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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]
CistromeMap a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. database website [5]
CTCFBSDB a database for CTCF binding sites and genome organization database website [6]
Factorbook a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. database website [7]
hmChIP a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. database website [8]
HOCOMOCO a comprehensive collection of human transcription factor binding sites models. database website [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. database website [10][11]
SwissRegulon a database of genome-wide annotations of regulatory sites. database website [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. {{cite journal}}: no-break space character in |last6= at position 4 (help)
  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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