Figure 2.
ChIP-seq method comparison. (A) Proportion of peaks with a CArG-box (CCW6GG or CCW7G) within a distance of 50 bp among the significant regions detected by each method in the comparison of S1 to Sc. (B) Proportion of peaks detected by each method in the comparison of A1 to Ac with at least one target gene differentially expressed. Only peaks near a gene (3 kb upstream or 1kb downstream) represented in the microarray experiments were considered. The list of genes which expression is affected by AP1 was downloaded from [19], we used the list denoted "Agilent and_or Operon_BH-0h". Default options for QuEST results in the identification of only 66 significant peaks, therefore we used the option "Relaxed peak calling parameters" for Figure 2B. For comparison purposes, all scores reported by the different methods were transformed into rank scores with zero as the rank of the most significant peak.