Plant Promoter Database (PPDB).
Identifieur interne : 001258 ( Main/Exploration ); précédent : 001257; suivant : 001259Plant Promoter Database (PPDB).
Auteurs : Kazutaka Kusunoki [Japon] ; Yoshiharu Y. Yamamoto [Japon]Source :
- Methods in molecular biology (Clifton, N.J.) [ 1940-6029 ] ; 2017.
Descripteurs français
- KwdFr :
- Bases de données d'acides nucléiques (MeSH), Biologie informatique (méthodes), Boite TATA (MeSH), Gènes de plante (MeSH), Navigateur (MeSH), Plantes (génétique), Régions promotrices (génétique) (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Site d'initiation de la transcription (MeSH), Éléments de réponse (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
ppdb ( http://ppdb.agr.gifu-u.ac.jp ) is a web-based plant promoter database that provides promoter information of each gene in genomes of Arabidopsis, rice, poplar, and Physcomitrella patens. In this database, recognition of a promoter structure is achieved by annotating genome sequences with our sequence lists of bioinformatically identified octamers for core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA Elements) and regulatory element groups (REGs), together with information of transcription start sites (TSSs) that have been experimentally identified. Our promoter elements are octamer sequences that show strongly biased localization profiles in the promoter region, extracted by the local distribution of short sequence (LDSS) analysis. In addition, REGs are linked with the information of the PLACE database and also with their physiological roles that are predicted using large-scale gene expression data.
DOI: 10.1007/978-1-4939-6658-5_18
PubMed: 27987179
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Yamamoto</name><affiliation wicri:level="4"><nlm:affiliation>United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan. yyy@gifu-u.ac.jp.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193</wicri:regionArea><orgName type="university">Université de Gifu</orgName><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan. yyy@gifu-u.ac.jp.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193</wicri:regionArea><orgName type="university">Université de Gifu</orgName><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>RIKEN CSRS, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. yyy@gifu-u.ac.jp.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>RIKEN CSRS, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045</wicri:regionArea><wicri:noRegion>230-0045</wicri:noRegion></affiliation><affiliation wicri:level="3"><nlm:affiliation>JST ALCA, Tokyo, Japan. yyy@gifu-u.ac.jp.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>JST ALCA, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author></analytic><series><title level="j">Methods in molecular biology (Clifton, N.J.)</title><idno type="eISSN">1940-6029</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Plants (genetics)</term><term>Promoter Regions, Genetic (MeSH)</term><term>Response Elements (MeSH)</term><term>TATA Box (MeSH)</term><term>Transcription Initiation Site (MeSH)</term><term>Web Browser (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données d'acides nucléiques (MeSH)</term><term>Biologie informatique (méthodes)</term><term>Boite TATA (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Navigateur (MeSH)</term><term>Plantes (génétique)</term><term>Régions promotrices (génétique) (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Site d'initiation de la transcription (MeSH)</term><term>Éléments de réponse (MeSH)</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></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Nucleic Acid</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Promoter Regions, Genetic</term><term>Response Elements</term><term>TATA Box</term><term>Transcription Initiation Site</term><term>Web Browser</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données d'acides nucléiques</term><term>Boite TATA</term><term>Gènes de plante</term><term>Navigateur</term><term>Régions promotrices (génétique)</term><term>Régulation de l'expression des gènes végétaux</term><term>Site d'initiation de la transcription</term><term>Éléments de réponse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">ppdb ( http://ppdb.agr.gifu-u.ac.jp ) is a web-based plant promoter database that provides promoter information of each gene in genomes of Arabidopsis, rice, poplar, and Physcomitrella patens. In this database, recognition of a promoter structure is achieved by annotating genome sequences with our sequence lists of bioinformatically identified octamers for core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA Elements) and regulatory element groups (REGs), together with information of transcription start sites (TSSs) that have been experimentally identified. Our promoter elements are octamer sequences that show strongly biased localization profiles in the promoter region, extracted by the local distribution of short sequence (LDSS) analysis. In addition, REGs are linked with the information of the PLACE database and also with their physiological roles that are predicted using large-scale gene expression data.