Transcription factor binding site databases

Transcription factors are proteins that bind genomic regulatory sites. 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]
TRANSFAC	A long-standing curated database of regulatory sites, enhancers, binding site predictions, PSSMs and related analytical software.	database	website	[16]

References

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Kel A, Voss N, Jauregui R, Kel-Margoulis O, Wingender E (September 2006). "Beyond microarrays: find key transcription factors controlling signal transduction pathways". BMC Bioinformatics. 7 (Suppl 2): S2–S13. doi:10.1186/1471-2105-7-S2-S13. PMC 1683568. PMID 17118134.

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[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.

[16] Kel A, Voss N, Jauregui R, Kel-Margoulis O, Wingender E (September 2006). "Beyond microarrays: find key transcription factors controlling signal transduction pathways". BMC Bioinformatics. 7 (Suppl 2): S2–S13. doi:10.1186/1471-2105-7-S2-S13. PMC 1683568. PMID 17118134.