starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

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ID: 289497
2013
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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 miRNApseudogene 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 miRNAmediated 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.
Reference Key
openalex_W2117977572 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Jun-Hao Li, Shun Liu, Hui Zhou, Liang‐Hu Qu, Jian-Hua Yang
Journal Nucleic Acids Research
Year 2013
DOI
10.1093/nar/gkt1248
URL
https://doi.org/10.1093/nar/gkt1248
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