starBase swMATH ID: 23121 Software Authors: Li JH, Liu S, Zhou H et al Description: starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. 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. Homepage: http://starbase.sysu.edu.cn/ Related Software: LncDisease; lncRNAdb; miRBase; igraph; BioGRID; ARACNE; BLAT; KEGG; edgeR; Rfam; GitHub; DeepWalk; LncADeep; node2vec; ncPred; word2vec; miRcode; PARAssign; Numbat; WhatsHap Cited in: 9 Publications all top 5 Cited by 32 Authors 3 Wang, Lei 3 Xuan, Zhanwei 2 Ping, Pengyao 2 Zhao, Haochen 1 Aransay, Ana M. 1 Buffa, Francesca M. 1 Dhawan, Andrew 1 Engström, Christopher 1 Feng, Xiang 1 Fu, Benjamin M. M. 1 Hackenberg, Michael 1 Han, Hillary S. W. 1 Harris, Adrian L. 1 Hui, Zhang 1 Johansson, Patrik 1 Keith, Jonathan M. 1 Kuang, Linai 1 Nelander, Sven 1 Pei, Tingrui 1 Reidys, Christian Michael 1 Rodríguez-Ezpeleta, Naiara 1 Scott, Jacob G. 1 Silvestrov, Sergei D. 1 Siyu, Han 1 Swartling, Fredrik J. 1 Wei, Du 1 Weishaupt, Holger 1 Yanchun, Liang 1 Ying, Li 1 Yu, Jingwen 1 Zhou, Shunxian 1 Zhu, Xianyou Cited in 4 Serials 3 Computational & Mathematical Methods in Medicine 2 Mathematical Biosciences 1 Journal of Theoretical Biology 1 Methods in Molecular Biology Cited in 5 Fields 9 Biology and other natural sciences (92-XX) 2 General and overarching topics; collections (00-XX) 2 Combinatorics (05-XX) 1 Ordinary differential equations (34-XX) 1 Computer science (68-XX) Citations by Year