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Relations of the differentially expressed genes and the transcription factor binding motifs were further investigated using the Pubgene Ontology Database (www.pubgene.org).org
To reduce false positive peaks, we re-processed the raw data using stringent parameters to identify 92 314 high-confidence binding loci for 15 different cell lines, and 157 158 binding motifs were further predicted from these regions.
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This binding motif was further discovered to also exist in streptavidin-binding aptamers (SBAs) selected by three other laboratories using different methods.
Interestingly, when the HNF4α binding motif was further searched using a web-based search tool, HNF4 Motif Finder [ 40], a potential HNF4 binding site was identified in the promoter region of MMP15, which could lead to a direct binding of HNF4α when HNF4α antibody was used to immunoprecipitate chromatin.
(C) MalR, CcpA, and Fnr binding motifs were predicted from the pathways.
Apparent interactions that do not match the known binding motifs are a cause for concern and should be further validated.
The ion binding motifs are shown.
In Fig. 1D the different binding motifs are illustrated.
The predicted TF-binding motifs were compared using Pearson correlation coefficients calculated using Tomtom [ 62] and further clustered using Hierarchical Clustering Explorer 3.5 [ 63].
In total, 68,000 OCRs were identified, and a number of TF-binding motifs were predicted.
For example, an SGF-1 binding motif was located 441 bp upstream from Sericin-1B, and Br- and Kr-binding motifs were located 712 bp upstream from Sericin-1B.
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