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Association studies of affected individuals with Cystic Fibrosis identified the causal variant, a regulatory SNP rs7910656 on the non-coding region of FAS gene on human chromosome 10q24.1, which includes the binding site of many transcription factors especially the NFκB complex, but no molecular alterations were detected by conventional approaches.
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In addition, the binding sites of many TFs are so similar that they do not allow a reliable prediction of function; clearly, sequence preferences can be altered by the binding context [23].
MacIsaac et al. used evolutionarily conservative criteria to computationally identify the binding sites of many TFs.
The in vitro binding sites of many AP2/ERF superfamily proteins have been studied in detail.
The ambiguity in binding sites of many of the probes (Table 2 and Figure 7) prohibits detailed interpretation.
The drawback of open chromatin assays is their lack of specificity, as the identified sites typically correlate with the binding sites of many different transcription factors 32.
In the TFCONES database, a considerable fraction of conserved elements were annotated overlapping with the binding sites of many transcription factors [ 28].
Interestingly, the binding sites of many of the anti-retroviral protease inhibitors like nelfinavir and lopinavir were also observed to have similarity to the predicted binding site in PknD.
We also confirmed that 5hmC is highly enriched at the core of distal binding sites of many TFs, such as Zfx and Esrrb (Additional file 1: Figure S1B) [ 11, 12].
Although recent study showed that it was possible to identify binding sites of more than one TFs using a single ChIP-seq experiment [ 9], the cost is still prohibitively expensive to identify binding sites of many TFs in various cell types and conditions.
NKX2-5Y191C pealsoalshowedwed over-representation of the motif 5′TAATC3′, which is similar to the binding sites of many non-NK-2 class HD proteins, including HOX proteins, as well as that of NK-2 proteins that lack HD tyrosine 54, such as NKX1-2 (Betger et al., 2008).
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