UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.
Identifieur interne : 002070 ( PubMed/Curation ); précédent : 002069; suivant : 002071UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.
Auteurs : Daniel E. Newburger [États-Unis] ; Martha L. BulykSource :
- Nucleic acids research [ 1362-4962 ] ; 2009.
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 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/.
DOI: 10.1093/nar/gkn660
PubMed: 18842628
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Newburger</name><affiliation wicri:level="1"><nlm:affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology, 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. 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Newburger</name><affiliation wicri:level="1"><nlm:affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology, 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></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2009" type="published">2009</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">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/.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18842628</PMID><DateCompleted><Year>2009</Year><Month>03</Month><Day>03</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>37</Volume><Issue>Database issue</Issue><PubDate><Year>2009</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation></Journal><ArticleTitle>UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.</ArticleTitle><Pagination><MedlinePgn>D77-82</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkn660</ELocationID><Abstract><AbstractText>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. 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