Transcription factor binding site databases

From HandWiki

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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