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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 ...
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.
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.
Regulatory elements are binding sites for transcription factors, which are involved in gene regulation. [1] Cis-regulatory modules perform a large amount of developmental information processing. [1] Cis-regulatory modules are non-random clusters at their specified target site that contain transcription factor binding sites. [1]
GeneProf database and analysis tool: GeneProf is a freely accessible, easy-to-use analysis environment for ChIP-seq and RNA-seq data and comes with a large database of ready-analysed public experiments, e.g. for transcription factor binding and histone modifications.
EGR1 is a transcription factor important for regulation of methylation of CpG islands. An EGR1 transcription factor binding site is frequently located in enhancer or promoter sequences. [20] There are about 12,000 binding sites for EGR1 in the mammalian genome and about half of EGR1 binding sites are located in promoters and half in enhancers. [20]
Analysis of transcription factor binding site analysis showed that the risk allele disrupt a binding site for AP-2 alpha. [ 20 ] Mutations in the AP-2 alpha gene also cause branchio-oculo-facial syndrome, [ 19 ] which has overlapping features with Van der Woude syndrome such as orofacial clefting and occasional lip pits what make rs642961 a ...
This way, the fragments produced by DNaseI digestion will contain FAM, and will be detectable by the capillary electrophoresis machine. Typically, carboxytetramethyl-rhodamine (ROX)-labelled size standards are also added to the mixture of fragments to be analyzed. Binding sites of transcription factors have been successfully identified this way ...