starBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA Interaction Networks From Large-Scale CLIP-Seq Data

Nucleic Acids Res. 2014 Jan;42(Database issue):D92-7. doi: 10.1093/nar/gkt1248. Epub 2013 Dec 1.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Argonaute Proteins / metabolism
  • Binding Sites
  • Databases, Nucleic Acid*
  • Gene Regulatory Networks
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Immunoprecipitation / methods
  • Internet
  • Mice
  • MicroRNAs / metabolism*
  • Molecular Sequence Annotation
  • Oncogenes
  • Pseudogenes
  • RNA / metabolism*
  • RNA, Circular
  • RNA, Long Noncoding / metabolism
  • RNA, Messenger / metabolism
  • RNA, Untranslated / metabolism*
  • RNA-Binding Proteins / metabolism*
  • Sequence Analysis, RNA

Substances

  • Argonaute Proteins
  • MicroRNAs
  • RNA, Circular
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA, Untranslated
  • RNA-Binding Proteins
  • RNA