Energy walk across 5 potential regulatory regions for CNC and CPC pairs.

*For these regions, both strands were examined, explaining the higher number of binding sites.
For each miRNA/mRNA of a CNC (A) pair and CPC pair (B), we analyzed 5 predicted regulatory regions of the mRNA for enrichment in binding sites for the corresponding miRNA. The number of sequences from each of these 5 regions containing high energy binding sites (number of high energy binding sites in CNC and CPC pairs) for the miRNA was recorded. The miRNA/mRNA pairs were then shuffled, each miRNA reassigned to a randomly selected mRNA. The same analysis was performed on this control set (number of high energy binding sites in shuffled pairs). By comparing the number of high energy binding sites in the CNC and CPC pairs with the number of high energy binding sites in the same number of shuffled pairs for each region, we were able to find regions that were significantly enriched in binding sites for miRNAs. This comparison was done using Fisher's exact test for categorical data with p-values<0.05 defined as significant.