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).