UniPROBE: an online database of protein binding microarray data on protein–DNA interactions
Identifieur interne : 000F42 ( Pmc/Curation ); précédent : 000F41; suivant : 000F43UniPROBE: 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.
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
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Daniel E. Newburger<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 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="1"><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></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="1"><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></affiliation>Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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="1"><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></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></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="1"><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></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></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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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><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18842628</article-id><article-id pub-id-type="pmc">2686578</article-id><article-id pub-id-type="doi">10.1093/nar/gkn660</article-id><article-id pub-id-type="publisher-id">gkn660</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>UniPROBE: an online database of protein binding microarray data on protein–DNA interactions</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Newburger</surname><given-names>Daniel E.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bulyk</surname><given-names>Martha L.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Division of Genetics, Department of Medicine,<sup>2</sup>Department of Pathology, Brigham and Women's Hospital and Harvard Medical School and<sup>3</sup>Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115, USA</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>+1 617 525 4725</phone>; Fax: <fax>+1 617 525 4705</fax>; Email: <email>mlbulyk@receptor.med.harvard.edu</email></corresp></author-notes><pub-date pub-type="ppub"><month>1</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>8</day><month>10</month><year>2008</year></pub-date><pub-date pub-type="pmc-release"><day>7</day><month>10</month><year>2008</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<pmc-comment> oupReleaseDelayRemoved from OA Article (10.1093/nar/gkn660gkn660ArticlesUniPROBE: an online database of protein binding microarray data on protein–DNA interactionsNewburgerDaniel E.1BulykMartha L.123*1Division of Genetics, Department of Medicine, 2Department of Pathology, Brigham and Women's Hospital and Harvard Medical School and 3Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115, USA*To whom correspondence should be addressed. Tel: +1 617 525 4725; Fax: +1 617 525 4705; Email: mlbulyk@receptor.med.harvard.edu12009710200837suppl_1Database issueD77D82158200818920082192008© 2008 The Author(s)2008This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro 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 k (‘k-mers’), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database hosts DNA-binding data for over 175 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, 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 http://thebrain.bwh.harvard.edu/uniprobe/.) </pmc-comment>
<volume>37</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D77</fpage><lpage>D82</lpage><history><date date-type="received"><day>15</day><month>8</month><year>2008</year></date><date date-type="rev-recd"><day>18</day><month>9</month><year>2008</year></date><date date-type="accepted"><day>21</day><month>9</month><year>2008</year></date></history><permissions><copyright-statement>© 2008 The Author(s)</copyright-statement><copyright-year>2008</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/">http://creativecommons.org/licenses/by-nc/2.0/uk/</ext-link>) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><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></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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