Transcription factor binding site databases - Revision history

Ymblanter: /* Transcription factor binding site databases */

2024-01-22T20:06:05Z

Transcription factor binding site databases

← Previous revision		Revision as of 20:06, 22 January 2024
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	\|a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.\|\| database \|\| [http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl website] \|\| <ref>{{cite journal \| vauthors = Chen L, Wu G, Ji H \| title = hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data \| journal = Bioinformatics \| volume = 27 \| issue = 10 \| pages = 1447–1448 \| date = May 2011 \| pmid = 21450710 \| pmc = 3087956 \| doi = 10.1093/bioinformatics/btr156 }}</ref>		\|a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.\|\| database \|\| [http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl website] \|\| <ref>{{cite journal \| vauthors = Chen L, Wu G, Ji H \| title = hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data \| journal = Bioinformatics \| volume = 27 \| issue = 10 \| pages = 1447–1448 \| date = May 2011 \| pmid = 21450710 \| pmc = 3087956 \| doi = 10.1093/bioinformatics/btr156 }}</ref>
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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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← Previous revision		Revision as of 15:26, 11 December 2023
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	{{Orphan\|date=November 2016}}

	[[Transcription factor\|Transcription factors]] are proteins that bind genomic regulatory sites. Identification of [[Regulation of gene expression\|genomic regulatory]] elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in [[chromatin immunoprecipitation]] followed by sequencing ([[ChIP-sequencing\|ChIP-seq]]) have provided powerful ways to identify genome-wide profiling of [[DNA-binding protein]]s and [[histone]] modifications.<ref>{{cite journal \| vauthors = Park PJ \| title = ChIP-seq: advantages and challenges of a maturing technology \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 10 \| pages = 669–680 \| date = October 2009 \| pmid = 19736561 \| pmc = 3191340 \| doi = 10.1038/nrg2641 }}</ref><ref>{{cite journal \| vauthors = Farnham PJ \| title = Insights from genomic profiling of transcription factors \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 9 \| pages = 605–616 \| date = September 2009 \| pmid = 19668247 \| pmc = 2846386 \| doi = 10.1038/nrg2636 }}</ref> The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.		[[Transcription factor\|Transcription factors]] are proteins that bind genomic regulatory sites. Identification of [[Regulation of gene expression\|genomic regulatory]] elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in [[chromatin immunoprecipitation]] followed by sequencing ([[ChIP-sequencing\|ChIP-seq]]) have provided powerful ways to identify genome-wide profiling of [[DNA-binding protein]]s and [[histone]] modifications.<ref>{{cite journal \| vauthors = Park PJ \| title = ChIP-seq: advantages and challenges of a maturing technology \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 10 \| pages = 669–680 \| date = October 2009 \| pmid = 19736561 \| pmc = 3191340 \| doi = 10.1038/nrg2641 }}</ref><ref>{{cite journal \| vauthors = Farnham PJ \| title = Insights from genomic profiling of transcription factors \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 9 \| pages = 605–616 \| date = September 2009 \| pmid = 19668247 \| pmc = 2846386 \| doi = 10.1038/nrg2636 }}</ref> The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.

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← Previous revision		Revision as of 02:30, 1 December 2023
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	\|TRANSFAC		\|TRANSFAC
	\| A long-standing curated database of regulatory sites, enhancers, binding site predictions, PSSMs and related analytical software. \|\| database \|\| [https://genexplain.com/transfac/ website] \|\| <ref>{{cite journal \| vauthors = Kel A, Voss N, Jauregui R, Kel-Margoulis O, Wingender E \| title = Beyond microarrays: find key transcription factors controlling signal transduction pathways \| journal = BMC Bioinformatics \| volume = 7 \| issue = Suppl 2 \| pages = ~~S2-S13~~ \| date = September 2006 \| pmid = 17118134 \| pmc = 1683568 \| doi = 10.1186/1471-2105-7-S2-S13 }}</ref>		\| A long-standing curated database of regulatory sites, enhancers, binding site predictions, PSSMs and related analytical software. \|\| database \|\| [https://genexplain.com/transfac/ website] \|\| <ref>{{cite journal \| vauthors = Kel A, Voss N, Jauregui R, Kel-Margoulis O, Wingender E \| title = Beyond microarrays: find key transcription factors controlling signal transduction pathways \| journal = BMC Bioinformatics \| volume = 7 \| issue = Suppl 2 \| pages = S2–S13 \| date = September 2006 \| pmid = 17118134 \| pmc = 1683568 \| doi = 10.1186/1471-2105-7-S2-S13 \| doi-access = free }}</ref>
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2023-07-24T01:10:00Z

