title: starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.
abstract: 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.
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China.
authors.forename: Jun-Hao
authors.initials: JH
authors.lastname: Li
authors.forename: Shun
authors.initials: S
authors.lastname: Liu
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Yang
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000378:metabolism; D001665:Binding Sites; D030561:Databases, Nucleic Acid; D053263:Gene Regulatory Networks; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D009857:Oncogenes; D011544:Pseudogenes; D012313:RNA / Q000378:metabolism*; D000079962:RNA, Circular; D062085:RNA, Long Noncoding / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D060565:Argonaute Proteins; D035683:MicroRNAs; D000079962:RNA, Circular; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D012313:RNA