Transcription factor binding site databases

Identification of genomic regulatory elements is essential for understanding the dynamics of cellular processes. Recent advances in chromatin immunoprecipitation followed by sequencing (ChIP-seq) have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.

Transcription factor binding site databases

Comprehensive List of transcription factor binding sites (TFBSs) databases based on ChIP-seq data as follows:

Name	Description	type	Link	References
ChIPBase	ChIPBase a database for transcription factor binding sites, motifs (~1290 transcrition 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	database	[website
ChEA	transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.	database	website
CistromeMap	a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.	database	website
CTCFBSDB	a database for CTCF binding sites and genome organization	database	website
Factorbook	a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.	database	website
hmChIP	a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.	database	website
HOCOMOCO	a comprehensive collection of human transcription factor binding sites models.	database	website
JASPAR	The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes.	database	[website
SwissRegulon	a database of genome-wide annotations of regulatory sites.	database	[website
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