Transcription factor binding site databases
Подписчиков: 0, рейтинг: 0
Transcription factors are proteins that bind genomic regulatory sites. Identification of genomic regulatory elements is essential for understanding the dynamics of developmental, physiological and pathological 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 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 | database | website | ||||||
| ChEA | transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. | database | website | ||||||
| CIS-BP | collection of transcription factor binding sites models inferred by binding domains. | 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 and mouse 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 | ||||||
| MethMotif | An integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles. | database | website | ||||||
| SwissRegulon | a database of genome-wide annotations of regulatory sites. | database | website | ||||||
| TFLink | TFLink gateway provides comprehensive and highly accurate information on transcription factor - target gene interactions, nucleotide sequences and genomic locations of transcription factor binding sites for human and six model organisms. | database | website | ||||||