Figure 2  Best and median ranks of known motifs at 70th, 80th and 90th percentiles. ChIP-seq datasets were ordered by observed best or median ranks of motifs known for respective target TFs. Log-odds: Binding sites scored using Log-odds scores; Match: Binding sites scored using MATCH [26] scores; CI99: Correction with confidence interval of 99% as in Equation (4); BI99: Correction based on the Beta quantile function as in Equation (6); Site: Enrichment accounted for all binding sites; Seq: Enrichment accounted for sequences with at least on site. (A) Best ranks for site enrichment (B) Best ranks for sequence enrichment (C) Median ranks for site enrichment (D) Median ranks for sequence enrichment.