2.6 Analysis of miRNA-mRNA regulatory networks
TargetScan (http://www.targetscan.org/) is a database that can be used to predict miRNA targets by matching conserved 8mer and 7mer sites with the seed region of an input miRNA (Lewis et al., 2005). MiRDB (http://www.mirdb.org/ ) is an online database that predicts miRNA target genes based on high throughput sequencing data (Wong and Wang, 2015). In addition, miRTarBase (http://mirtarbase.mbc.nctu.edu.tw/) is an experimentally-verified miRNA target gene database (Chou et al., 2016). Target genes that were verified by at least 1 of the 3 databases (TargetScan, miRDB, or miRTarBase) were selected as final sreened-out target genes for significant DEMs, and were used to build a miRNA-mRNA pairing file. Finally, the miRNA–mRNA regulatory network was constructed using Cytoscape, an open source bioinformatics software program used to visualize molecular interaction networks (Shannon et al., 2003).