Figure 1

Base composition differs in active versus inactive ZFP target sites. A) Total base counts for active and inactive ZFP target sites (from ZFTS135, a dataset of 135 experimentally validated 9-bp target sites, see Additional File 1 - Table S1) reveal that variation in the average frequency of each base differentiates active versus inactive target sites. The total number of G and T residues relative to A and C is inflated because currently available OPEN pools are designed to target GNN and TNN triplets. B) Positional base counts, i.e., average base counts for each position within target site triplets (1^st, 2^nd, 3^rd), suggest that thymine bases negatively impact ZFP binding at all three positions. C) An iceLogo [50] generated from ZFTS135 illustrates the difference in percentage composition of nucleotides at each position, from 1 - 9 (5' to 3'), between the positive class and the entire dataset. For example, 78% of all sites in ZFTS135 have a G in position 1, whereas 88% of all active sites have a G at position 1, resulting in a difference of 10%. Positive difference values indicate that, on average, the indicated bases are favored at those positions in active sites; negative difference values indicate that the indicated bases are disfavored. These position-specific differences in percentage composition also support the conclusion that thymine bases tend to occur in inactive targets (i.e., they have large negative propensities).