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	\|[https://tflink.net/ website]		\|[https://tflink.net/ website]
	\|<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>		\|<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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			\|TRANSFAC
			\| A long-standing curated database of regulatory sites, enhancers, binding site predictions, PSSMs and related analytical software. \|\| database \|\| [https://genexplain.com/transfac/ website] \|\| <ref>{{cite journal \| vauthors = Kel A, Voss N, Jauregui R, Kel-Margoulis O, Wingender E \| title = Beyond microarrays: find key transcription factors controlling signal transduction pathways \| journal = BMC Bioinformatics \| volume = 7 \| issue = Suppl 2 \| pages = S2-S13 \| date = September 2006 \| pmid = 17118134 \| pmc = 1683568 \| doi = 10.1186/1471-2105-7-S2-S13 }}</ref>
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WikiCleanerBot: v2.05b - Bot T18 CW#553 - Fix errors for CW project ( tags)

2023-01-30T23:54:45Z

v2.05b - Bot T18 CW#553 - Fix errors for CW project (<nowiki> tags)

← Previous revision		Revision as of 23:54, 30 January 2023
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	{{Orphan\|date=November 2016}}		{{Orphan\|date=November 2016}}

	[[Transcription factor\|Transcription factors]]~~<nowiki/>~~ are proteins that bind genomic regulatory sites. Identification of [[Regulation of gene expression\|genomic regulatory]] elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in [[chromatin immunoprecipitation]] followed by sequencing ([[ChIP-sequencing\|ChIP-seq]]) have provided powerful ways to identify genome-wide profiling of [[DNA-binding protein]]s and [[histone]] modifications.<ref>{{cite journal \| vauthors = Park PJ \| title = ChIP-seq: advantages and challenges of a maturing technology \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 10 \| pages = 669–680 \| date = October 2009 \| pmid = 19736561 \| pmc = 3191340 \| doi = 10.1038/nrg2641 }}</ref><ref>{{cite journal \| vauthors = Farnham PJ \| title = Insights from genomic profiling of transcription factors \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 9 \| pages = 605–616 \| date = September 2009 \| pmid = 19668247 \| pmc = 2846386 \| doi = 10.1038/nrg2636 }}</ref> The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.		[[Transcription factor\|Transcription factors]] are proteins that bind genomic regulatory sites. Identification of [[Regulation of gene expression\|genomic regulatory]] elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in [[chromatin immunoprecipitation]] followed by sequencing ([[ChIP-sequencing\|ChIP-seq]]) have provided powerful ways to identify genome-wide profiling of [[DNA-binding protein]]s and [[histone]] modifications.<ref>{{cite journal \| vauthors = Park PJ \| title = ChIP-seq: advantages and challenges of a maturing technology \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 10 \| pages = 669–680 \| date = October 2009 \| pmid = 19736561 \| pmc = 3191340 \| doi = 10.1038/nrg2641 }}</ref><ref>{{cite journal \| vauthors = Farnham PJ \| title = Insights from genomic profiling of transcription factors \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 9 \| pages = 605–616 \| date = September 2009 \| pmid = 19668247 \| pmc = 2846386 \| doi = 10.1038/nrg2636 }}</ref> The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.

	==Transcription factor binding site databases==		==Transcription factor binding site databases==

Jaredroach: Improve lede. Add link.

2023-01-11T18:54:53Z

Improve lede. Add link.

