  • AGO-RBP interactions, Stringent Ago Clusters overlapping with binding sites of other RNA Binding Proteins(RBPs).

  • Protein-RNA interactions, Binding peaks for RBPs: FOX2, IGF2BP1, IGF2BP2, IGF2BP3, PTB, PUM2, QKI, TDP-43, TNRC6, AGOs/ALG1, HuR, and Nova.

  • High-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from
    Six organisms: Human, Mouse, Worm, Rice, Arabidopsis and Grapevine

  • Our deepView genome browser   was developed to provide an integrated view of multidimensional data.

  • Target site intersections:   Search for intersections among targets predicted by different target prediction programs.

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

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