Regulatory subnetworks for two time points following transient retinal ischemia-reperfusion injury. The networks contain three types of molecules: miRNAs (shown in the left column), TFs (shown as trapezoids in the center), and coding gene targets (shown in the right column). All of these molecules changed their expression in response to IR injury twofold or more, relative to their sham controls. The arrows next to each gene correspond to gene regulation: uppointed arrows indicate increased gene expression; downpointed arrows indicate decreased gene expression. TFs, miRNAs, and coding genes that are linked with the same colored line indicate that the miRNAs target the TFs and at the same time, both of these regulators cotarget the coding genes. With the notable exception of Cebpb, there were no common target coding genes or TFs in the 2 subnetworks, even though they shared 19 common miRNAs. (a) Regulatory subnetwork consisting of miRNAs, TFs, and target genes, which changed their expression at the 24 h IR injury time point relative to their sham controls (FC 2). At this post-IR time point, six TFs were fine-tuned by 29 miRNAs to jointly regulate 17 target genes. (b) Regulatory subnetwork consisting of miRNAs, TFs, and target genes, which changed their expression at 7 days after IR injury relative to their sham controls (FC 2). At this post-IR time point, eight TFs were regulated by 30 miRNAs to jointly control the expression of 31 target genes.
