UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions
Identifieur interne : 001347 ( Pmc/Checkpoint ); précédent : 001346; suivant : 001348UniPROBE, 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.
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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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></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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<front><journal-meta><journal-id journal-id-type="nlm-ta">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">21037262</article-id><article-id pub-id-type="pmc">3013812</article-id><article-id pub-id-type="doi">10.1093/nar/gkq992</article-id><article-id pub-id-type="publisher-id">gkq992</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Robasky</surname><given-names>Kimberly</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF1"><sup>2</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>3</sup></xref><xref ref-type="aff" rid="AFF1"><sup>4</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Department of Medicine, Division of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115,<sup>2</sup>Bioinformatics Program, Boston University, Boston, MA 02215,<sup>3</sup>Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School and<sup>4</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><pmc-comment>For NAR both ppub and collection dates generated for PMC processing 1/27/05 beck</pmc-comment>
<pub-date pub-type="collection"><month>1</month><year>2011</year></pub-date><pub-date pub-type="ppub"><month>1</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>30</day><month>10</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>30</day><month>10</month><year>2010</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>39</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D124</fpage><lpage>D128</lpage><history><date date-type="received"><day>13</day><month>9</month><year>2010</year></date><date date-type="accepted"><day>5</day><month>10</month><year>2010</year></date></history><permissions><copyright-statement>© The Author(s) 2010. Published by Oxford University Press.</copyright-statement><copyright-year>2010</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.5"><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/2.5">http://creativecommons.org/licenses/by-nc/2.5</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 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></abstract></article-meta></front></pmc><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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