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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<series><title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
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<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>
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</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="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
. </pmc-comment>
<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>
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