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27987179</PMID><DateCompleted><Year>2018</Year><Month>01</Month><Day>29</Day></DateCompleted><DateRevised><Year>2018</Year><Month>04</Month><Day>25</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1940-6029</ISSN><JournalIssue CitedMedium="Internet"><Volume>1533</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>Methods in molecular biology (Clifton, N.J.)</Title><ISOAbbreviation>Methods Mol Biol</ISOAbbreviation></Journal><ArticleTitle>Plant Promoter Database (PPDB).</ArticleTitle><Pagination><MedlinePgn>299-314</MedlinePgn></Pagination><Abstract><AbstractText>ppdb ( http://ppdb.agr.gifu-u.ac.jp ) is a web-based plant promoter database that provides promoter information of each gene in genomes of Arabidopsis, rice, poplar, and Physcomitrella patens. In this database, recognition of a promoter structure is achieved by annotating genome sequences with our sequence lists of bioinformatically identified octamers for core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA Elements) and regulatory element groups (REGs), together with information of transcription start sites (TSSs) that have been experimentally identified. Our promoter elements are octamer sequences that show strongly biased localization profiles in the promoter region, extracted by the local distribution of short sequence (LDSS) analysis. In addition, REGs are linked with the information of the PLACE database and also with their physiological roles that are predicted using large-scale gene expression data.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kusunoki</LastName><ForeName>Kazutaka</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yamamoto</LastName><ForeName>Yoshiharu Y</ForeName><Initials>YY</Initials><AffiliationInfo><Affiliation>United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan. yyy@gifu-u.ac.jp.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan. yyy@gifu-u.ac.jp.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>RIKEN CSRS, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. yyy@gifu-u.ac.jp.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>JST ALCA, Tokyo, Japan. yyy@gifu-u.ac.jp.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Methods Mol Biol</MedlineTA><NlmUniqueID>9214969</NlmUniqueID><ISSNLinking>1064-3745</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="Y">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011401" MajorTopicYN="Y">Promoter Regions, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020218" MajorTopicYN="N">Response Elements</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016385" MajorTopicYN="N">TATA Box</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D024363" MajorTopicYN="N">Transcription Initiation Site</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D064878" MajorTopicYN="Y">Web Browser</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Core element</Keyword><Keyword MajorTopicYN="Y">LDSS</Keyword><Keyword MajorTopicYN="Y">Promoter</Keyword><Keyword MajorTopicYN="Y">REG</Keyword><Keyword MajorTopicYN="Y">Transcription start site (TSS)</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>12</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>12</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>1</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27987179</ArticleId><ArticleId IdType="doi">10.1007/978-1-4939-6658-5_18</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country><region><li>Préfecture de Gifu</li><li>Région de Kantō</li><li>Région du Chūbu</li></region><settlement><li>Gifu (ville)</li><li>Tokyo</li></settlement><orgName><li>Université de Gifu</li></orgName></list><tree><country name="Japon"><region name="Région du Chūbu"><name sortKey="Kusunoki, Kazutaka" sort="Kusunoki, Kazutaka" uniqKey="Kusunoki K" first="Kazutaka" last="Kusunoki">Kazutaka Kusunoki</name></region><name sortKey="Yamamoto, Yoshiharu Y" sort="Yamamoto, Yoshiharu Y" uniqKey="Yamamoto Y" first="Yoshiharu Y" last="Yamamoto">Yoshiharu Y. Yamamoto</name><name sortKey="Yamamoto, Yoshiharu Y" sort="Yamamoto, Yoshiharu Y" uniqKey="Yamamoto Y" first="Yoshiharu Y" last="Yamamoto">Yoshiharu Y. Yamamoto</name><name sortKey="Yamamoto, Yoshiharu Y" sort="Yamamoto, Yoshiharu Y" uniqKey="Yamamoto Y" first="Yoshiharu Y" last="Yamamoto">Yoshiharu Y. Yamamoto</name><name sortKey="Yamamoto, Yoshiharu Y" sort="Yamamoto, Yoshiharu Y" uniqKey="Yamamoto Y" first="Yoshiharu Y" last="Yamamoto">Yoshiharu Y. Yamamoto</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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