A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.
Identifieur interne : 000053 ( PubMed/Checkpoint ); précédent : 000052; suivant : 000054A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.
Auteurs : Dominique Vlieghe [Belgique] ; Albin Sandelin ; Pieter J. De Bleser ; Kris Vleminckx ; Wyeth W. Wasserman ; Frans Van Roy ; Boris LenhardSource :
- Nucleic acids research [ 1362-4962 ] ; 2006.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- chemical , metabolism : DNA, Transcription Factors.
- Animals, Binding Sites, Computational Biology, Conserved Sequence, Databases, Nucleic Acid, Genomics, Internet, Regulatory Sequences, Nucleic Acid, User-Computer Interface.
Abstract
JASPAR is the most complete open-access collection of transcription factor binding site (TFBS) matrices. In this new release, JASPAR grows into a meta-database of collections of TFBS models derived by diverse approaches. We present JASPAR CORE--an expanded version of the original, non-redundant collection of annotated, high-quality matrix-based transcription factor binding profiles, JASPAR FAM--a collection of familial TFBS models and JASPAR phyloFACTS--a set of matrices computationally derived from statistically overrepresented, evolutionarily conserved regulatory region motifs from mammalian genomes. JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at http://jaspar.genereg.net.
DOI: 10.1093/nar/gkj115
PubMed: 16381983
Affiliations:
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De Bleser</name></author><author><name sortKey="Vleminckx, Kris" sort="Vleminckx, Kris" uniqKey="Vleminckx K" first="Kris" last="Vleminckx">Kris Vleminckx</name></author><author><name sortKey="Wasserman, Wyeth W" sort="Wasserman, Wyeth W" uniqKey="Wasserman W" first="Wyeth W" last="Wasserman">Wyeth W. 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De Bleser</name></author><author><name sortKey="Vleminckx, Kris" sort="Vleminckx, Kris" uniqKey="Vleminckx K" first="Kris" last="Vleminckx">Kris Vleminckx</name></author><author><name sortKey="Wasserman, Wyeth W" sort="Wasserman, Wyeth W" uniqKey="Wasserman W" first="Wyeth W" last="Wasserman">Wyeth W. Wasserman</name></author><author><name sortKey="Van Roy, Frans" sort="Van Roy, Frans" uniqKey="Van Roy F" first="Frans" last="Van Roy">Frans Van Roy</name></author><author><name sortKey="Lenhard, Boris" sort="Lenhard, Boris" uniqKey="Lenhard B" first="Boris" last="Lenhard">Boris Lenhard</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>Computational Biology</term><term>Conserved Sequence</term><term>DNA (chemistry)</term><term>DNA (metabolism)</term><term>Databases, Nucleic Acid</term><term>Genomics</term><term>Internet</term><term>Regulatory Sequences, Nucleic Acid</term><term>Transcription Factors (metabolism)</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>Computational Biology</term><term>Conserved Sequence</term><term>Databases, Nucleic Acid</term><term>Genomics</term><term>Internet</term><term>Regulatory Sequences, Nucleic Acid</term><term>User-Computer Interface</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">JASPAR is the most complete open-access collection of transcription factor binding site (TFBS) matrices. In this new release, JASPAR grows into a meta-database of collections of TFBS models derived by diverse approaches. We present JASPAR CORE--an expanded version of the original, non-redundant collection of annotated, high-quality matrix-based transcription factor binding profiles, JASPAR FAM--a collection of familial TFBS models and JASPAR phyloFACTS--a set of matrices computationally derived from statistically overrepresented, evolutionarily conserved regulatory region motifs from mammalian genomes. JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at http://jaspar.genereg.net.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16381983</PMID><DateCreated><Year>2005</Year><Month>12</Month><Day>29</Day></DateCreated><DateCompleted><Year>2006</Year><Month>02</Month><Day>28</Day></DateCompleted><DateRevised><Year>2014</Year><Month>9</Month><Day>9</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>34</Volume><Issue>Database issue</Issue><PubDate><Year>2006</Year><Month>Jan</Month><Day>1</Day></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation></Journal><ArticleTitle>A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.</ArticleTitle><Pagination><MedlinePgn>D95-7</MedlinePgn></Pagination><Abstract><AbstractText>JASPAR is the most complete open-access collection of transcription factor binding site (TFBS) matrices. In this new release, JASPAR grows into a meta-database of collections of TFBS models derived by diverse approaches. We present JASPAR CORE--an expanded version of the original, non-redundant collection of annotated, high-quality matrix-based transcription factor binding profiles, JASPAR FAM--a collection of familial TFBS models and JASPAR phyloFACTS--a set of matrices computationally derived from statistically overrepresented, evolutionarily conserved regulatory region motifs from mammalian genomes. JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at http://jaspar.genereg.net.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vlieghe</LastName><ForeName>Dominique</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department for Molecular Biomedical Research (DMBR), VIB-Ghent University, Technologiepark 927 B-9052, Ghent (Zwijnaarde), Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sandelin</LastName><ForeName>Albin</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>De Bleser</LastName><ForeName>Pieter J</ForeName><Initials>PJ</Initials></Author><Author ValidYN="Y"><LastName>Vleminckx</LastName><ForeName>Kris</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Wasserman</LastName><ForeName>Wyeth W</ForeName><Initials>WW</Initials></Author><Author ValidYN="Y"><LastName>van Roy</LastName><ForeName>Frans</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Lenhard</LastName><ForeName>Boris</ForeName><Initials>B</Initials></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2000 Jan;16(1):16-23</RefSource><PMID 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Version="1">15215389</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Science. 2004 Oct 22;306(5696):636-40</RefSource><PMID Version="1">15499007</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2004 Dec;36(12):1331-9</RefSource><PMID Version="1">15543148</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2005 Mar 17;434(7031):338-45</RefSource><PMID Version="1">15735639</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Bioinformatics. 2005;6:79</RefSource><PMID Version="1">15799782</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2005;33(10):3154-64</RefSource><PMID Version="1">15933209</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W393-6</RefSource><PMID Version="1">15980497</PMID></CommentsCorrections><CommentsCorrections 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MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="Y">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012045" MajorTopicYN="Y">Regulatory Sequences, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014584" MajorTopicYN="N">User-Computer Interface</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC1347477</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate 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De Bleser</name><name sortKey="Lenhard, Boris" sort="Lenhard, Boris" uniqKey="Lenhard B" first="Boris" last="Lenhard">Boris Lenhard</name><name sortKey="Sandelin, Albin" sort="Sandelin, Albin" uniqKey="Sandelin A" first="Albin" last="Sandelin">Albin Sandelin</name><name sortKey="Van Roy, Frans" sort="Van Roy, Frans" uniqKey="Van Roy F" first="Frans" last="Van Roy">Frans Van Roy</name><name sortKey="Vleminckx, Kris" sort="Vleminckx, Kris" uniqKey="Vleminckx K" first="Kris" last="Vleminckx">Kris Vleminckx</name><name sortKey="Wasserman, Wyeth W" sort="Wasserman, Wyeth W" uniqKey="Wasserman W" first="Wyeth W" last="Wasserman">Wyeth W. Wasserman</name></noCountry><country name="Belgique"><noRegion><name sortKey="Vlieghe, Dominique" sort="Vlieghe, Dominique" uniqKey="Vlieghe D" first="Dominique" last="Vlieghe">Dominique Vlieghe</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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