starbase

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…]

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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 http://starbase.sysu.edu.cn/.

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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 http://starbase.sysu.edu.cn/.

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]

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