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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] CTCFBSDB a database for CTCF binding sites and genome organization: database: website [7] Factorbook
Upon infection, STING from infected cells can sense the presence of nucleic acids from intracellular pathogens, and then induce interferon β and more than 10 forms of interferon α production. Type I interferon produced by infected cells can find and bind to Interferon-alpha/beta receptor of nearby cells to protect cells from local infection.
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.
TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites .
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]
CollecTF is a database of transcription factor binding sites in the Bacteria domain. [1]CollecTF compiles only experimentally validated TF-binding sites. This is accomplished through the manual curation of peer-reviewed literature with a special focus on the experimental process used to identify TF-binding sites.
The DNA sequence that a transcription factor binds to is called a transcription factor-binding site or response element. [62] Transcription factors interact with their binding sites using a combination of electrostatic (of which hydrogen bonds are a special case) and Van der Waals forces. Due to the nature of these chemical interactions, most ...
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]