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ChIPBase a database for Transcription factor-binding sites, motifs (~1290 transcription factors) and decoding the transcriptional regulation of LncRNAs, miRNAs and protein-coding genes from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species
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.
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.
The Open Regulatory Annotation Database (also known as ORegAnno) is designed to promote community-based curation of regulatory information. Specifically, the database contains information about regulatory regions, transcription factor binding sites, regulatory variants, and haplotypes.
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.
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.
RegulonDB provides a database of such regulatory elements, their binding sites and the transcription factors that bind to these sites in E. coli. RegulonDB 9.0 includes 184 experimentally determined transcription factors (TFs) as well as 120 computationally predicted TFs, that is, a total of 304.