UniPROBE: an online database of protein binding microarray data on protein–DNA interactions
Identifieur interne : 002937 ( Main/Exploration ); précédent : 002936; suivant : 002938UniPROBE: an online database of protein binding microarray data on protein–DNA interactions
Auteurs : Daniel E. Newburger ; Martha L. Bulyk [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : DNA-Binding Proteins, Transcription Factors.
- Animals, Binding Sites, Databases, Protein, Humans, Internet, Mice, Protein Array Analysis, Sequence Analysis, DNA, User-Computer Interface.
Abstract
The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the
Url:
DOI: 10.1093/nar/gkn660
PubMed: 18842628
PubMed Central: 2686578
Affiliations:
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Le document en format XML
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Bulyk</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine,</nlm:aff><wicri:noCountry code="subfield">Department of Medicine</wicri:noCountry></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></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18842628</idno><idno type="pmc">2686578</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686578</idno><idno type="RBID">PMC:2686578</idno><idno type="doi">10.1093/nar/gkn660</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000F42</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F42</idno><idno type="wicri:Area/Pmc/Curation">000F42</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F42</idno><idno type="wicri:Area/Pmc/Checkpoint">001391</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001391</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:18842628</idno><idno type="wicri:Area/PubMed/Corpus">002070</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002070</idno><idno type="wicri:Area/PubMed/Curation">002070</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002070</idno><idno type="wicri:Area/PubMed/Checkpoint">001E74</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001E74</idno><idno type="wicri:Area/Ncbi/Merge">000639</idno><idno type="wicri:Area/Ncbi/Curation">000639</idno><idno type="wicri:Area/Ncbi/Checkpoint">000639</idno><idno type="wicri:doubleKey">0305-1048:2008:Newburger D:uniprobe:an:online</idno><idno type="wicri:Area/Main/Merge">002963</idno><idno type="wicri:Area/Main/Curation">002937</idno><idno type="wicri:Area/Main/Exploration">002937</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">UniPROBE: an online database of protein binding microarray data on protein–DNA interactions</title><author><name sortKey="Newburger, Daniel E" sort="Newburger, Daniel E" uniqKey="Newburger D" first="Daniel E." last="Newburger">Daniel E. Newburger</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine,</nlm:aff><wicri:noCountry code="subfield">Department of Medicine</wicri:noCountry></affiliation></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine,</nlm:aff><wicri:noCountry code="subfield">Department of Medicine</wicri:noCountry></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="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>DNA-Binding Proteins (metabolism)</term><term>Databases, Protein</term><term>Humans</term><term>Internet</term><term>Mice</term><term>Protein Array Analysis</term><term>Sequence Analysis, DNA</term><term>Transcription Factors (metabolism)</term><term>User-Computer Interface</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Analyse par réseau de protéines</term><term>Animaux</term><term>Bases de données de protéines</term><term>Facteurs de transcription (métabolisme)</term><term>Humains</term><term>Interface utilisateur</term><term>Internet</term><term>Protéines de liaison à l'ADN (métabolisme)</term><term>Sites de fixation</term><term>Souris</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA-Binding Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</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>Mice</term><term>Protein Array Analysis</term><term>Sequence Analysis, DNA</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Analyse par réseau de protéines</term><term>Animaux</term><term>Bases de données de protéines</term><term>Humains</term><term>Interface utilisateur</term><term>Internet</term><term>Sites de fixation</term><term>Souris</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the <italic>in vitro</italic> DNA-binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive PBM data on the preferences of proteins for all possible 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 total, the database hosts DNA-binding data for over 175 nonredundant proteins from a diverse collection of organisms, including the prokaryote <italic>Vibrio harveyi</italic>, the eukaryotic malarial parasite <italic>Plasmodium falciparum</italic>, the parasitic Apicomplexan <italic>Cryptosporidium parvum</italic>, the yeast <italic>Saccharomyces cerevisiae</italic>, the worm <italic>Caenorhabditis elegans</italic>, mouse and human. Current web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. The UniPROBE database is available at <ext-link ext-link-type="uri" xlink:href="http://thebrain.bwh.harvard.edu/uniprobe/">http://thebrain.bwh.harvard.edu/uniprobe/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name></author><author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name></author><author><name sortKey="Qureshi, Am" uniqKey="Qureshi A">AM Qureshi</name></author><author><name sortKey="He, Fs" uniqKey="He F">FS He</name></author><author><name sortKey="Estep, P W" uniqKey="Estep P">P.W. 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sortKey="Park, J" uniqKey="Park J">J Park</name></author><author><name sortKey="Binkley, G" uniqKey="Binkley G">G Binkley</name></author><author><name sortKey="Costanzo, Mc" uniqKey="Costanzo M">MC Costanzo</name></author><author><name sortKey="Dwight, Ss" uniqKey="Dwight S">SS Dwight</name></author><author><name sortKey="Engel, Sr" uniqKey="Engel S">SR Engel</name></author><author><name sortKey="Fisk, Dg" uniqKey="Fisk D">DG Fisk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rogers, A" uniqKey="Rogers A">A Rogers</name></author><author><name sortKey="Antoshechkin, I" uniqKey="Antoshechkin I">I Antoshechkin</name></author><author><name sortKey="Bieri, T" uniqKey="Bieri T">T Bieri</name></author><author><name sortKey="Blasiar, D" uniqKey="Blasiar D">D Blasiar</name></author><author><name sortKey="Bastiani, C" uniqKey="Bastiani C">C Bastiani</name></author><author><name sortKey="Canaran, P" uniqKey="Canaran P">P Canaran</name></author><author><name sortKey="Chan, J" uniqKey="Chan J">J Chan</name></author><author><name sortKey="Chen, Wj" uniqKey="Chen W">WJ Chen</name></author><author><name sortKey="Davis, P" uniqKey="Davis P">P Davis</name></author><author><name sortKey="Fernandes, J" uniqKey="Fernandes J">J Fernandes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pruitt, Kd" uniqKey="Pruitt K">KD Pruitt</name></author><author><name sortKey="Tatusova, T" uniqKey="Tatusova T">T Tatusova</name></author><author><name sortKey="Maglott, Dr" uniqKey="Maglott D">DR Maglott</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Gupta, S" uniqKey="Gupta S">S Gupta</name></author><author><name sortKey="Stamatoyannopoulos, Ja" uniqKey="Stamatoyannopoulos J">JA Stamatoyannopoulos</name></author><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name></author><author><name sortKey="Noble, Ws" uniqKey="Noble W">WS Noble</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huber, Br" uniqKey="Huber B">BR Huber</name></author><author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Massachusetts</li></region></list><tree><noCountry><name sortKey="Newburger, Daniel E" sort="Newburger, Daniel E" uniqKey="Newburger D" first="Daniel E." last="Newburger">Daniel E. Newburger</name></noCountry><country name="États-Unis"><region name="Massachusetts"><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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