plantsUPS: a database of plants' Ubiquitin Proteasome System.
Identifieur interne : 003420 ( Main/Exploration ); précédent : 003419; suivant : 003421plantsUPS: a database of plants' Ubiquitin Proteasome System.
Auteurs : Zhou Du [République populaire de Chine] ; Xin Zhou ; Li Li ; Zhen SuSource :
- BMC genomics [ 1471-2164 ] ; 2009.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Proteasome Endopeptidase Complex.
- genetics : Plants.
- Databases, Genetic, Genes, Plant, Genomics, Oligonucleotide Array Sequence Analysis, Phylogeny, Sequence Alignment, User-Computer Interface.
Abstract
BACKGROUND
The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes involved in this system, but are not identified in many species. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. Genomics data of plants such as Populus trichocarpa, Medicago truncatula, Glycine max and others are now publicly accessible. It is time to integrate information on classes of genes for complex protein systems such as UPS.
RESULTS
We developed a database of higher plants' UPS, named 'plantsUPS'. Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.
CONCLUSION
The plantsUPS enables the exploration and comparative analysis of UPS in higher plants. It now archives > 8000 genes from seven plant species distributed in 11 UPS-involved gene families. The plantsUPS is freely available now to all users at http://bioinformatics.cau.edu.cn/plantsUPS.
DOI: 10.1186/1471-2164-10-227
PubMed: 19445698
PubMed Central: PMC2690602
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Li</name></author><author><name sortKey="Su, Zhen" sort="Su, Zhen" uniqKey="Su Z" first="Zhen" last="Su">Zhen Su</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19445698</idno><idno type="pmid">19445698</idno><idno type="doi">10.1186/1471-2164-10-227</idno><idno type="pmc">PMC2690602</idno><idno type="wicri:Area/Main/Corpus">003566</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003566</idno><idno type="wicri:Area/Main/Curation">003566</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003566</idno><idno type="wicri:Area/Main/Exploration">003566</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">plantsUPS: a database of plants' Ubiquitin Proteasome System.</title><author><name sortKey="Du, Zhou" sort="Du, Zhou" uniqKey="Du Z" first="Zhou" last="Du">Zhou Du</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, PR China. adugduzhou@gmail.com</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhou, Xin" sort="Zhou, Xin" uniqKey="Zhou X" first="Xin" last="Zhou">Xin Zhou</name></author><author><name sortKey="Li, Li" sort="Li, Li" uniqKey="Li L" first="Li" last="Li">Li Li</name></author><author><name sortKey="Su, Zhen" sort="Su, Zhen" uniqKey="Su Z" first="Zhen" last="Su">Zhen Su</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genomics (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plants (genetics)</term><term>Proteasome Endopeptidase Complex (genetics)</term><term>Sequence Alignment (MeSH)</term><term>User-Computer Interface (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Bases de données génétiques (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génomique (MeSH)</term><term>Interface utilisateur (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Plantes (génétique)</term><term>Proteasome endopeptidase complex (génétique)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Proteasome Endopeptidase Complex</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Plantes</term><term>Proteasome endopeptidase complex</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Genes, Plant</term><term>Genomics</term><term>Oligonucleotide Array Sequence Analysis</term><term>Phylogeny</term><term>Sequence Alignment</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Bases de données génétiques</term><term>Gènes de plante</term><term>Génomique</term><term>Interface utilisateur</term><term>Phylogenèse</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes involved in this system, but are not identified in many species. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. Genomics data of plants such as Populus trichocarpa, Medicago truncatula, Glycine max and others are now publicly accessible. It is time to integrate information on classes of genes for complex protein systems such as UPS.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We developed a database of higher plants' UPS, named 'plantsUPS'. Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>The plantsUPS enables the exploration and comparative analysis of UPS in higher plants. It now archives > 8000 genes from seven plant species distributed in 11 UPS-involved gene families. The plantsUPS is freely available now to all users at http://bioinformatics.cau.edu.cn/plantsUPS.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19445698</PMID><DateCompleted><Year>2009</Year><Month>06</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><PubDate><Year>2009</Year><Month>May</Month><Day>16</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>plantsUPS: a database of plants' Ubiquitin Proteasome System.</ArticleTitle><Pagination><MedlinePgn>227</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-10-227</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes involved in this system, but are not identified in many species. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. Genomics data of plants such as Populus trichocarpa, Medicago truncatula, Glycine max and others are now publicly accessible. It is time to integrate information on classes of genes for complex protein systems such as UPS.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We developed a database of higher plants' UPS, named 'plantsUPS'. Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The plantsUPS enables the exploration and comparative analysis of UPS in higher plants. It now archives > 8000 genes from seven plant species distributed in 11 UPS-involved gene families. 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Xin" uniqKey="Zhou X" first="Xin" last="Zhou">Xin Zhou</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Du, Zhou" sort="Du, Zhou" uniqKey="Du Z" first="Zhou" last="Du">Zhou Du</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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