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Snyder's grant will fund the Stanford ENCODE Production Center for Mapping of Regulatory Regions, where researchers will, among other things, map the binding sites for most of the gene activity that regulates molecules called transcription factors in five cell lines.
The presence of a TAAT motif in the binding sites for most other homeodomain proteins suggests the existence of a conserved mechanism for recognition of this core sequence, with further specificity conferred by interactions with bases flanking this core.
This result suggests that PWMs may be sufficient to model binding sites for most of the transcription factors in this study, whereas perhaps other transcription factors may require more complex binding site models.
However, the number of binding sites for most transcription factors modelled in TRANSFAC is fairly low and this limits the conclusions that can be drawn from this analysis.
A previous global analysis of DNA binding sites for most of the transcription factors of yeast provided the first evidence to suggest that Yap1p may regulate the expression of transcription factors [ 30].
Additional support for the notion that many yeast TFs are condition-specific regulators is that binding sites for most TFs confer little effect on reporter expression in typical laboratory growth conditions.
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The heparin binding domain 3 (HBD-3), also located at the C-terminal end, is the major binding site for most studied bacterial Vn-binding proteins8.
The active site is formed at the interface of these two domains and is the binding site for most known AGC kinase small molecule inhibitors.
Inspection of the 3' UTR of Eln revealed four potential binding sites for the most highly up-regulated miRNA, miR-29 (Fig. 4A).
However, as both SgI and SgII harbor at least ten binding sites for Zn2+, most of the seminal plasma Zn2+ will eventually be chelated leading to the activation the prostatic KLKs.
Binding sites for the NF-κB family were the most highly enriched within the innate immune gene signature, whereas binding sites for STAT1 were most highly enriched among the IFN-γ-stimulated genes.
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