Transcription factor binding site databases

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 DescriptiontypeLinkReferences
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 speciesdatabasewebsite[3]
ChEA transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.databasewebsite[4]
CistromeMap a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.databasewebsite[5]
CTCFBSDB a database for CTCF binding sites and genome organizationdatabasewebsite[6]
Factorbook a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.databasewebsite[7]
hmChIP a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.databasewebsite[8]
HOCOMOCO a comprehensive collection of human transcription factor binding sites models.databasewebsite[9]
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.databasewebsite[10][11]
SwissRegulon a database of genome-wide annotations of regulatory sites.databasewebsite[12]

References

  1. ↑ Park, Peter J. (1 October 2009). "ChIP–seq: advantages and challenges of a maturing technology". Nature Reviews Genetics. 10 (10): 669–680. doi:10.1038/nrg2641. ISSN 1471-0056. PMC 3191340. PMID 19736561.
  2. ↑ Farnham, Peggy J. (1 September 2009). "Insights from genomic profiling of transcription factors". Nature Reviews Genetics. 10 (9): 605–616. doi:10.1038/nrg2636. ISSN 1471-0056. PMC 2846386. 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. PMC 3531181. 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. PMC 2944209. PMID 20709693.
  5. ↑ Qin, Bo; Zhou, Meng; Ge, Ying; Taing, Len; Liu, Tao; Wang, Qian; Wang, Su; Chen, Junsheng; Shen, Lingling; Duan, Xikun; Hu, Sheng'en; Li, Wei; Long, Henry; Zhang, Yong; Liu, X. Shirley (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. PMC 3348563. PMID 22495751.
  6. ↑ 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. PMC 3531215. PMID 23193294.
  7. ↑ Wang, Jie; Zhuang, Jiali; Iyer, Sowmya; Lin, Xin-Ying; Greven, Melissa C.; Kim, Bong-Hyun; Moore, Jill; Pierce, Brian G.; Dong, Xianjun; Virgil, Daniel; Birney, Ewan; Hung, Jui-Hung; Weng, Zhiping (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. PMC 3531197. PMID 23203885.
  8. ↑ 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. PMC 3087956. PMID 21450710.
  9. ↑ Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Yevshin, Ivan S.; Soboleva, Anastasiia V.; Kasianov, Artem S.; Ashoor, Haitham; Ba-Alawi, Wail; Bajic, Vladimir B.; Medvedeva, Yulia A.; Kolpakov, Fedor A.; Makeev, Vsevolod J. (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. PMC 4702883. PMID 26586801.
  10. ↑ 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.
  11. ↑ Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A.; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R.; Tan, Ge; Baranasic, Damir; Arenillas, David J.; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoît; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony (13 November 2017). "JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework". Nucleic Acids Research. doi:10.1093/nar/gkx1126.
  12. ↑ 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. PMC 3531101. PMID 23180783.
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