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Figure 5 | Genome Biology

Figure 5

From: Discovery of estrogen receptor α target genes and response elements in breast tumor cells

Figure 5

ERE-like sequences are enriched in the extended promoter regions of putative target gene. (a) ERE predictions were made using a previously published model and optimized sensitivity setting. Prediction models were tested on the extended promoter regions (-3,000 to +500, both strands) from the most significant putative ER target and non-responsive genes, ordered by statistical significance. The y-axis represents the relative frequency of binding-site predictions as determined by the number of genes with predicted sites divided by the total number of genes. The number of most significant genes queried is indicated on the x-axis. Frequency of ERE predictions in putative target genes is significantly greater (p = 0.0027) than the similarly ranked non-responsive genes. Binding-site predictions were also carried out using position weight matrices describing sites for (b) Sp1, (c) AP-1 and (d) GATA1. Both Sp1 and AP-1 are known to be involved in regulating ER binding in certain target genes. GATA1 sites were included as negative controls. There is no significant enrichment of these sites in the putative target genes (see p-values in figure).

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