starBase v2.0 logoStarBase has been updated to explore Pan-Cancer pattern of lncRNAs, miRNAs, RNA-binding proteins (RBP) and their regulatory networks (ceRNA, coexpression) by mining expression profiles of miRNAs, lncRNAs and mRNAs across 14 cancer types (>6000 samples) from The Cancer Genome Atlas (TCGA) Data Portal (all data available without limitations).
StarBase provides the following Pan-Cancer Analysis Services:
  1. starBase constructed Pan-Cancer expression profiles of lncRNAs, miRNAs from TCGA RNA-Seq and miRNA-Seq data.
  2. starBase generated Pan-Cancer networks of CLIP-Seq experimentally supported miRNA-lncRNA and miRNA-mRNA interactions.
  3. starBase identified Pan-Cancer ceRNA networks involving lncRNAs and mRNAs by analyzing >6000 tumor and normal samples and [click to continue…]


starBase v2.0 logostarBase v2.0 update available

starBase is a database that can be used for decoding miRNA-mRNA, miRNA-ceRNA, miRNA-lncRNA, miRNA-circRNA, miRNA-pseudogene and protein-RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. starBase v2.0 now also provides visualization, analysis, discovery and downloading of above-mentioned large-scale functional genomics data.

Currently, starBase v.20 includes (1)108 CLIP-Seq datasets, (2)~500,000 miRNA-mRNA interactions, (3)~10,000 miRNA-lncRNA interactions(4)~16,000 miRNA-pseudogene interactions, (5)~9,000 miRNA-circRNA interactions, (6)~10,000 ceRNA pairs, (7)~300,000 protein-RNA interactions, (8) two tools for functional annotation from ceRNA and miRNA regulatory networks.
starBase v2.0 is freely available at

Incoming search terms for this article:


starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

UPDATE: starBase v2.0 released

Assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively.

Researchers at Sun Yat-sen University, China have developed a novel database, starBase (sRNA target Base), to facilitate the comprehensive exploration of miRNA–target interaction maps from CLIP-Seq and Degradome-Seq data. The current version includes high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms. By analyzing millions of mapped CLIP-Seq and Degradome-Seq reads, the authors identified ∼1 million Ago-binding clusters and ∼2 million cleaved target clusters in animals and plants, respectively. Analyses of these clusters, and of target sites predicted by 6 miRNA target prediction programs, resulted in identification of approximately 400 000 and approximately 66 000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively.

Two web servers are provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. The web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways.

The starBase is available at

Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. (2010) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res [Epub ahead of print]. [article]

Incoming search terms for this article: