CoP: a database for characterizing co-expressed gene modules with biological information in plants.
Identifieur interne : 003337 ( Main/Exploration ); précédent : 003336; suivant : 003338CoP: a database for characterizing co-expressed gene modules with biological information in plants.
Auteurs : Yoshiyuki Ogata [Japon] ; Hideyuki Suzuki ; Nozomu Sakurai ; Daisuke ShibataSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2010.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Arabidopsis (génétique), Bases de données génétiques (MeSH), Biologie informatique (méthodes), Gènes de plante (MeSH), Génome végétal (MeSH), Modèles génétiques (MeSH), Plantes (génétique), Plantes (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Séquençage par oligonucléotides en batterie (MeSH).
- MESH :
- génétique : Arabidopsis, Plantes.
- métabolisme : Plantes.
- méthodes : Biologie informatique.
- Algorithmes, Bases de données génétiques, Gènes de plante, Génome végétal, Modèles génétiques, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Algorithms (MeSH), Arabidopsis (genetics), Computational Biology (methods), Databases, Genetic (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Genes, Plant (MeSH), Genome, Plant (MeSH), Models, Genetic (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Plants (genetics), Plants (metabolism).
- MESH :
- genetics : Arabidopsis, Plants.
- metabolism : Plants.
- methods : Computational Biology.
- Algorithms, Databases, Genetic, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genes, Plant, Genome, Plant, Models, Genetic, Oligonucleotide Array Sequence Analysis.
Abstract
UNLABELLED
Using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the CoP database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. The Confeito algorithm developed previously in our laboratory, which is suitable to calculate the interconnectivity between genes in co-expressed gene network, was applied to extract co-expressed gene modules. The database includes the gene modules for Arabidopsis thaliana (thale cress) and seven crops, Glycine max (soybean), Hordeum vulgare (barley), Oryza sativa (rice), Populus trichocarpa (poplar), Triticum aestivum (wheat), Vitis vinifera (grape) and Zea mays (maize).
AVAILABILITY
The CoP database is available at: http://webs2.kazusa.or.jp/kagiana/cop0911/.
DOI: 10.1093/bioinformatics/btq121
PubMed: 20305269
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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The Confeito algorithm developed previously in our laboratory, which is suitable to calculate the interconnectivity between genes in co-expressed gene network, was applied to extract co-expressed gene modules. The database includes the gene modules for Arabidopsis thaliana (thale cress) and seven crops, Glycine max (soybean), Hordeum vulgare (barley), Oryza sativa (rice), Populus trichocarpa (poplar), Triticum aestivum (wheat), Vitis vinifera (grape) and Zea mays (maize).</p></div><div type="abstract" xml:lang="en"><p><b>AVAILABILITY</b></p><p>The CoP database is available at: http://webs2.kazusa.or.jp/kagiana/cop0911/.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20305269</PMID><DateCompleted><Year>2010</Year><Month>10</Month><Day>22</Day></DateCompleted><DateRevised><Year>2013</Year><Month>05</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>26</Volume><Issue>9</Issue><PubDate><Year>2010</Year><Month>May</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>CoP: a database for characterizing co-expressed gene modules with biological information in plants.</ArticleTitle><Pagination><MedlinePgn>1267-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btq121</ELocationID><Abstract><AbstractText Label="UNLABELLED">Using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the CoP database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. 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