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Transcription factors (TFs) are proteins that bind DNA and thus regulate the trasncription process. The binding is sequence-specific. 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 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.
This program uses a database of confirmed transcription factor binding sites that were annotated across the human genome. 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.
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]
Chromatin Immunoprecipitation sequencing, also known as ChIP-seq, is an experimental technique used to identify transcription factor binding events throughout an entire genome. Knowing how the proteins in the human body interact with DNA to regulate gene expression is a key component of our knowledge of human diseases and biological processes.
The DNA template labeled at the 3' or 5' end, depending on the location of the binding site(s). Labels that can be used are: radioactivity and fluorescence.Radioactivity has been traditionally used to label DNA fragments for footprinting analysis, as the method was originally developed from the Maxam-Gilbert chemical sequencing technique.
It is thought that interactions with other proteins (eg: Modulator of the activity of Ets called Mae) is one way in which specific binding to DNA is achieved. Transcription factor Ets are a site of signalling convergence. [10] ETS factors act as transcriptional repressors, transcriptional activators, or both. [11]