UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions
Identifieur interne : 000F39 ( Pmc/Curation ); précédent : 000F38; suivant : 000F40UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions
Auteurs : Maxwell A. Hume [États-Unis] ; Luis A. Barrera [États-Unis] ; Stephen S. Gisselbrecht [États-Unis] ; Martha L. Bulyk [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2014.
Abstract
The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides
Url:
DOI: 10.1093/nar/gku1045
PubMed: 25378322
PubMed Central: 4383892
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Hume</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115</wicri:regionArea></affiliation></author><author><name sortKey="Barrera, Luis A" sort="Barrera, Luis A" uniqKey="Barrera L" first="Luis A." last="Barrera">Luis A. Barrera</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF3">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115</wicri:regionArea></affiliation></author><author><name sortKey="Gisselbrecht, Stephen S" sort="Gisselbrecht, Stephen S" uniqKey="Gisselbrecht S" first="Stephen S." last="Gisselbrecht">Stephen S. Gisselbrecht</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115</wicri:regionArea></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 wicri:level="1"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF3">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF5">Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, Brigham and Women's Hospital and 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="2014">2014</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) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides <italic>in vitro</italic> data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length <italic>k</italic> (‘<italic>k</italic>-mers’). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of <italic>k</italic>-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. 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="Berger, M F" uniqKey="Berger M">M.F. 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<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="hwp">nar</journal-id><journal-id journal-id-type="publisher-id">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">25378322</article-id><article-id pub-id-type="pmc">4383892</article-id><article-id pub-id-type="doi">10.1093/nar/gku1045</article-id><article-categories><subj-group subj-group-type="heading"><subject>Database Issue</subject></subj-group></article-categories><title-group><article-title>UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hume</surname><given-names>Maxwell A.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF2"><sup>2</sup></xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-2877-8079</contrib-id></contrib><contrib contrib-type="author"><name><surname>Barrera</surname><given-names>Luis A.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF3"><sup>3</sup></xref><xref ref-type="aff" rid="AFF4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gisselbrecht</surname><given-names>Stephen S.</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="AFF3"><sup>3</sup></xref><xref ref-type="aff" rid="AFF4"><sup>4</sup></xref><xref ref-type="aff" rid="AFF5"><sup>5</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><aff id="AFF1"><label>1</label>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</aff><aff id="AFF2"><label>2</label>Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115, USA</aff><aff id="AFF3"><label>3</label>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</aff><aff id="AFF4"><label>4</label>Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</aff><aff id="AFF5"><label>5</label>Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</aff></contrib-group><author-notes><corresp id="COR1"><label>*</label>To whom correspondence should be addressed. Tel: +1 617 525 4725; Fax: +1 617 525 4705; Email: <email>mlbulyk@receptor.med.harvard.edu</email></corresp></author-notes><pub-date pub-type="ppub"><day>28</day><month>1</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>05</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>05</day><month>11</month><year>2014</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>43</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D117</fpage><lpage>D122</lpage><history><date date-type="accepted"><day>12</day><month>10</month><year>2014</year></date><date date-type="received"><day>15</day><month>9</month><year>2014</year></date></history><permissions><copyright-statement>© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.</copyright-statement><copyright-year>2015</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact <email>journals.permissions@oup.com</email></license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="gku1045.pdf"></self-uri><abstract><p>The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides <italic>in vitro</italic> data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length <italic>k</italic> (‘<italic>k</italic>-mers’). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of <italic>k</italic>-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at <ext-link ext-link-type="uri" xlink:href="http://uniprobe.org">http://uniprobe.org</ext-link>.</p></abstract><counts><page-count count="6"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>28 January 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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