Supplemental Material, Figure 2 (http://www.ehponline.org/docs/2009/0800485/suppl.pdf) shows differential binding profiles for a select group of genes chosen from among the 750 top-ranked genes.
The clinical efficacy of antipsychotic drugs has been associated with a certain binding profile for a set of G protein-coupled receptors (GPCR s.
We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, following transient expression in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility.
We compiled a list of 118 binding matrices for this analysis, but if binding profiles for other TFs can be generated from a reasonable number of known binding sites, we could identify more TFs that possibly regulate the accumulation of seed storage reserves.
Zoomed binding profiles for both TFs are highly similar, which is a striking observation given that both profiles were recorded in different growth conditions (sucrose-supplemented for LysM-specific ChIP versus tryptone-supplemented medium for Ss-LrpB-specific ChIP).
Detailed binding profiles for αH3K27ac, αH3K27me3 and αMi2β were compared across a ∼6 Kb region spanning the transcription start sites for these genes in both Mbd3 flox/− and Mbd3 −/− ES cells.
The binding profiles for these target gene loci showed that most have a strong enrichment for Esg-Dam binding at the 5′ UTR of their transcript isoforms, that is, close to the transcription start site (Fig 4C).
We next determined the primary binding profiles for each protein by aligning the enriched sequences to a seed sequence, and calculating a position weight matrix (PWM) using the background corrected multinomial method as described previously (Jolma et al., 2010, 2013).
To address the conservation of the binding specificities, we first calculated motif similarity score of all previously existing B1H and HT-SELEX binding profiles for Drosophila and mammals, respectively, and illustrated their similarities as a network map.
