PoplarV1, Main, Exploration, bibRecord, 003202

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.

Identifieur interne : 003202 ( Main/Exploration ); précédent : 003201; suivant : 003203

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.

Auteurs : Keiichi Mochida [Japon] ; Takuhiro Yoshida ; Tetsuya Sakurai ; Kazuko Yamaguchi-Shinozaki ; Kazuo Shinozaki ; Lam-Son Phan Tran

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2010.

RBID : pubmed:19933159

Descripteurs français

KwdFr :
- Bases de données de protéines (MeSH), Bases de données génétiques (MeSH), Fabaceae (génétique), Facteurs de transcription (composition chimique), Génome végétal (MeSH), Génomique (méthodes), Logiciel (MeSH), Loteae (génétique), Medicago truncatula (génétique), Protéines végétales (composition chimique), Soja (génétique).
MESH :
- composition chimique : Facteurs de transcription, Protéines végétales.
- génétique : Fabaceae, Loteae, Medicago truncatula, Soja.
- méthodes : Génomique.
- Bases de données de protéines, Bases de données génétiques, Génome végétal, Logiciel.

English descriptors

KwdEn :
- Databases, Genetic (MeSH), Databases, Protein (MeSH), Fabaceae (genetics), Genome, Plant (MeSH), Genomics (methods), Lotus (genetics), Medicago truncatula (genetics), Plant Proteins (chemistry), Software (MeSH), Soybeans (genetics), Transcription Factors (chemistry).
MESH :
- chemical , chemistry : Plant Proteins, Transcription Factors.
- genetics : Fabaceae, Lotus, Medicago truncatula, Soybeans.
- methods : Genomics.
- Databases, Genetic, Databases, Protein, Genome, Plant, Software.

Abstract

UNLABELLED

We have established a database named LegumeTFDB to provide access to transcription factor (TF) repertoires of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula. LegumeTFDB integrates unique information for each TF gene and family, including sequence features, gene promoters, domain alignments, gene ontology (GO) assignment and sequence comparison data derived from comparative analysis with TFs found within legumes, in Arabidopsis, rice and poplar as well as with proteins in NCBI nr and UniProt. We also analyzed the promoter regions for all of the TFs to identify all types of cis-motifs provided by the PLACE database. Additionally, we supply hyperlinks to make available expression data of 2411 soybean TF genes. LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in agriculturally important legumes.

AVAILABILITY

http://legumetfdb.psc.riken.jp/.

SUPPLEMENTARY INFORMATION

Supplementary data available at Bioinformatics online.

DOI: 10.1093/bioinformatics/btp645
PubMed: 19933159

Affiliations:

Japon

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Le document en format XML

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<author><name sortKey="Mochida, Keiichi" sort="Mochida, Keiichi" uniqKey="Mochida K" first="Keiichi" last="Mochida">Keiichi Mochida</name>
<affiliation wicri:level="1"><nlm:affiliation>Plant Science Center, Gene Discovery Research Group, RIKEN, Yokohama 230-0045 Japan. mochida@psc.riken.jp</nlm:affiliation>
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<author><name sortKey="Yoshida, Takuhiro" sort="Yoshida, Takuhiro" uniqKey="Yoshida T" first="Takuhiro" last="Yoshida">Takuhiro Yoshida</name>
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<author><name sortKey="Sakurai, Tetsuya" sort="Sakurai, Tetsuya" uniqKey="Sakurai T" first="Tetsuya" last="Sakurai">Tetsuya Sakurai</name>
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<term>Genomics (methods)</term>
<term>Lotus (genetics)</term>
<term>Medicago truncatula (genetics)</term>
<term>Plant Proteins (chemistry)</term>
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<term>Bases de données génétiques (MeSH)</term>
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<term>Facteurs de transcription (composition chimique)</term>
<term>Génome végétal (MeSH)</term>
<term>Génomique (méthodes)</term>
<term>Logiciel (MeSH)</term>
<term>Loteae (génétique)</term>
<term>Medicago truncatula (génétique)</term>
<term>Protéines végétales (composition chimique)</term>
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<term>Protéines végétales</term>
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<front><div type="abstract" xml:lang="en"><p><b>UNLABELLED</b>
</p>
<p>We have established a database named LegumeTFDB to provide access to transcription factor (TF) repertoires of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula. LegumeTFDB integrates unique information for each TF gene and family, including sequence features, gene promoters, domain alignments, gene ontology (GO) assignment and sequence comparison data derived from comparative analysis with TFs found within legumes, in Arabidopsis, rice and poplar as well as with proteins in NCBI nr and UniProt. We also analyzed the promoter regions for all of the TFs to identify all types of cis-motifs provided by the PLACE database. Additionally, we supply hyperlinks to make available expression data of 2411 soybean TF genes. LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in agriculturally important legumes.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>AVAILABILITY</b>
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<p>http://legumetfdb.psc.riken.jp/.</p>
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<div type="abstract" xml:lang="en"><p><b>SUPPLEMENTARY INFORMATION</b>
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<p>Supplementary data available at Bioinformatics online.</p>
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<Abstract><AbstractText Label="UNLABELLED">We have established a database named LegumeTFDB to provide access to transcription factor (TF) repertoires of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula. LegumeTFDB integrates unique information for each TF gene and family, including sequence features, gene promoters, domain alignments, gene ontology (GO) assignment and sequence comparison data derived from comparative analysis with TFs found within legumes, in Arabidopsis, rice and poplar as well as with proteins in NCBI nr and UniProt. We also analyzed the promoter regions for all of the TFs to identify all types of cis-motifs provided by the PLACE database. Additionally, we supply hyperlinks to make available expression data of 2411 soybean TF genes. LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in agriculturally important legumes.</AbstractText>
<AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">http://legumetfdb.psc.riken.jp/.</AbstractText>
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<country name="Japon"><noRegion><name sortKey="Mochida, Keiichi" sort="Mochida, Keiichi" uniqKey="Mochida K" first="Keiichi" last="Mochida">Keiichi Mochida</name>
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LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki