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DiffBind was used to identify the set of Dichaete-Dam binding intervals unique to D. melanogaster and the set conserved in all four species [ 87].
The highly conserved intervals contain significantly more Sox motifs on average (mean = 4.53) than the binding intervals unique to D. melanogaster (mean = 1.29, p = 3.03e-193, Wilcoxon rank sum test with continuity correction), showing that the presence and number of Sox motifs is positively correlated with Dichaete binding conservation.
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We also used the translated binding data to determine the location of binding intervals with respect to transcription start sites.
The distances from binding intervals to TSSs were calculated and plotted using ChIPpeakAnno [ 125].
Interestingly, binding sites unique to either PU.1 or Spi-B demonstrated distinct profiles.
Specifically, binding sites unique to K562 cells show reduced nucleosome occupancy relative to the same genomic loci in GM12878 cells.
ADA binding is unique to DPP-4 among DASH family and DPP-4 inhibitor was reported not to affect this binding [ 14].
There is a very large binding cooperativity unique to Stemloop IV that favors formation of the SLIV/SNF/U2A′ complex.
On average, GR binding sites unique to A549 do not show nucleosome depletion in RS4; 11 (Fig. 1b, top panel).
There is huge variation between individual ESR1 ChIP experiments with most binding sites unique to a single experiment.
Interestingly, only one common binding motif was found in the two sets, while the rest of the binding motifs were unique to each set (Tables 11 and 12).
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