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Furthermore, about 12% of Pol II binding sites (detected with the 8WG16 antibody which recognizes the unphosphorylated form of the C-terminal domain of Rpb1) [ 35] are within sLADs, and the binding site density in non-sLADs is about four folds of that in sLADs.
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Vasarhelyi, B. et al. Three mechanisms in the pathogenesis of pre-eclampsia suggested by over-represented transcription factor-binding sites detected with comparative promoter analysis.
They describe the number of AhR binding sites detected as a ratio with regard to the number of gene promoters analyzed.
The fold occurrences describe the number of c-Myc binding sites detected as a ratio with regard to the number of gene promoters analyzed.
This is consistent with the high percentage of p63 motif-containing p63 binding sites detected by p63scan (90%).
Pocket-Finder 28 was used to compare pocket detection with our ligand binding site detected by Q-sitefinder.
Fluorescence quenching studies with the spin-labeled analogue showed that the binding site detected in the EPR experiments could not be one of the annular or nonannular binding sites.
To remove experimental noise and/or artifacts [ 26] and to avoid possible false positives in binding site detecting, SeqSite filters clusters with fewer than 10 tags or of less than 100-nt length.
The SeqA binding sites we detected with our modified method were exclusively canonical binding sites with binding signals being proportional to the number of GATC sites in the respective regions.
Potential binding sites were detected with the grid-based cavity prediction algorithm.
ISRE (IFN-stimulated response element), GAS (gamma-activated sequence), and hepatocyte nuclear factors HNF1 and HNF3 [34] binding sites were detected with CONSITE (http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite/ 8090/cgi-bin/CONSITE/consite/ally.
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