Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

starBase (starBase)

General information

Description: starBase is designed for decoding Pan-Cancer and Interaction Networks of lncRNAs,miRNAs,competing endogenous RNAs(ceRNAs),RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP,PAR-CLIP,iCLIP,CLASH) data and tumor samples
Year founded: 2011
Last update: 2013-9
Version: v2.0
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Sun Yat-sen University
Address: Guangzhou 510275,PR China
City: Guangzhou
Province/State: Guangdong
Country/Region: China
Contact name (PI/Team): Liang-Hu Qu
Contact email (PI/Helpdesk): lssqlh@mail.sysu.edu.cn

Record metadata

Created on: 2015-06-20
Curated by:
Lin Xia [2016-03-28]
Lin Xia [2015-11-20]
Lina Ma [2015-11-18]
Lina Ma [2015-11-10]
Lin Xia [2015-06-26]

Ranking

All databases:
63/4692 (98.679%)
Interaction:
9/698 (98.854%)
63
Total Rank
1,293
Citations
143.667
z-index

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Publications

24297251
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. [PMID: 24297251]
Li JH, Liu S, Zhou H, Qu LH, Yang JH.

Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs) (e.g. lncRNAs, pseudogenes and circRNAs) and competing endogenous RNAs (ceRNAs) have been implicated in cell-fate determination and in various human diseases, surprisingly little is known about the regulatory interaction networks among the multiple classes of RNAs. In this study, we developed starBase v2.0 (http://starbase.sysu.edu.cn/) to systematically identify the RNA-RNA and protein-RNA interaction networks from 108 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH) data sets generated by 37 independent studies. By analyzing millions of RNA-binding protein binding sites, we identified ?9000 miRNA-circRNA, 16 000 miRNA-pseudogene and 285,000 protein-RNA regulatory relationships. Moreover, starBase v2.0 has been updated to provide the most comprehensive CLIP-Seq experimentally supported miRNA-mRNA and miRNA-lncRNA interaction networks to date. We identified ?10,000 ceRNA pairs from CLIP-supported miRNA target sites. By combining 13 functional genomic annotations, we developed miRFunction and ceRNAFunction web servers to predict the function of miRNAs and other ncRNAs from the miRNA-mediated regulatory networks. Finally, we developed interactive web implementations to provide visualization, analysis and downloading of the aforementioned large-scale data sets. This study will greatly expand our understanding of ncRNA functions and their coordinated regulatory networks.

Nucleic Acids Res. 2014:42(Database issue) | 939 Citations (from Europe PMC, 2020-09-19)
21037263
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. [PMID: 21037263]
Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH.

MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, 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. In this study, we introduce a novel database, starBase (sRNA target Base), which we have developed 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, we 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 our identification of approximately 400,000 and approximately 66,000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively. Furthermore, two web servers were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our 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/.

Nucleic Acids Res. 2011:39(Database issue) | 354 Citations (from Europe PMC, 2020-09-19)