Examples of how miRNA regulation of hub genes indirectly affect the expression of large numbers of downstream genes. (A) Among genes differentially expressed after miR-7 transfection, RELA/NF-κB (circled in red) acts as a hub gene, and is found to target many of the differentially expressed genes. One of these, IL1-beta (circled in red) is significantly down-regulated and targets additional differentially expressed genes, thus, amplifying the effect of NF-κB down-regulation. (B) Caveolin-1 (circled in red) is a significantly down-regulated hub gene and a predicted target of miR-128. One of CAV1’s many direct downstream target genes is SMAD2 (also circled in red; regulation shown by arrow/edge pointing from Caveolin-1 to SMAD2), which itself acts as another hub gene. Several downstream targets of SMAD2 are also differentially expressed following miR-128 transfection. Thus by targeting the hub gene CAV1, miR-128 can regulate the non-target hub gene SMAD2 and trigger a ripple effect on the expression of down-stream genes. Key: blue filled circle - significantly down-regulated gene as determined by microarray analysis; red filled circle – significantly up-regulated gene as determined by microarray analysis; green edges: established activating interaction; red edges: established inhibitory interaction; grey edges: predicted interaction of unknown significance.