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Figure 5 | BMC Genomics

Figure 5

From: Relationship between estrogen receptor α location and gene induction reveals the importance of downstream sites and cofactors

Figure 5

Response to hERα increases in function of the number of ChIP sites along transcripts. Ranks of the induction scores are shown as boxplots in function of the number of ChIP sites. In B-D, ChIP sites are further filtered according to the presence or absence of consensus elements for hERα (A) or FOX (C, D). A motif is assigned to a binding site if the occupancy, computed using posterior decoding, is greater than 0.5 (cf. Methods). The ranks of the induction scores of the cancer expression compendium and of the study on primary estrogen receptor targets have been pooled to avoid small sample size effects. Significance of the comparisons is assessed using the Wilcoxon rank sum test, i.e. comparison between equally colored distributions are made. A-B. Effect of ERE motifs. For ChIP-pet sites the presence of an ERE improves the correlation between ranks and number of sites (orange boxes). No statistically significant improvement is detected for the ChIP-chip sites (blue boxes). C-D. Effect of FOX motifs. In addition to the presence of an ERE, the presence of a FOX motif improves significantly the association for the ChIP-pet sites (red box). Comparison with panel B (black boxes) indicates that many ChIP-pet sites with EREs also have FOX sites. Despite a shift in the distribution to higher ranks, no statistically significant improvement is detected for the ChIP-chip sites (purple boxes) with a FOX site.

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