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Lists of genes associated with Twist1 binding peaks unique to each cell type or shared among multiple cell types were examined for pathway identification and interactions using ToppGene Suite and GeneMANIA (http://www.genemania.org) [ 26, 49].
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Equally seductive to me was their setting of mountains with the deep ravines, clefts and peaks unique to the region.
While the two samples shared some common peaks, the spectra were different, with some peaks unique to each sample.
If the brands had formed separate groups, we might have found peaks unique to each brand.
Proportional Venn diagrams show peaks unique to WT NKX2-5 (A sets); common to WT and mutant proteins (B sets); unique to mutant proteins (C sets).
The MTX treatment unique peaks, compared with the peaks unique to no-treatment, are much less likely to be in CpG islands and exons and more likely to be in LTRs.
In MCF7-T cells, 3,596 ERα binding peaks corresponded to 1,743 annotated genes and 4,644 Pol-II binding peaks corresponded to 3,207 genes were found.
We identified peaks that, among all 3dpf peaks, were unique to MTX treatment and unique to the no-treatment set.
More than 201,000 peaks were shared across subsets and less than 5% of the peaks were unique to any individual subset.
Next, we removed the peaks shared by control and Dex-exposed cells, so that the remaining peaks were unique to each specific sample, and referred to as DMRs.
Only 17%% of cChIP-seq peaks were unique to cChIP-seq, similar to SYDH (17.8 %) and lower than Broad (29.6 % unique).
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