Figure 5.

Identification of mammalian tissue specific miRNA target sites by CompMoby. (A) Output file format generated by CompMoby given a user defined Bonferroni corrected -log₁₀ p-value cutoff of greater than 0. These results represent the top motif cluster from two independent runs of CompMoby on two different sets of co-regulated genes that were significantly down-regulated with miR-1 or miR-124 overexpression in HeLa cells [34]. "Species" column represents the sequence source of the predicted "Motif". "# Cluster" represents the number of occurrences of the motif cluster from the reference species sequence set and "# Background" the number of occurrences in the background sequence set. The "-log₁₀ p-value" and "Expected" columns are calculated as described in Figure 3B. (B) WebLogo (v. 2.8) representation of the miR-1 site identified by CompMoby. Also shown is the match between the predicted motif cluster to the miR-1 seed region. U (mRNA) is equivalent to T (DNA). (C) WebLogo (v. 2.8) representation of the miR-124 site identified by CompMoby. Also shown is the match between the predicted motif cluster to the miR-124 seed region.