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Human protein reference database as a discovery resource for proteomics

Nucleic Acids Research
Oxford University Press
Publication Date
DOI: 10.1093/nar/gkh070
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  • Biology
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OP-NARE131248 92..97 starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data Jun-Hao Li, Shun Liu, Hui Zhou, Liang-Hu Qu* and Jian-Hua Yang* 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 Received September 15, 2013; Revised October 28, 2013; Accepted November 9, 2013 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 determin- ation 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. 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 rela- tionships. Moreover, starBase v2.0 has been updated to provide the most comprehensive CLIP-Seq experi- mentally 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 visualiza- tion, 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. INTRODUCTION Eukaryotic genomes encode thousands of short and long non-coding RNAs (ncRNAs

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