Indeed, when the spatial distribution of the H3Y41ph peaks are determined relative to the STAT5 peaks, we find that the location of H3Y41ph is directly coincident with the STAT5 binding event.
Of the 1928 high confidence Suz12 binding peaks we identified in Mbd3 Flox/− ES cells, 330 of these were not found in Mbd3 −/− ES cells (17.1%; Supplementary Table 5).
For ERα binding peaks, we considered all binding peaks except those in the gene desert regions (larger than 100 kb away from a TSS).
To quantify this we carried out overlap analysis of the binding peaks and found, for example, that 89 % of Ubx peaks overlap with Abd-A peaks (Fig. 1b).
In addition, we directly searched for matches to TGATNNAT[g/t][g/a] and TGATTTAT/TGATTTATTT/ATGATTTATGG in both the top 1000 embryo Ubx binding peaks and the 1875 haltere binding peaks but found none of these motifs significantly enriched in either dataset.
When the MACS identified 7693 Tip60 binding peaks were annotated to promoter-TSS, 5′- or 3′-untranslated regions (UTRs), exons, introns and intergenic regions, about 42 % of all high-confidence Tip60 binding peaks were found at promoter-TSS regions (Fig. 4a).
Some of these tools [ 33, 39] use the locations of binding peaks to help find the CREs of a ChIP-ed TF.
Despite BRD4 peak signal intensity being similar in SEs and typical enhancers (TEs) in hESCs, more BRD4-binding peaks were found in SEs than in TEs.
In a region of 2 kb up- and downstream of transcription start sites, AIRE-binding peaks were found in 30% of AIRE-upregulated genes present on the array.
Using discriminative motif discovery on the 10% highest and 10% lowest c-Fos peaks (see Methods), we found that the highest c-Fos peaks in K562 had motif sequences such as CCAAT and CGCGG, which resemble binding profiles for NF-Y and parts of AP-2, but we did not find any AP-1 binding motif or variant thereof.
