UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions
Identifieur interne : 002603 ( Main/Exploration ); précédent : 002602; suivant : 002604UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions
Auteurs : Kimberly Robasky [États-Unis] ; Martha L. Bulyk [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, DNA-Binding Proteins.
- chemical , metabolism : DNA, DNA-Binding Proteins.
- Animals, Binding Sites, Databases, Protein, Humans, Internet, Protein Array Analysis, Sequence Analysis, Protein, Software.
Abstract
The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants (‘words’) of length
Url:
DOI: 10.1093/nar/gkq992
PubMed: 21037262
PubMed Central: 3013812
Affiliations:
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Le document en format XML
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Bulyk</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Department of Medicine, Division of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Department of Medicine, Division of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston</wicri:cityArea></affiliation><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School</nlm:aff><wicri:noCountry code="subfield">Brigham and Women’s Hospital and Harvard Medical School</wicri:noCountry></affiliation><affiliation wicri:level="2"><nlm:aff id="AFF1">Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>DNA (chemistry)</term><term>DNA (metabolism)</term><term>DNA-Binding Proteins (chemistry)</term><term>DNA-Binding Proteins (metabolism)</term><term>Databases, Protein</term><term>Humans</term><term>Internet</term><term>Protein Array Analysis</term><term>Sequence Analysis, Protein</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (métabolisme)</term><term>Analyse de séquence de protéine</term><term>Analyse par réseau de protéines</term><term>Animaux</term><term>Bases de données de protéines</term><term>Humains</term><term>Internet</term><term>Logiciel</term><term>Protéines de liaison à l'ADN ()</term><term>Protéines de liaison à l'ADN (métabolisme)</term><term>Sites de fixation</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>DNA-Binding Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>DNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Protéines de liaison à l'ADN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>Databases, Protein</term><term>Humans</term><term>Internet</term><term>Protein Array Analysis</term><term>Sequence Analysis, Protein</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Analyse de séquence de protéine</term><term>Analyse par réseau de protéines</term><term>Animaux</term><term>Bases de données de protéines</term><term>Humains</term><term>Internet</term><term>Logiciel</term><term>Protéines de liaison à l'ADN</term><term>Sites de fixation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants (‘words’) of length <italic>k</italic> (‘<italic>k</italic>-mers’), as well as position weight matrix (PWM) and graphical sequence logo representations of the <italic>k</italic>-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at <ext-link ext-link-type="uri" xlink:href="http://uniprobe.org">http://uniprobe.org</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name></author><author><name sortKey="Huang, X" uniqKey="Huang X">X Huang</name></author><author><name sortKey="Choo, Y" uniqKey="Choo Y">Y Choo</name></author><author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mukherjee, S" uniqKey="Mukherjee S">S Mukherjee</name></author><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name></author><author><name sortKey="Jona, 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sortKey="Newburger, De" uniqKey="Newburger D">DE Newburger</name></author><author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Portales Casamar, E" uniqKey="Portales Casamar E">E Portales-Casamar</name></author><author><name sortKey="Thongjuea, S" uniqKey="Thongjuea S">S Thongjuea</name></author><author><name sortKey="Kwon, At" uniqKey="Kwon A">AT Kwon</name></author><author><name sortKey="Arenillas, D" uniqKey="Arenillas D">D Arenillas</name></author><author><name sortKey="Zhao, X" uniqKey="Zhao X">X Zhao</name></author><author><name sortKey="Valen, E" uniqKey="Valen E">E Valen</name></author><author><name sortKey="Yusuf, D" uniqKey="Yusuf D">D Yusuf</name></author><author><name sortKey="Lenhard, B" uniqKey="Lenhard B">B Lenhard</name></author><author><name sortKey="Wasserman, Ww" uniqKey="Wasserman W">WW Wasserman</name></author><author><name sortKey="Sandelin, A" uniqKey="Sandelin A">A 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uniqKey="Bulyk M">ML Bulyk</name></author><author><name sortKey="Serrano, L" uniqKey="Serrano L">L Serrano</name></author><author><name sortKey="Stricher, F" uniqKey="Stricher F">F Stricher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Madden, Tl" uniqKey="Madden T">TL Madden</name></author><author><name sortKey="Sch Ffer, Aa" uniqKey="Sch Ffer A">AA Schäffer</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Massachusetts</li></region></list><tree><country name="États-Unis"><region name="Massachusetts"><name sortKey="Robasky, Kimberly" sort="Robasky, Kimberly" uniqKey="Robasky K" first="Kimberly" last="Robasky">Kimberly Robasky</name></region><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><name sortKey="Robasky, Kimberly" sort="Robasky, Kimberly" uniqKey="Robasky K" first="Kimberly" last="Robasky">Kimberly Robasky</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|area= MersV1
|flux= Main
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|texte= UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions
}}
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