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a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. database: website [8] hmChIP a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. database: website [9] HOCOMOCO: a comprehensive collection of human and mouse transcription factor binding sites ...
The DNA binding sites of 519 transcription factors were evaluated. [50] Of these, 169 transcription factors (33%) did not have CpG dinucleotides in their binding sites, and 33 transcription factors (6%) could bind to a CpG-containing motif but did not display a preference for a binding site with either a methylated or unmethylated CpG.
DNA binding sites can be categorized according to their biological function. Thus, we can distinguish between transcription factor-binding sites, restriction sites and recombination sites. Some authors have proposed that binding sites could also be classified according to their most convenient mode of representation. [3]
Phylogenetic footprinting is a technique used to identify transcription factor binding sites (TFBS) within a non-coding region of DNA of interest by comparing it to the orthologous sequence in different species. When this technique is used with a large number of closely related species, this is called phylogenetic shadowing. [1]
Compared to ChIP-chip, ChIP-seq data can be used to locate the binding site within few tens of base pairs of the actual protein binding site. Tag densities at the binding sites are a good indicator of protein–DNA binding affinity, [14] which makes it easier to quantify and compare binding affinities of a protein to different DNA sites. [15]
The TRANSFAC database can be used as an encyclopedia of eukaryotic transcription factors. The target sequences and the regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new transcription factor binding sites (TFBS) recognition algorithms. [12]
Transcription factors (TFs) are proteins that bind DNA and thus regulate the trasncription process. The binding is sequence-specific. A sequence motif [5] is a model that describes the common pattern of the DNA binding sites [6] that a particular TF prefers to bind.
A search algorithm is applied to the data set to identify possible combinations of transcription factors, which have binding sites that are close to the promoter of the gene set of interest. The possible cis-regulatory modules are then statistically analyzed and the significant combinations are graphically represented [ 16 ]