Bacteriome.org--an integrated protein interaction database for E. coli.
Identifieur interne : 002216 ( Main/Exploration ); précédent : 002215; suivant : 002217Bacteriome.org--an integrated protein interaction database for E. coli.
Auteurs : Chong Su [Canada] ; Jose M. Peregrin-Alvarez ; Gareth Butland ; Sadhna Phanse ; Vincent Fong ; Andrew Emili ; John ParkinsonSource :
- Nucleic acids research [ 1362-4962 ] ; 2008.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Escherichia coli Proteins.
- metabolism : Escherichia coli, Escherichia coli Proteins.
- Databases, Protein, Internet, Protein Interaction Mapping, Proteomics, Systems Integration, User-Computer Interface.
Abstract
High throughput methods are increasingly being used to examine the functions and interactions of gene products on a genome-scale. These include systematic large-scale proteomic studies of protein complexes and protein-protein interaction networks, functional genomic studies examining patterns of gene expression and comparative genomics studies examining patterns of conservation. Since these datasets offer different yet highly complementary perspectives on cell behavior it is expected that integration of these datasets will lead to conceptual advances in our understanding of the fundamental design and evolutionary principles that underlie the organization and function of proteins within biochemical pathways. Here we present Bacteriome.org, a resource that combines locally generated interaction and evolutionary datasets with a previously generated knowledgebase, to provide an integrated view of the Escherichia coli interactome. Tools are provided which allow the user to select and visualize functional, evolutionary and structural relationships between groups of interacting proteins and to focus on genes of interest. Currently the database contains three interaction datasets: a functional dataset consisting of 3989 interactions between 1927 proteins; a 'core' high quality experimental dataset of 4863 interactions between 1100 proteins and an 'extended' experimental dataset of 9860 interactions between 2131 proteins. Bacteriome.org is available online at http://www.bacteriome.org.
DOI: 10.1093/nar/gkm807
PubMed: 17942431
Affiliations:
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Peregrin-Alvarez</name></author><author><name sortKey="Butland, Gareth" sort="Butland, Gareth" uniqKey="Butland G" first="Gareth" last="Butland">Gareth Butland</name></author><author><name sortKey="Phanse, Sadhna" sort="Phanse, Sadhna" uniqKey="Phanse S" first="Sadhna" last="Phanse">Sadhna Phanse</name></author><author><name sortKey="Fong, Vincent" sort="Fong, Vincent" uniqKey="Fong V" first="Vincent" last="Fong">Vincent Fong</name></author><author><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:17942431</idno><idno type="pmid">17942431</idno><idno type="doi">10.1093/nar/gkm807</idno><idno type="wicri:Area/PubMed/Corpus">001025</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001025</idno><idno type="wicri:Area/PubMed/Curation">001025</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001025</idno><idno type="wicri:Area/PubMed/Checkpoint">001025</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001025</idno><idno type="wicri:Area/Ncbi/Merge">000824</idno><idno type="wicri:Area/Ncbi/Curation">000824</idno><idno type="wicri:Area/Ncbi/Checkpoint">000824</idno><idno type="wicri:Area/Main/Merge">002409</idno><idno type="wicri:Area/Main/Curation">002216</idno><idno type="wicri:Area/Main/Exploration">002216</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Bacteriome.org--an integrated protein interaction database for E. coli.</title><author><name sortKey="Su, Chong" sort="Su, Chong" uniqKey="Su C" first="Chong" last="Su">Chong Su</name><affiliation wicri:level="1"><nlm:affiliation>Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8</wicri:regionArea><wicri:noRegion>ON M5G 1X8</wicri:noRegion></affiliation></author><author><name sortKey="Peregrin Alvarez, Jose M" sort="Peregrin Alvarez, Jose M" uniqKey="Peregrin Alvarez J" first="Jose M" last="Peregrin-Alvarez">Jose M. Peregrin-Alvarez</name></author><author><name sortKey="Butland, Gareth" sort="Butland, Gareth" uniqKey="Butland G" first="Gareth" last="Butland">Gareth Butland</name></author><author><name sortKey="Phanse, Sadhna" sort="Phanse, Sadhna" uniqKey="Phanse S" first="Sadhna" last="Phanse">Sadhna Phanse</name></author><author><name sortKey="Fong, Vincent" sort="Fong, Vincent" uniqKey="Fong V" first="Vincent" last="Fong">Vincent Fong</name></author><author><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Protein</term><term>Escherichia coli (metabolism)</term><term>Escherichia coli Proteins (genetics)</term><term>Escherichia coli Proteins (metabolism)</term><term>Internet</term><term>Protein Interaction Mapping</term><term>Proteomics</term><term>Systems Integration</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Escherichia coli Proteins</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Escherichia coli</term><term>Escherichia coli Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Protein</term><term>Internet</term><term>Protein Interaction Mapping</term><term>Proteomics</term><term>Systems Integration</term><term>User-Computer Interface</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">High throughput methods are increasingly being used to examine the functions and interactions of gene products on a genome-scale. These include systematic large-scale proteomic studies of protein complexes and protein-protein interaction networks, functional genomic studies examining patterns of gene expression and comparative genomics studies examining patterns of conservation. Since these datasets offer different yet highly complementary perspectives on cell behavior it is expected that integration of these datasets will lead to conceptual advances in our understanding of the fundamental design and evolutionary principles that underlie the organization and function of proteins within biochemical pathways. Here we present Bacteriome.org, a resource that combines locally generated interaction and evolutionary datasets with a previously generated knowledgebase, to provide an integrated view of the Escherichia coli interactome. Tools are provided which allow the user to select and visualize functional, evolutionary and structural relationships between groups of interacting proteins and to focus on genes of interest. Currently the database contains three interaction datasets: a functional dataset consisting of 3989 interactions between 1927 proteins; a 'core' high quality experimental dataset of 4863 interactions between 1100 proteins and an 'extended' experimental dataset of 9860 interactions between 2131 proteins. Bacteriome.org is available online at http://www.bacteriome.org.</div></front></TEI><affiliations><list><country><li>Canada</li></country></list><tree><noCountry><name sortKey="Butland, Gareth" sort="Butland, Gareth" uniqKey="Butland G" first="Gareth" last="Butland">Gareth Butland</name><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name><name sortKey="Fong, Vincent" sort="Fong, Vincent" uniqKey="Fong V" first="Vincent" last="Fong">Vincent Fong</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Peregrin Alvarez, Jose M" sort="Peregrin Alvarez, Jose M" uniqKey="Peregrin Alvarez J" first="Jose M" last="Peregrin-Alvarez">Jose M. Peregrin-Alvarez</name><name sortKey="Phanse, Sadhna" sort="Phanse, Sadhna" uniqKey="Phanse S" first="Sadhna" last="Phanse">Sadhna Phanse</name></noCountry><country name="Canada"><noRegion><name sortKey="Su, Chong" sort="Su, Chong" uniqKey="Su C" first="Chong" last="Su">Chong Su</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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