Transcription factor binding site databases

From HandWiki

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.[1][2] 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 [3]
ChEA 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]
CTCFBSDB a database for CTCF binding sites and genome organization database website [7]
Factorbook a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. database website [8]
hmChIP a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. database website [9]
HOCOMOCO a comprehensive collection of human and mouse transcription factor binding sites models. database website [10]
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 [11][12]
MethMotif
SwissRegulon a database of genome-wide annotations of regulatory sites. database website [13]
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 [14]
TRANSFAC A long-standing curated database of regulatory sites, enhancers, binding site predictions, PSSMs and related analytical software. database website [15]

References

  1. ↑ "ChIP-seq: advantages and challenges of a maturing technology". Nature Reviews. Genetics 10 (10): 669–680. October 2009. doi:10.1038/nrg2641. PMID 19736561. 
  2. ↑ "Insights from genomic profiling of transcription factors". Nature Reviews. Genetics 10 (9): 605–616. September 2009. doi:10.1038/nrg2636. PMID 19668247. 
  3. ↑ "ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data". Nucleic Acids Research 41 (Database issue): D177–D187. January 2013. doi:10.1093/nar/gks1060. PMID 23161675. 
  4. ↑ "ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments". Bioinformatics 26 (19): 2438–2444. October 2010. doi:10.1093/bioinformatics/btq466. PMID 20709693. 
  5. ↑ "Determination and inference of eukaryotic transcription factor sequence specificity". Cell 158 (6): 1431–1443. September 2014. doi:10.1016/j.cell.2014.08.009. PMID 25215497. 
  6. ↑ "CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human". Bioinformatics 28 (10): 1411–1412. May 2012. doi:10.1093/bioinformatics/bts157. PMID 22495751. 
  7. ↑ "CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization". Nucleic Acids Research 41 (Database issue): D188–D194. January 2013. doi:10.1093/nar/gks1165. PMID 23193294. 
  8. ↑ "Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium". Nucleic Acids Research 41 (Database issue): D171–D176. January 2013. doi:10.1093/nar/gks1221. PMID 23203885. 
  9. ↑ "hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data". Bioinformatics 27 (10): 1447–1448. May 2011. doi:10.1093/bioinformatics/btr156. PMID 21450710. 
  10. ↑ "HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models". Nucleic Acids Research 44 (D1): D116–D125. January 2016. doi:10.1093/nar/gkv1249. PMID 26586801. 
  11. ↑ "JASPAR: an open-access database for eukaryotic transcription factor binding profiles". Nucleic Acids Research 32 (Database issue): D91–D94. January 2004. doi:10.1093/nar/gkh012. PMID 14681366. 
  12. ↑ "JASPAR 2020: update of the open-access database of transcription factor binding profiles". Nucleic Acids Research 48 (D1): D87–D92. January 2020. doi:10.1093/nar/gkz1001. PMID 31701148. 
  13. ↑ "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates". Nucleic Acids Research 41 (Database issue): D214–D220. January 2013. doi:10.1093/nar/gks1145. PMID 23180783. 
  14. ↑ "TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species". Database 2022. September 2022. doi:10.1093/database/baac083. PMID 36124642. 
  15. ↑ "Beyond microarrays: find key transcription factors controlling signal transduction pathways". BMC Bioinformatics 7 (Suppl 2): S2–S13. September 2006. doi:10.1186/1471-2105-7-S2-S13. PMID 17118134. 



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