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词条 Transcription factor binding site databases
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  1. Transcription factor binding site databases

  2. References

{{Orphan|date=November 2016}}

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
ChIPBaseChIPBase 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]
ChEAtranscription factor regulation inferred from integrating genome-wide ChIP-X experiments. database website [4]
CistromeMapa knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. database website [5]
CTCFBSDBa database for CTCF binding sites and genome organization database website [6]
Factorbooka Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. database website [7]
hmChIPa database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. database website [8]
HOCOMOCOa comprehensive collection of human transcription factor binding sites models. database website [9]
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 [10][11]
MethMotifAn integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles. database website [12]
[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] [13]

References

1. ^{{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}}
2. ^{{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}}
3. ^{{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}}
4. ^{{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}}
5. ^{{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}}
6. ^{{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}}
7. ^{{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}}
8. ^{{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}}
9. ^{{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}}
10. ^{{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}}
11. ^{{cite journal|last1=Khan|first1=Aziz|last2=Fornes|first2=Oriol|last3=Stigliani|first3=Arnaud|last4=Gheorghe|first4=Marius|last5=Castro-Mondragon|first5=Jaime A.|last6=van der Lee|first6=Robin|last7=Bessy|first7=Adrien|last8=Chèneby|first8=Jeanne|last9=Kulkarni|first9=Shubhada R.|last10=Tan|first10=Ge|last11=Baranasic|first11=Damir|last12=Arenillas|first12=David J.|last13=Sandelin|first13=Albin|last14=Vandepoele|first14=Klaas|last15=Lenhard|first15=Boris|last16=Ballester|first16=Benoît|last17=Wasserman|first17=Wyeth W.|last18=Parcy|first18=François|last19=Mathelier|first19=Anthony|title=JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework|journal=Nucleic Acids Research|volume=46|issue=D1|pages=D260–D266|date=13 November 2017|doi=10.1093/nar/gkx1126|pmid=29140473|pmc=5753243}}
12. ^{{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 }}
13. ^{{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}}

2 : Bioinformatics|Scientific databases
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