← Previous revision		Revision as of 18:54, 11 January 2023
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	{{Orphan\|date=November 2016}}		{{Orphan\|date=November 2016}}

	Identification of [[Regulation of gene expression\|genomic regulatory]] elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in [[chromatin immunoprecipitation]] followed by sequencing ([[ChIP-sequencing\|ChIP-seq]]) have provided powerful ways to identify genome-wide profiling of [[DNA-binding protein]]s and [[histone]] modifications.<ref>{{cite journal \| vauthors = Park PJ \| title = ChIP-seq: advantages and challenges of a maturing technology \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 10 \| pages = 669–680 \| date = October 2009 \| pmid = 19736561 \| pmc = 3191340 \| doi = 10.1038/nrg2641 }}</ref><ref>{{cite journal \| vauthors = Farnham PJ \| title = Insights from genomic profiling of transcription factors \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 9 \| pages = 605–616 \| date = September 2009 \| pmid = 19668247 \| pmc = 2846386 \| doi = 10.1038/nrg2636 }}</ref> The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.		[[Transcription factor\|Transcription factors]]<nowiki/> are proteins that bind genomic regulatory sites. Identification of [[Regulation of gene expression\|genomic regulatory]] elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in [[chromatin immunoprecipitation]] followed by sequencing ([[ChIP-sequencing\|ChIP-seq]]) have provided powerful ways to identify genome-wide profiling of [[DNA-binding protein]]s and [[histone]] modifications.<ref>{{cite journal \| vauthors = Park PJ \| title = ChIP-seq: advantages and challenges of a maturing technology \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 10 \| pages = 669–680 \| date = October 2009 \| pmid = 19736561 \| pmc = 3191340 \| doi = 10.1038/nrg2641 }}</ref><ref>{{cite journal \| vauthors = Farnham PJ \| title = Insights from genomic profiling of transcription factors \| journal = Nature Reviews. Genetics \| volume = 10 \| issue = 9 \| pages = 605–616 \| date = September 2009 \| pmid = 19668247 \| pmc = 2846386 \| doi = 10.1038/nrg2636 }}</ref> The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.

	==Transcription factor binding site databases==		==Transcription factor binding site databases==

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← Previous revision		Revision as of 10:16, 1 January 2023
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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>
	\|-		\|-
	\|[[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>
	\|-		\|-
	\|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>
	\|-		\|-
	\|TFLink		\|TFLink

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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>		\|<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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Boghog: /* Transcription factor binding site databases */ removed redundant external links; removed excessive bolding

2023-01-01T09:52:50Z

Transcription factor binding site databases: removed redundant external links; removed excessive bolding

← Previous revision		Revision as of 09:52, 1 January 2023
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	==Transcription factor binding site databases==		==Transcription factor binding site databases==

	~~'''~~Comprehensive List of transcription factor binding sites (TFBSs) databases based on ChIP-seq data as follows:~~'''~~		Comprehensive List of transcription factor binding sites (TFBSs) databases based on ChIP-seq data as follows:

	{\| class="wikitable"		{\| class="wikitable"
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	! Description \|\| type\|\| Link \|\| References		! Description \|\| type\|\| Link \|\| References
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			\|ChIPBase
	\|'''[http://rna.sysu.edu.cn/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>
	\|-		\|-
			\|ChEA
	\|'''[http://amp.pharm.mssm.edu/lib/chea.jsp ChEA]'''
	\|transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. \|\| database \|\| [http://amp.pharm.mssm.edu/lib/chea.jsp website] \|\| <ref>{{cite journal \| vauthors = Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A \| title = ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments \| journal = Bioinformatics \| volume = 26 \| issue = 19 \| pages = 2438–2444 \| date = October 2010 \| pmid = 20709693 \| pmc = 2944209 \| doi = 10.1093/bioinformatics/btq466 }}</ref>		\|transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. \|\| database \|\| [http://amp.pharm.mssm.edu/lib/chea.jsp website] \|\| <ref>{{cite journal \| vauthors = Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A \| title = ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments \| journal = Bioinformatics \| volume = 26 \| issue = 19 \| pages = 2438–2444 \| date = October 2010 \| pmid = 20709693 \| pmc = 2944209 \| doi = 10.1093/bioinformatics/btq466 }}</ref>
	\|-		\|-
			\|CIS-BP
	\|'''[http://cisbp.ccbr.utoronto.ca/ CIS-BP]'''
	\|collection of transcription factor binding sites models inferred by binding domains.\|\| database \|\| [http://cisbp.ccbr.utoronto.ca/ website] \|\| <ref>{{cite journal \| vauthors = Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR \| display-authors = 6 \| title = Determination and inference of eukaryotic transcription factor sequence specificity \| journal = Cell \| volume = 158 \| issue = 6 \| pages = 1431–1443 \| date = September 2014 \| pmid = 25215497 \| pmc = 4163041 \| doi = 10.1016/j.cell.2014.08.009 }}</ref>		\|collection of transcription factor binding sites models inferred by binding domains.\|\| database \|\| [http://cisbp.ccbr.utoronto.ca/ website] \|\| <ref>{{cite journal \| vauthors = Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR \| display-authors = 6 \| title = Determination and inference of eukaryotic transcription factor sequence specificity \| journal = Cell \| volume = 158 \| issue = 6 \| pages = 1431–1443 \| date = September 2014 \| pmid = 25215497 \| pmc = 4163041 \| doi = 10.1016/j.cell.2014.08.009 }}</ref>
	\|-		\|-
	\|~~'''[http://cistrome.dfci.harvard.edu/pc/~~ CistromeMap~~]'''~~		\|CistromeMap
	\|a knowledgebase and web server for ChIP-Seq and [[DNase-Seq]] studies in mouse and human. \|\| database \|\| [http://cistrome.dfci.harvard.edu/pc/ website] \|\| <ref>{{cite journal \| vauthors = Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y, Liu XS \| display-authors = 6 \| title = CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human \| journal = Bioinformatics \| volume = 28 \| issue = 10 \| pages = 1411–1412 \| date = May 2012 \| pmid = 22495751 \| pmc = 3348563 \| doi = 10.1093/bioinformatics/bts157 }}</ref>		\|a knowledgebase and web server for ChIP-Seq and [[DNase-Seq]] studies in mouse and human. \|\| database \|\| [http://cistrome.dfci.harvard.edu/pc/ website] \|\| <ref>{{cite journal \| vauthors = Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y, Liu XS \| display-authors = 6 \| title = CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human \| journal = Bioinformatics \| volume = 28 \| issue = 10 \| pages = 1411–1412 \| date = May 2012 \| pmid = 22495751 \| pmc = 3348563 \| doi = 10.1093/bioinformatics/bts157 }}</ref>
	\|-		\|-
			\|CTCFBSDB
	\|'''[http://insulatordb.uthsc.edu/ 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>
	\|-		\|-
	\|~~'''[http://www.factorbook.org/~~ 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>
	\|-		\|-
			\|hmChIP
	\|'''[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl hmChIP]'''
	\|a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.\|\| database \|\| [http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl website] \|\| <ref>{{cite journal \| vauthors = Chen L, Wu G, Ji H \| title = hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data \| journal = Bioinformatics \| volume = 27 \| issue = 10 \| pages = 1447–1448 \| date = May 2011 \| pmid = 21450710 \| pmc = 3087956 \| doi = 10.1093/bioinformatics/btr156 }}</ref>		\|a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.\|\| database \|\| [http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl website] \|\| <ref>{{cite journal \| vauthors = Chen L, Wu G, Ji H \| title = hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data \| journal = Bioinformatics \| volume = 27 \| issue = 10 \| pages = 1447–1448 \| date = May 2011 \| pmid = 21450710 \| pmc = 3087956 \| doi = 10.1093/bioinformatics/btr156 }}</ref>
	\|-		\|-
			\|HOCOMOCO
	\|'''[http://hocomoco.autosome.ru/ 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>
	\|-		\|-
	\|~~'''~~[[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>

	\|-		\|-
			\|MethMotif
	\|'''[http://bioinfo-csi.nus.edu.sg/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>
	\|-		\|-
			\|SwissRegulon
	\|'''[https://web.archive.org/web/20140529224906/http://swissregulon.unibas.ch/fcgi/sr/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>
	\|-		\|-
			\|TFLink
	\|'''[https://tflink.net/ 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.		\|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		\|database
Line 51:		Line 51:
	\|<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>		\|<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>
	\|-		\|-
	\|colspan="5" \| ~~<small></small>~~		\|colspan="5" \|
	\|}		\|}

Boghog: consistent citation formatting

2023-01-01T09:49:41Z

consistent citation formatting

Show changes