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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|last1=Park|first1=Peter J.|title=ChIP–seq: advantages and challenges of a maturing technology|journal=Nature Reviews Genetics|date=1 October 2009|volume=10|issue=10|pages=669–680|doi=10.1038/nrg2641|pmid=19736561|language=en|issn=1471-0056|pmc=3191340}}</ref><ref>{{cite journal|last1=Farnham|first1=Peggy J.|title=Insights from genomic profiling of transcription factors|journal=Nature Reviews Genetics|date=1 September 2009|volume=10|issue=9|pages=605–616|doi=10.1038/nrg2636|pmid=19668247|language=en|issn=1471-0056|pmc=2846386}}</ref> The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification 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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|-
|-
|'''[http://rna.sysu.edu.cn/chipbase/ 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|last1=Yang|first1=Jian-Hua|last2=Li|first2=Jun-Hao|last3=Jiang|first3=Shan|last4=Zhou|first4=Hui|last5=Qu|first5=Liang-Hu|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|date=1 January 2013|volume=41|issue=Database issue|pages=D177–187|doi=10.1093/nar/gks1060|issn=1362-4962|pmid=23161675|pmc=3531181}}</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>
|-
|-
|'''[http://amp.pharm.mssm.edu/lib/chea.jsp 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|last1=Lachmann|first1=Alexander|last2=Xu|first2=Huilei|last3=Krishnan|first3=Jayanth|last4=Berger|first4=Seth I.|last5=Mazloom|first5=Amin R.|last6=Ma'ayan|first6=Avi|title=ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments|journal=Bioinformatics|date=1 October 2010|volume=26|issue=19|pages=2438–2444|doi=10.1093/bioinformatics/btq466|pmid=20709693|issn=1367-4811|pmc=2944209}}</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>
|-
|-
|'''[http://cisbp.ccbr.utoronto.ca/ 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|title=Determination and inference of eukaryotic transcription factor sequence specificity.|year=2014|pmid=25215497|last1=Weirauch|first1=M. T.|last2=Yang|first2=A.|last3=Albu|first3=M.|last4=Cote|first4=A. G.|last5=Montenegro-Montero|first5=A.|last6=Drewe|first6=P.|last7=Najafabadi|first7=H. S.|last8=Lambert|first8=S. A.|last9=Mann|first9=I.|last10=Cook|first10=K.|last11=Zheng|first11=H.|last12=Goity|first12=A.|last13=Van Bakel|first13=H.|last14=Lozano|first14=J. C.|last15=Galli|first15=M.|last16=Lewsey|first16=M. G.|last17=Huang|first17=E.|last18=Mukherjee|first18=T.|last19=Chen|first19=X.|last20=Reece-Hoyes|first20=J. S.|last21=Govindarajan|first21=S.|last22=Shaulsky|first22=G.|author23=Walhout AJM|last24=Bouget|first24=F. Y.|last25=Ratsch|first25=G.|last26=Larrondo|first26=L. F.|last27=Ecker|first27=J. R.|last28=Hughes|first28=T. R.|journal=Cell|volume=158|issue=6|pages=1431–1443|doi=10.1016/j.cell.2014.08.009|pmc=4163041}}</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]'''
|'''[http://cistrome.dfci.harvard.edu/pc/ 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|last1=Qin|first1=Bo|last2=Zhou|first2=Meng|last3=Ge|first3=Ying|last4=Taing|first4=Len|last5=Liu|first5=Tao|last6=Wang|first6=Qian|last7=Wang|first7=Su|last8=Chen|first8=Junsheng|last9=Shen|first9=Lingling|last10=Duan|first10=Xikun|last11=Hu|first11=Sheng'en|last12=Li|first12=Wei|last13=Long|first13=Henry|last14=Zhang|first14=Yong|last15=Liu|first15=X. Shirley|title=CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human|journal=Bioinformatics|date=15 May 2012|volume=28|issue=10|pages=1411–1412|doi=10.1093/bioinformatics/bts157|issn=1367-4811|pmid=22495751|pmc=3348563}}</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>
|-
|-
|'''[http://insulatordb.uthsc.edu/ CTCFBSDB]'''
|'''[http://insulatordb.uthsc.edu/ CTCFBSDB]'''
|a database for [[CTCF]] binding sites and genome organization || database|| [http://insulatordb.uthsc.edu/ website] || <ref>{{cite journal|last1=Ziebarth|first1=Jesse D.|last2=Bhattacharya|first2=Anindya|last3=Cui|first3=Yan|title=CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization|journal=Nucleic Acids Research|date=1 January 2013|volume=41|issue=Database issue|pages=D188–194|doi=10.1093/nar/gks1165|issn=1362-4962|pmid=23193294|pmc=3531215}}</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]'''
|'''[http://www.factorbook.org/ Factorbook]'''
|a Wiki-based database for transcription factor-binding data generated by the [[ENCODE]] consortium. || database || [http://www.factorbook.org/ website] || <ref>{{cite journal|last1=Wang|first1=Jie|last2=Zhuang|first2=Jiali|last3=Iyer|first3=Sowmya|last4=Lin|first4=Xin-Ying|last5=Greven|first5=Melissa C.|last6=Kim|first6=Bong-Hyun|last7=Moore|first7=Jill|last8=Pierce|first8=Brian G.|last9=Dong|first9=Xianjun|last10=Virgil|first10=Daniel|last11=Birney|first11=Ewan|last12=Hung|first12=Jui-Hung|last13=Weng|first13=Zhiping|title=Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium|journal=Nucleic Acids Research|date=1 January 2013|volume=41|issue=Database issue|pages=D171–176|doi=10.1093/nar/gks1221|issn=1362-4962|pmid=23203885|pmc=3531197}}</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>
