Transcription factor binding site databases

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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]

References

  1. ↑ Park, Peter J. (1 October 2009). "ChIP–seq: advantages and challenges of a maturing technology" (in en). Nature Reviews Genetics 10 (10): 669–680. doi:10.1038/nrg2641. ISSN 1471-0056. PMID 19736561. 
  2. ↑ Farnham, Peggy J. (1 September 2009). "Insights from genomic profiling of transcription factors" (in en). Nature Reviews Genetics 10 (9): 605–616. doi:10.1038/nrg2636. ISSN 1471-0056. PMID 19668247. 
  3. ↑ Yang, Jian-Hua; Li, Jun-Hao; Jiang, Shan; Zhou, Hui; Qu, Liang-Hu (1 January 2013). "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): D177–187. doi:10.1093/nar/gks1060. ISSN 1362-4962. PMID 23161675. 
  4. ↑ Lachmann, Alexander; Xu, Huilei; Krishnan, Jayanth; Berger, Seth I.; Mazloom, Amin R.; Ma'ayan, Avi (1 October 2010). "ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments". Bioinformatics 26 (19): 2438–2444. doi:10.1093/bioinformatics/btq466. ISSN 1367-4811. PMID 20709693. 
  5. ↑ Determination and inference of eukaryotic transcription factor sequence specificity.. PMID 25215497. 
  6. ↑ Qin, Bo; Zhou, Meng; Ge, Ying; Taing, Len; Liu, Tao; Wang, Qian; Wang, Su; Chen, Junsheng et al. (15 May 2012). "CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human". Bioinformatics 28 (10): 1411–1412. doi:10.1093/bioinformatics/bts157. ISSN 1367-4811. PMID 22495751. 
  7. ↑ Ziebarth, Jesse D.; Bhattacharya, Anindya; Cui, Yan (1 January 2013). "CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization". Nucleic Acids Research 41 (Database issue): D188–194. doi:10.1093/nar/gks1165. ISSN 1362-4962. PMID 23193294. 
  8. ↑ Wang, Jie; Zhuang, Jiali; Iyer, Sowmya; Lin, Xin-Ying; Greven, Melissa C.; Kim, Bong-Hyun; Moore, Jill; Pierce, Brian G. et al. (1 January 2013). "Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium". Nucleic Acids Research 41 (Database issue): D171–176. doi:10.1093/nar/gks1221. ISSN 1362-4962. PMID 23203885. 
  9. ↑ Chen, Li; Wu, George; Ji, Hongkai (15 May 2011). "hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data". Bioinformatics 27 (10): 1447–1448. doi:10.1093/bioinformatics/btr156. ISSN 1367-4811. PMID 21450710. 
  10. ↑ Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Yevshin, Ivan S.; Soboleva, Anastasiia V.; Kasianov, Artem S.; Ashoor, Haitham; Ba-Alawi, Wail; Bajic, Vladimir B. et al. (4 January 2016). "HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models". Nucleic Acids Research 44 (D1): D116–125. doi:10.1093/nar/gkv1249. ISSN 1362-4962. PMID 26586801. 
  11. ↑ Sandelin, A; Alkema, W; Engström, P; Wasserman, WW; Lenhard, B (1 January 2004). "JASPAR: an open-access database for eukaryotic transcription factor binding profiles.". Nucleic Acids Research 32 (Database issue): D91–4. doi:10.1093/nar/gkh012. PMID 14681366. 
  12. ↑ Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A.; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne et al. (13 November 2017). "JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework". Nucleic Acids Research 46 (D1): D260–D266. doi:10.1093/nar/gkx1126. PMID 29140473. 
  13. ↑ Pachkov, Mikhail; Balwierz, Piotr J.; Arnold, Phil; Ozonov, Evgeniy; van Nimwegen, Erik (1 January 2013). "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates". Nucleic Acids Research 41 (Database issue): D214–220. doi:10.1093/nar/gks1145. ISSN 1362-4962. PMID 23180783. 




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