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transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. database: website [4] CIS-BP collection of transcription factor binding sites models inferred by binding domains. database: website [5] CistromeMap a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. database: website [6 ...
The goal of ChIP-on-chip is to locate protein binding sites that may help identify functional elements in the genome. For example, in the case of a transcription factor as a protein of interest, one can determine its transcription factor binding sites throughout the genome.
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]
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]
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.
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.
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 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.