|-
|-
|'''[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl 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|last1=Chen|first1=Li|last2=Wu|first2=George|last3=Ji|first3=Hongkai|title=hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data|journal=Bioinformatics|date=15 May 2011|volume=27|issue=10|pages=1447–1448|doi=10.1093/bioinformatics/btr156|issn=1367-4811|pmid=21450710|pmc=3087956}}</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>
|-
|-
|'''[http://hocomoco.autosome.ru/ 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|last1=Kulakovskiy|first1=Ivan V.|last2=Vorontsov|first2=Ilya E.|last3=Yevshin|first3=Ivan S.|last4=Soboleva|first4=Anastasiia V.|last5=Kasianov|first5=Artem S.|last6=Ashoor|first6=Haitham|last7=Ba-Alawi|first7=Wail|last8=Bajic|first8=Vladimir B.|last9=Medvedeva|first9=Yulia A.|last10=Kolpakov|first10=Fedor A.|last11=Makeev|first11=Vsevolod J.|title=HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models|journal=Nucleic Acids Research|date=4 January 2016|volume=44|issue=D1|pages=D116–125|doi=10.1093/nar/gkv1249|issn=1362-4962|pmid=26586801|pmc=4702883}}</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|last1=Sandelin|first1=A|last2=Alkema|first2=W|last3=Engström|first3=P|last4=Wasserman|first4=WW|last5=Lenhard|first5=B|title=JASPAR: an open-access database for eukaryotic transcription factor binding profiles.|journal=Nucleic Acids Research|date=1 January 2004|volume=32|issue=Database issue|pages=D91–4|doi=10.1093/nar/gkh012|pmid=14681366|pmc=308747}}</ref><ref>{{cite journal|last1=Fornes|first1=Oriol|last2=Castro-Mondragon|first2=Jaime A.|last3=Khan|first3=Aziz|last4=van der Lee|first4=Robin|last5=Zhang|first5=Xi|last6=Richmond|first6=Phillip A.|last7=Modi|first7=Bhavi P.|last8=Correard|first8=Solenne|last9=Gheorghe|first9=Marius|last10=Baranašić|first10=Damir|last11=Santana-Garcia|first11=Walter|last12=Tan|first12=Ge|last13=Chèneby|first13=Jeanne|last14=Ballester|first14=Benoit|last15=Parcy|first15=François|last16=Sandelin|first16=Albin|last17=Lenhard|first17=Boris|last18=Wasserman|first18=Wyeth W.|last19=Mathelier|first19=Anthony|title=JASPAR 2020: update of the open-access database of transcription factor binding profiles|journal=Nucleic Acids Research|date=8 January 2020|doi=10.1093/nar/gkz1001|volume=48|issue=D1|pages=D87–D92|pmid=31701148|pmc=7145627}}</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>


|-
|-
|'''[http://bioinfo-csi.nus.edu.sg/methmotif/ 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 |last1=Lin |first1=Quy Xiao Xuan |last2=Sian |first2=Stephanie |last3=An |first3=Omer |last4=Thieffry |first4=Denis |last5=Jha |first5=Sudhakar |last6=Benoukraf |first6=Touati | author-link6 = Touati Benoukraf|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=31 October 2018 |doi=10.1093/nar/gky1005|pmid=30380113 |pmc=6323897 }}</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>
|-
|-
|'''[https://web.archive.org/web/20140529224906/http://swissregulon.unibas.ch/fcgi/sr/swissregulon 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|last1=Pachkov|first1=Mikhail|last2=Balwierz|first2=Piotr J.|last3=Arnold|first3=Phil|last4=Ozonov|first4=Evgeniy|last5=van Nimwegen|first5=Erik|title=SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates|journal=Nucleic Acids Research|date=1 January 2013|volume=41|issue=Database issue|pages=D214–220|doi=10.1093/nar/gks1145|issn=1362-4962|pmid=23180783|pmc=3531101}}</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>
|-
|-
|'''[https://tflink.net/ TFLink]'''
|'''[https://tflink.net/ TFLink]'''
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|database
|database
|[https://tflink.net/ website]
|[https://tflink.net/ website]
|<ref>{{Cite journal |last=Liska |first=Orsolya |last2=Bohár |first2=Balázs |last3=Hidas |first3=András |last4=Korcsmáros |first4=Tamás |last5=Papp |first5=Balázs |last6=Fazekas |first6=Dávid |last7=Ari |first7=Eszter |date=2022-01-01 |title=TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species |url=https://doi.org/10.1093/database/baac083 |journal=Database |volume=2022 |doi=10.1093/database/baac083 |issn=1758-0463 |pmc=PMC9480832 |pmid=36124642}}</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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|colspan="5" | <small></small>
|colspan="5" | <small></small>
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==References==
== References ==
{{Reflist}}
{{Reflist}}


Revision as of 09:49, 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.
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