GeneBrowser 2: an application to explore and identify common biological traits in a set of genes
Identifieur interne : 000B22 ( Main/Exploration ); précédent : 000B21; suivant : 000B23GeneBrowser 2: an application to explore and identify common biological traits in a set of genes
Auteurs : Joel P. Arrais [Portugal] ; João Fernandes [Portugal] ; João Pereira [Portugal] ; José Luís Oliveira [Portugal]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2010.
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English descriptors
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Abstract
The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relevant biological roles for the problem at hand. The required information is typically available in public databases, and usually, this information must be manually retrieved to complement the analysis. This process is a very time-consuming task that should be automated as much as possible.
GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways.
GeneBrowser provides a unique entry point to several visualisation and analysis methods, providing fast and easy analysis of a set of genes. GeneBrowser fills the gap between Web portals that analyse one gene at a time and functional analysis tools that are limited in scope and usually desktop-based.
Url:
DOI: 10.1186/1471-2105-11-389
PubMed: 20663121
PubMed Central: 2919517
Affiliations:
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Le document en format XML
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Arrais</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro</wicri:regionArea><wicri:noRegion>3810-193 Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Fernandes, Joao" sort="Fernandes, Joao" uniqKey="Fernandes J" first="João" last="Fernandes">João Fernandes</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro</wicri:regionArea><wicri:noRegion>3810-193 Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Pereira, Joao" sort="Pereira, Joao" uniqKey="Pereira J" first="João" last="Pereira">João Pereira</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro</wicri:regionArea><wicri:noRegion>3810-193 Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Oliveira, Jose Luis" sort="Oliveira, Jose Luis" uniqKey="Oliveira J" first="José Luís" last="Oliveira">José Luís Oliveira</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro</wicri:regionArea><wicri:noRegion>3810-193 Aveiro</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Computational Biology (methods)</term><term>Databases, Genetic</term><term>Gene Expression Profiling</term><term>Genomics (methods)</term><term>Information Storage and Retrieval</term><term>Internet</term><term>Saccharomyces cerevisiae (genetics)</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de profil d'expression de gènes</term><term>Bases de données génétiques</term><term>Biologie informatique ()</term><term>Génomique ()</term><term>Interface utilisateur</term><term>Internet</term><term>Logiciel</term><term>Mémorisation et recherche des informations</term><term>Saccharomyces cerevisiae (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Databases, Genetic</term><term>Gene Expression Profiling</term><term>Information Storage and Retrieval</term><term>Internet</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de profil d'expression de gènes</term><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Génomique</term><term>Interface utilisateur</term><term>Internet</term><term>Logiciel</term><term>Mémorisation et recherche des informations</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relevant biological roles for the problem at hand. The required information is typically available in public databases, and usually, this information must be manually retrieved to complement the analysis. This process is a very time-consuming task that should be automated as much as possible.</p></sec><sec><title>Results</title><p>GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways.</p></sec><sec><title>Conclusions</title><p>GeneBrowser provides a unique entry point to several visualisation and analysis methods, providing fast and easy analysis of a set of genes. GeneBrowser fills the gap between Web portals that analyse one gene at a time and functional analysis tools that are limited in scope and usually desktop-based.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lee, Hk" uniqKey="Lee H">HK Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Westerhoff, H" uniqKey="Westerhoff H">H Westerhoff</name></author><author><name sortKey="Palsson, B" uniqKey="Palsson B">B Palsson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Duggan, Dj" uniqKey="Duggan D">DJ Duggan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blake, Ja" uniqKey="Blake J">JA Blake</name></author><author><name sortKey="Harris, Ma" uniqKey="Harris M">MA Harris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Draghici, S" uniqKey="Draghici S">S 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sortKey="Arrais, Joel P" sort="Arrais, Joel P" uniqKey="Arrais J" first="Joel P" last="Arrais">Joel P. Arrais</name></noRegion><name sortKey="Fernandes, Joao" sort="Fernandes, Joao" uniqKey="Fernandes J" first="João" last="Fernandes">João Fernandes</name><name sortKey="Oliveira, Jose Luis" sort="Oliveira, Jose Luis" uniqKey="Oliveira J" first="José Luís" last="Oliveira">José Luís Oliveira</name><name sortKey="Pereira, Joao" sort="Pereira, Joao" uniqKey="Pereira J" first="João" last="Pereira">João Pereira</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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