Prediction for CircRNA/miRNA/mRNA Interactions

The ceRNA hypothesis is that RNA transcripts can crosstalk by competing for common miRNAs, where MREs are the foundation of this interaction (Salmena et al., 2011). Any RNA transcript with MREs might act as a ceRNA, and ceRNAs include pseudogene transcripts, circRNAs and mRNAs; these transcripts can compete for the same MER to mutually regulate it. We constructed the ceRNA network by merging common targeted miRNAs. The circRNA/miRNA/mRNA interactions were predicted in combination with in-house miRNA target prediction software according to TargetScan and miRanda software (Friedman et al., 2009; Huang et al., 2016) to identify the potential targets of miRNAs. Three conditions must exist for the ceRNA network to occur (Salmena et al., 2011). First, the relative concentration of ceRNAs and their miRNAs is clearly important; second, the effectiveness of a ceRNA depends on the number of miRNAs that it can “sponge”; third, not all of the MREs on ceRNAs are equal. Therefore, we accept only the ceRNA-pair relations that passed filtering measures (P < 0.05). A graph of the circRNA/miRNA/mRNA network was made using Cytoscape software (version 3.5.1) to visualize these relationships.

Next, we used Gene Ontology (GO²) to reveal the biological process, cellular component and molecular function of the target mRNAs. Significant pathways were identified using pathways in the Kyoto Encyclopedia of Genes and Genomes database (KEGG³). A P < 0.05 indicates the significance of GO and KEGG pathway terms. The FDR was calculated to correct the P.