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|<ref>{{cite journal | vauthors = Liska O, Bohár B, Hidas A, Korcsmáros T, Papp B, Fazekas D, Ari E | title = TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species | journal = Database | volume = 2022 | date = September 2022 | pmid = 36124642 | pmc = 9480832 | doi = 10.1093/database/baac083 }}</ref>
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Revision as of 09:53, 1 January 2023

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 An integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles. database website [13]
SwissRegulon a database of genome-wide annotations of regulatory sites. database website [14]
TFLink TFLink gateway provides comprehensive and highly accurate information on transcription factor - target gene interactions, nucleotide sequences and genomic locations of transcription factor binding sites for human and six model organisms. database website [15]

References

  1. ^ Park PJ (October 2009). "ChIP-seq: advantages and challenges of a maturing technology". Nature Reviews. Genetics. 10 (10): 669–680. doi:10.1038/nrg2641. PMC 3191340. PMID 19736561.
  2. ^ Farnham PJ (September 2009). "Insights from genomic profiling of transcription factors". Nature Reviews. Genetics. 10 (9): 605–616. doi:10.1038/nrg2636. PMC 2846386. PMID 19668247.
  3. ^ Yang JH, Li JH, Jiang S, Zhou H, Qu LH (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 – D187. doi:10.1093/nar/gks1060. PMC 3531181. PMID 23161675.
  4. ^ Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A (October 2010). "ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments". Bioinformatics. 26 (19): 2438–2444. doi:10.1093/bioinformatics/btq466. PMC 2944209. PMID 20709693.
  5. ^ Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, et al. (September 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 B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, et al. (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. PMC 3348563. PMID 22495751.
  7. ^ Ziebarth JD, Bhattacharya A, Cui Y (January 2013). "CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization". Nucleic Acids Research. 41 (Database issue): D188 – D194. doi:10.1093/nar/gks1165. PMC 3531215. PMID 23193294.
  8. ^ Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, et al. (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 – D176. doi:10.1093/nar/gks1221. PMC 3531197. PMID 23203885.
  9. ^ Chen L, Wu G, Ji H (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. PMC 3087956. PMID 21450710.
  10. ^ Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, et al. (January 2016). "HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models". Nucleic Acids Research. 44 (D1): D116 – D125. doi:10.1093/nar/gkv1249. PMC 4702883. PMID 26586801.
  11. ^ Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B (January 2004). "JASPAR: an open-access database for eukaryotic transcription factor binding profiles". Nucleic Acids Research. 32 (Database issue): D91 – D94. doi:10.1093/nar/gkh012. PMC 308747. PMID 14681366.
  12. ^ Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, et al. (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. ^ Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T (January 2019). "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 M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E (January 2013). "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates". Nucleic Acids Research. 41 (Database issue): D214 – D220. doi:10.1093/nar/gks1145. PMC 3531101. PMID 23180783.
  15. ^ Liska O, Bohár B, Hidas A, Korcsmáros T, Papp B, Fazekas D, Ari E (September 2022). "TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species". Database. 2022. doi:10.1093/database/baac083. PMC 9480832. PMID 36124642.
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