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|ChIPBase
|ChIPBase
|ChIPBase a database for [[Transcription factor-binding site]]s, motifs (~1290 transcription factors) and decoding the transcriptional regulation of [[LncRNA]]s, [[miRNAs]] and protein-coding genes from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species || database || [http://rna.sysu.edu.cn/chipbase/ website] || <ref>{{cite journal | vauthors = Yang JH, Li JH, Jiang S, Zhou H, Qu LH | title = ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D177-D187 | date = January 2013 | pmid = 23161675 | pmc = 3531181 | doi = 10.1093/nar/gks1060 }}</ref>
|ChIPBase a database for [[Transcription factor-binding site]]s, motifs (~1290 transcription factors) and decoding the transcriptional regulation of [[LncRNA]]s, [[miRNAs]] and protein-coding genes from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species || database || [http://rna.sysu.edu.cn/chipbase/ website] || <ref>{{cite journal | vauthors = Yang JH, Li JH, Jiang S, Zhou H, Qu LH | title = ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D177–D187 | date = January 2013 | pmid = 23161675 | pmc = 3531181 | doi = 10.1093/nar/gks1060 }}</ref>
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|ChEA
|ChEA
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|CTCFBSDB
|CTCFBSDB
|a database for [[CTCF]] binding sites and genome organization || database|| [http://insulatordb.uthsc.edu/ website] || <ref>{{cite journal | vauthors = Ziebarth JD, Bhattacharya A, Cui Y | title = CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D188-D194 | date = January 2013 | pmid = 23193294 | pmc = 3531215 | doi = 10.1093/nar/gks1165 }}</ref>
|a database for [[CTCF]] binding sites and genome organization || database|| [http://insulatordb.uthsc.edu/ website] || <ref>{{cite journal | vauthors = Ziebarth JD, Bhattacharya A, Cui Y | title = CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D188–D194 | date = January 2013 | pmid = 23193294 | pmc = 3531215 | doi = 10.1093/nar/gks1165 }}</ref>
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|Factorbook
|Factorbook
|a Wiki-based database for transcription factor-binding data generated by the [[ENCODE]] consortium. || database || [http://www.factorbook.org/ website] || <ref>{{cite journal | vauthors = Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z | display-authors = 6 | title = Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D171-D176 | date = January 2013 | pmid = 23203885 | pmc = 3531197 | doi = 10.1093/nar/gks1221 }}</ref>
|a Wiki-based database for transcription factor-binding data generated by the [[ENCODE]] consortium. || database || [http://www.factorbook.org/ website] || <ref>{{cite journal | vauthors = Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z | display-authors = 6 | title = Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D171–D176 | date = January 2013 | pmid = 23203885 | pmc = 3531197 | doi = 10.1093/nar/gks1221 }}</ref>
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|hmChIP
|hmChIP
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|HOCOMOCO
|HOCOMOCO
|a comprehensive collection of human and mouse transcription factor binding sites models.|| database || [http://hocomoco.autosome.ru/ website] || <ref>{{cite journal | vauthors = Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ | display-authors = 6 | title = HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D116-D125 | date = January 2016 | pmid = 26586801 | pmc = 4702883 | doi = 10.1093/nar/gkv1249 }}</ref>
|a comprehensive collection of human and mouse transcription factor binding sites models.|| database || [http://hocomoco.autosome.ru/ website] || <ref>{{cite journal | vauthors = Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ | display-authors = 6 | title = HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D116–D125 | date = January 2016 | pmid = 26586801 | pmc = 4702883 | doi = 10.1093/nar/gkv1249 }}</ref>
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|[[JASPAR]]
|[[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 || [http://jaspar.genereg.net/ website] || <ref>{{cite journal | vauthors = Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B | title = JASPAR: an open-access database for eukaryotic transcription factor binding profiles | journal = Nucleic Acids Research | volume = 32 | issue = Database issue | pages = D91-D94 | date = January 2004 | pmid = 14681366 | pmc = 308747 | doi = 10.1093/nar/gkh012 }}</ref><ref>{{cite journal | vauthors = Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A | display-authors = 6 | title = JASPAR 2020: update of the open-access database of transcription factor binding profiles | journal = Nucleic Acids Research | volume = 48 | issue = D1 | pages = D87-D92 | date = January 2020 | pmid = 31701148 | pmc = 7145627 | doi = 10.1093/nar/gkz1001 }}</ref>
| 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 || [http://jaspar.genereg.net/ website] || <ref>{{cite journal | vauthors = Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B | title = JASPAR: an open-access database for eukaryotic transcription factor binding profiles | journal = Nucleic Acids Research | volume = 32 | issue = Database issue | pages = D91–D94 | date = January 2004 | pmid = 14681366 | pmc = 308747 | doi = 10.1093/nar/gkh012 }}</ref><ref>{{cite journal | vauthors = Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A | display-authors = 6 | title = JASPAR 2020: update of the open-access database of transcription factor binding profiles | journal = Nucleic Acids Research | volume = 48 | issue = D1 | pages = D87–D92 | date = January 2020 | pmid = 31701148 | pmc = 7145627 | doi = 10.1093/nar/gkz1001 }}</ref>


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|MethMotif
|MethMotif
|An integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles.|| database || [http://bioinfo-csi.nus.edu.sg/methmotif/ website] || <ref>{{cite journal | vauthors = Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T | title = MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles | journal = Nucleic Acids Research | volume = 47 | issue = D1 | pages = D145-D154 | date = January 2019 | pmid = 30380113 | pmc = 6323897 | doi = 10.1093/nar/gky1005 | author-link6 = Touati Benoukraf }}</ref>
|An integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles.|| database || [http://bioinfo-csi.nus.edu.sg/methmotif/ website] || <ref>{{cite journal | vauthors = Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T | title = MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles | journal = Nucleic Acids Research | volume = 47 | issue = D1 | pages = D145–D154 | date = January 2019 | pmid = 30380113 | pmc = 6323897 | doi = 10.1093/nar/gky1005 | author-link6 = Touati Benoukraf }}</ref>
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|SwissRegulon
|SwissRegulon
| a database of genome-wide annotations of regulatory sites. || database || [https://web.archive.org/web/20140529224906/http://swissregulon.unibas.ch/fcgi/sr/swissregulon website] || <ref>{{cite journal | vauthors = Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E | title = SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D214-D220 | date = January 2013 | pmid = 23180783 | pmc = 3531101 | doi = 10.1093/nar/gks1145 }}</ref>
| a database of genome-wide annotations of regulatory sites. || database || [https://web.archive.org/web/20140529224906/http://swissregulon.unibas.ch/fcgi/sr/swissregulon website] || <ref>{{cite journal | vauthors = Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E | title = SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D214–D220 | date = January 2013 | pmid = 23180783 | pmc = 3531101 | doi = 10.1093/nar/gks1145 }}</ref>
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|TFLink
|TFLink

Revision as of 10:16, 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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