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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]
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 ...
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA.ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
The ChIA-PET method combines ChIP-based methods, [2] and Chromosome conformation capture (3C) based methods, [3] to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify transciption factor binding sites (TFBS) while 3C has been used to identify long-range chromatin interactions.
Chromatin immunoprecipitation allows binding sites of proteins to be identified. A genome-wide variation of this is known as ChIP-on-chip. Proteins that bind to chromatin are cross-linked in vivo, usually via fixation with formaldehyde. The chromatin is then fragmented and exposed to antibodies specific to the protein of interest. These ...
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.
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 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]