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]
CIS-BP collection of transcription factor binding sites models inferred by binding domains.databasewebsite[5]
CistromeMap a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.databasewebsite[6]
CTCFBSDB a database for CTCF binding sites and genome organizationdatabasewebsite[7]
Factorbook a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.databasewebsite[8]
hmChIP a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.databasewebsite[9]
HOCOMOCO a comprehensive collection of human and mouse transcription factor binding sites models.databasewebsite[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.databasewebsite[11][12]
MethMotif An integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles.databasewebsite[13]
SwissRegulon a database of genome-wide annotations of regulatory sites.databasewebsite[14]

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. Weirauch, M. T.; Yang, A.; Albu, M.; Cote, A. G.; Montenegro-Montero, A.; Drewe, P.; Najafabadi, H. S.; Lambert, S. A.; Mann, I.; Cook, K.; Zheng, H.; Goity, A.; Van Bakel, H.; Lozano, J. C.; Galli, M.; Lewsey, M. G.; Huang, E.; Mukherjee, T.; Chen, X.; Reece-Hoyes, J. S.; Govindarajan, S.; Shaulsky, G.; Walhout AJM; Bouget, F. Y.; Ratsch, G.; Larrondo, L. F.; Ecker, J. R.; Hughes, T. R. (2014). "Determination and inference of eukaryotic transcription factor sequence specificity". Cell. 158 (6): 1431–1443. doi:10.1016/j.cell.2014.08.009. PMC 4163041. PMID 25215497.
  6. 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.
  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. PMC 3531215. PMID 23193294.
  8. 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.
  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. PMC 3087956. 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.; 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.
  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. PMC 308747. PMID 14681366.
  12. Fornes, Oriol; Castro-Mondragon, Jaime A.; Khan, Aziz; van der Lee, Robin; Zhang, Xi; Richmond, Phillip A.; Modi, Bhavi P.; Correard, Solenne; Gheorghe, Marius; Baranašić, Damir; Santana-Garcia, Walter; Tan, Ge; Chèneby, Jeanne; Ballester, Benoit; Parcy, François; Sandelin, Albin; Lenhard, Boris; Wasserman, Wyeth W.; Mathelier, Anthony (8 January 2020). "JASPAR 2020: update of the open-access database of transcription factor binding profiles". Nucleic Acids Research. 48 (D1): D87–D92. doi:10.1093/nar/gkz1001. PMC 7145627. PMID 31701148.
  13. Lin, Quy Xiao Xuan; Sian, Stephanie; An, Omer; Thieffry, Denis; Jha, Sudhakar; Benoukraf, Touati (31 October 2018). "MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles". Nucleic Acids Research. 47 (D1): D145–D154. doi:10.1093/nar/gky1005. PMC 6323897. PMID 30380113.
  14. 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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