LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes.
Identifieur interne : 002A01 ( Main/Exploration ); précédent : 002A00; suivant : 002A02LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes.
Auteurs : Jun Li [États-Unis] ; Xinbin Dai ; Tingsong Liu ; Patrick Xuechun ZhaoSource :
- Nucleic acids research [ 1362-4962 ] ; 2012.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Bases de données génétiques (MeSH), Cytochrome P-450 enzyme system (génétique), Fabaceae (génétique), Fabaceae (microbiologie), Fabaceae (métabolisme), Glycosyltransferase (génétique), Gènes de plante (MeSH), Génome végétal (MeSH), Génomique (MeSH), Intégration de systèmes (MeSH), Logiciel (MeSH), Loteae (génétique), Medicago truncatula (génétique), Modèles génétiques (MeSH), Soja (génétique), Symbiose (MeSH).
- MESH :
- génétique : Cytochrome P-450 enzyme system, Fabaceae, Glycosyltransferase, Loteae, Medicago truncatula, Soja.
- microbiologie : Fabaceae.
- métabolisme : Fabaceae.
- Analyse de profil d'expression de gènes, Bases de données génétiques, Gènes de plante, Génome végétal, Génomique, Intégration de systèmes, Logiciel, Modèles génétiques, Symbiose.
English descriptors
- KwdEn :
- Cytochrome P-450 Enzyme System (genetics), Databases, Genetic (MeSH), Fabaceae (genetics), Fabaceae (metabolism), Fabaceae (microbiology), Gene Expression Profiling (MeSH), Genes, Plant (MeSH), Genome, Plant (MeSH), Genomics (MeSH), Glycosyltransferases (genetics), Lotus (genetics), Medicago truncatula (genetics), Models, Genetic (MeSH), Software (MeSH), Soybeans (genetics), Symbiosis (MeSH), Systems Integration (MeSH).
- MESH :
- chemical , genetics : Cytochrome P-450 Enzyme System, Glycosyltransferases.
- genetics : Fabaceae, Lotus, Medicago truncatula, Soybeans.
- metabolism : Fabaceae.
- microbiology : Fabaceae.
- Databases, Genetic, Gene Expression Profiling, Genes, Plant, Genome, Plant, Genomics, Models, Genetic, Software, Symbiosis, Systems Integration.
Abstract
Legumes play a vital role in maintaining the nitrogen cycle of the biosphere. They conduct symbiotic nitrogen fixation through endosymbiotic relationships with bacteria in root nodules. However, this and other characteristics of legumes, including mycorrhization, compound leaf development and profuse secondary metabolism, are absent in the typical model plant Arabidopsis thaliana. We present LegumeIP (http://plantgrn.noble.org/LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes. LegumeIP compiles gene and gene family information, syntenic and phylogenetic context and tissue-specific transcriptomic profiles. The database holds the genomic sequences of three model legumes, Medicago truncatula, Glycine max and Lotus japonicus plus two reference plant species, A. thaliana and Populus trichocarpa, with annotations based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. LegumeIP also contains large-scale microarray and RNA-Seq-based gene expression data. Our new database is capable of systematic synteny analysis across M. truncatula, G. max, L. japonicas and A. thaliana, as well as construction and phylogenetic analysis of gene families across the five hosted species. Finally, LegumeIP provides comprehensive search and visualization tools that enable flexible queries based on gene annotation, gene family, synteny and relative gene expression.
DOI: 10.1093/nar/gkr939
PubMed: 22110036
PubMed Central: PMC3245131
Affiliations:
Links toward previous steps (curation, corpus...)
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génétiques</term><term>Symbiose</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Legumes play a vital role in maintaining the nitrogen cycle of the biosphere. They conduct symbiotic nitrogen fixation through endosymbiotic relationships with bacteria in root nodules. However, this and other characteristics of legumes, including mycorrhization, compound leaf development and profuse secondary metabolism, are absent in the typical model plant Arabidopsis thaliana. We present LegumeIP (http://plantgrn.noble.org/LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes. LegumeIP compiles gene and gene family information, syntenic and phylogenetic context and tissue-specific transcriptomic profiles. The database holds the genomic sequences of three model legumes, Medicago truncatula, Glycine max and Lotus japonicus plus two reference plant species, A. thaliana and Populus trichocarpa, with annotations based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. LegumeIP also contains large-scale microarray and RNA-Seq-based gene expression data. Our new database is capable of systematic synteny analysis across M. truncatula, G. max, L. japonicas and A. thaliana, as well as construction and phylogenetic analysis of gene families across the five hosted species. Finally, LegumeIP provides comprehensive search and visualization tools that enable flexible queries based on gene annotation, gene family, synteny and relative gene expression.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22110036</PMID><DateCompleted><Year>2012</Year><Month>07</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>40</Volume><Issue>Database issue</Issue><PubDate><Year>2012</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res</ISOAbbreviation></Journal><ArticleTitle>LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes.</ArticleTitle><Pagination><MedlinePgn>D1221-9</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkr939</ELocationID><Abstract><AbstractText>Legumes play a vital role in maintaining the nitrogen cycle of the biosphere. They conduct symbiotic nitrogen fixation through endosymbiotic relationships with bacteria in root nodules. However, this and other characteristics of legumes, including mycorrhization, compound leaf development and profuse secondary metabolism, are absent in the typical model plant Arabidopsis thaliana. We present LegumeIP (http://plantgrn.noble.org/LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes. LegumeIP compiles gene and gene family information, syntenic and phylogenetic context and tissue-specific transcriptomic profiles. The database holds the genomic sequences of three model legumes, Medicago truncatula, Glycine max and Lotus japonicus plus two reference plant species, A. thaliana and Populus trichocarpa, with annotations based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. LegumeIP also contains large-scale microarray and RNA-Seq-based gene expression data. Our new database is capable of systematic synteny analysis across M. truncatula, G. max, L. japonicas and A. thaliana, as well as construction and phylogenetic analysis of gene families across the five hosted species. 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Jun" uniqKey="Li J" first="Jun" last="Li">Jun Li</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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