Role of sequence motifs for context-dependent target sites. (A) The fraction of context-dependent target sites that contain a certain number of discriminative k-mers. Only target sites that cannot be explained by mRNA levels were used. A k-mer is discriminative if it occurs n times in the positive set (e.g., cellular BCBL1-exclusive sites in red) and does not occur in the corresponding negative set (e.g., cellular DG75-exclusive sites) (see Table 1). We sorted discriminative k-mers according to their number of occurrences in decreasing order and chose a cutoff for n based on our randomization experiments (Supplemental Fig. S6; Supplemental Table S3). In all cases, between 75% and 90% of all context-dependent target sites can be explained by a discriminative k-mer. (B) Putative explanations for the full sets of context-dependent target sites are illustrated. On average, >90% can be explained by either differential mRNA levels or the presence of a discriminative k-mer.
