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Coupled with whole-genome DNA microarrays, ChIPs allow one to determine the entire spectrum of in vivo DNA binding sites for any given protein.
Assuming that we have access to the previous nucleotides before the start of the actual sequence, the likelihood of a sequence having no binding sites for any TF is, where.
It is challenging to rigorously assess subtle improvements due to the scarcity and unreliability of verified binding sites for any ChIP-seq dataset.
In many gene promoters it is possible to find multiple candidate binding sites for any particular transcription factor.
Only CNE 10 lacked binding sites for any of the twelve transcription factors in either species examined.
Careful analysis of the electron density maps verified that there are no secondary binding sites for any of the small molecules, ruling out allosteric contributions to stabilization.
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This hampers selection of a distinctive reference region lacking binding sites for a tau PET ligand.
We found that binding sites for a transcription factor that makes DNA accessible are required together with binding sites for transcriptional activators to produce a functional enhancer.
Nine RP genes had binding sites for all transcription factors.
We used Patser [31], [32] to scan this region for any potential binding site for any of the 263 mammalian transcription factors in TRANSFAC [33].
We used eight types of UniProt functional features: ACT_SITE: amino acid(s) involved in the activity of an enzyme BINDING: binding site for any chemical group (e.g. co-enzyme, prosthetic group, etc).
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