TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics.
Identifieur interne : 002435 ( Main/Exploration ); précédent : 002434; suivant : 002436TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics.
Auteurs : Keiichi Mochida [Japon] ; Takuhiro Yoshida ; Tetsuya Sakurai ; Kazuko Yamaguchi-Shinozaki ; Kazuo Shinozaki ; Lam-Son Phan TranSource :
- DNA research : an international journal for rapid publication of reports on genes and genomes [ 1756-1663 ] ; 2013.
Descripteurs français
- KwdFr :
- Arbres (génétique), Bases de données de protéines (MeSH), Bases de données factuelles (MeSH), Bases de données génétiques (MeSH), Facteurs de transcription (génétique), Génome végétal (MeSH), Génomique (méthodes), Interface utilisateur (MeSH), Logiciel (MeSH), Produits agricoles (MeSH), Protéines végétales (génétique), Protéines végétales (métabolisme), Régions promotrices (génétique) (MeSH).
- MESH :
- génétique : Arbres, Facteurs de transcription, Protéines végétales.
- métabolisme : Protéines végétales.
- méthodes : Génomique.
- Bases de données de protéines, Bases de données factuelles, Bases de données génétiques, Génome végétal, Interface utilisateur, Logiciel, Produits agricoles, Régions promotrices (génétique).
English descriptors
- KwdEn :
- Crops, Agricultural (MeSH), Databases, Factual (MeSH), Databases, Genetic (MeSH), Databases, Protein (MeSH), Genome, Plant (MeSH), Genomics (methods), Plant Proteins (genetics), Plant Proteins (metabolism), Promoter Regions, Genetic (MeSH), Software (MeSH), Transcription Factors (genetics), Trees (genetics), User-Computer Interface (MeSH).
- MESH :
- chemical , genetics : Plant Proteins, Transcription Factors.
- chemical , metabolism : Plant Proteins.
- genetics : Trees.
- methods : Genomics.
- Crops, Agricultural, Databases, Factual, Databases, Genetic, Databases, Protein, Genome, Plant, Promoter Regions, Genetic, Software, User-Computer Interface.
Abstract
Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB (http://treetfdb.bmep.riken.jp/index.pl) that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.
DOI: 10.1093/dnares/dss040
PubMed: 23284086
PubMed Central: PMC3628445
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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végétales</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Génomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Crops, Agricultural</term><term>Databases, Factual</term><term>Databases, Genetic</term><term>Databases, Protein</term><term>Genome, Plant</term><term>Promoter Regions, Genetic</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données de protéines</term><term>Bases de données factuelles</term><term>Bases de données génétiques</term><term>Génome végétal</term><term>Interface utilisateur</term><term>Logiciel</term><term>Produits agricoles</term><term>Régions promotrices (génétique)</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB (http://treetfdb.bmep.riken.jp/index.pl) that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23284086</PMID><DateCompleted><Year>2013</Year><Month>11</Month><Day>06</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1756-1663</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>2</Issue><PubDate><Year>2013</Year><Month>Apr</Month></PubDate></JournalIssue><Title>DNA research : an international journal for rapid publication of reports on genes and genomes</Title><ISOAbbreviation>DNA Res</ISOAbbreviation></Journal><ArticleTitle>TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics.</ArticleTitle><Pagination><MedlinePgn>151-62</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/dnares/dss040</ELocationID><Abstract><AbstractText>Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB (http://treetfdb.bmep.riken.jp/index.pl) that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mochida</LastName><ForeName>Keiichi</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. mochida@psc.riken.jp</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yoshida</LastName><ForeName>Takuhiro</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Sakurai</LastName><ForeName>Tetsuya</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Yamaguchi-Shinozaki</LastName><ForeName>Kazuko</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Shinozaki</LastName><ForeName>Kazuo</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Tran</LastName><ForeName>Lam-Son Phan</ForeName><Initials>LS</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>01</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>DNA Res</MedlineTA><NlmUniqueID>9423827</NlmUniqueID><ISSNLinking>1340-2838</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant 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sort="Shinozaki, Kazuo" uniqKey="Shinozaki K" first="Kazuo" last="Shinozaki">Kazuo Shinozaki</name><name sortKey="Tran, Lam Son Phan" sort="Tran, Lam Son Phan" uniqKey="Tran L" first="Lam-Son Phan" last="Tran">Lam-Son Phan Tran</name><name sortKey="Yamaguchi Shinozaki, Kazuko" sort="Yamaguchi Shinozaki, Kazuko" uniqKey="Yamaguchi Shinozaki K" first="Kazuko" last="Yamaguchi-Shinozaki">Kazuko Yamaguchi-Shinozaki</name><name sortKey="Yoshida, Takuhiro" sort="Yoshida, Takuhiro" uniqKey="Yoshida T" first="Takuhiro" last="Yoshida">Takuhiro Yoshida</name></noCountry><country name="Japon"><noRegion><name sortKey="Mochida, Keiichi" sort="Mochida, Keiichi" uniqKey="Mochida K" first="Keiichi" last="Mochida">Keiichi Mochida</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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