Figure 2

Clustered motifs found to be enriched among micro (mi)RNA low-accessibility targets in humans. (A) The motifs found to be enriched among miRNAs low-accessibility targets were clustered according to sequence similarity. Clusters containing at least three motifs are shown. For each cluster, we calculated the average GC content over all motifs in the cluster. The clusters were sorted according to their GC content. Note that the GC content axis is variable. (B) The multiple sequence alignment of the motifs belonging to the cluster with the lowest GC content is shown. For each member of the cluster, the miRNA family for which it was found and the enrichment P value are mentioned. (C) The logo of the motif enriched among miR-410 least accessible targets is shown. This motif holds the lowest GC content found. (D) On the left, the occurrences of UGUAUAUAU among miR-410 predicted targets are shown. The targets were ranked according to the miR-410 global accessibility score. The location of the miRNA binding site is marked with a pink rectangle on the x axis. In the middle, the occurrences vector plot illustrates the number of motif occurrences in each sequence (black for one occurrence, blue for two occurrences). On the right, the actual motif accumulated occurrences versus the expected motif accumulated occurrences in a random dataset are shown, highlighting the observed enrichment. The dashed line (and asterisk) indicates the minimum hypergeometric (mHG) cutoff used for partitioning the sequences into two subsets (such that the motif is enriched in the upper subset).