FIGURE 3 

Condition-specific regulation of PBM-only Rap1 target genes. (A) When ChIP–chip P-values for Rap1 for yeast grown in rich medium (Harbison et al, 2004) are used to rank genes in CRACR analysis, ChIP–chip-derived target genes are shown to be repressed after diamide treatment (P<0.001). (B) PBM P-values identify some target genes that are induced (P<0.05) and others that are repressed (P<0.001) in this same diamide treatment condition. (C) The genes induced by diamide treatment are enriched for targets identified by PBM but not ChIP–chip (P<0.05). Genes are ranked by log (PBM rank/ChIP–chip rank). (D) When the IGRs are ordered along the x axis by the significance of their Rap1 PBM P-values and the area statistic measures enrichment of downstream genes that are highly induced (positive signal) or highly repressed (negative signal) in diamide-treated cells, it is evident that the strongest Rap1 binding sites tend to be upstream of genes that are repressed, whereas intermediate affinity binding sites tend to regulate genes that are induced in this diamide condition.