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.