ppdb: plant promoter database version 3.0.
Identifieur interne : 001F39 ( Main/Exploration ); précédent : 001F38; suivant : 001F40ppdb: plant promoter database version 3.0.
Auteurs : Ayaka Hieno [Japon] ; Hushna Ara Naznin ; Mitsuro Hyakumachi ; Tetsuya Sakurai ; Mututomo Tokizawa ; Hiroyuki Koyama ; Naoki Sato ; Tomoaki Nishiyama ; Mitsuyasu Hasebe ; Andreas D. Zimmer ; Daniel Lang ; Ralf Reski ; Stefan A. Rensing ; Junichi Obokata ; Yoshiharu Y. YamamotoSource :
- Nucleic acids research [ 1362-4962 ] ; 2014.
Descripteurs français
- KwdFr :
- Arabidopsis (génétique), Bases de données d'acides nucléiques (MeSH), Bryopsida (génétique), Gènes de plante (MeSH), Génome végétal (MeSH), Internet (MeSH), Oryza (génétique), Régions promotrices (génétique) (MeSH), Site d'initiation de la transcription (MeSH), Éléments de régulation transcriptionnelle (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27,000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.
DOI: 10.1093/nar/gkt1027
PubMed: 24194597
PubMed Central: PMC3965062
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Kanazawa City, Ishikawa 920-0934, Japan, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki City, Aichi 444-8585 Japan, Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D79104 Freiburg, Germany, Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 9, 35043 Marburg, Germany and Graduate School of Environmental Life Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522 Japan.</nlm:affiliation><orgName type="university">Université de Gifu</orgName><country>Japon</country><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation></author><author><name sortKey="Naznin, Hushna Ara" sort="Naznin, Hushna Ara" uniqKey="Naznin H" first="Hushna Ara" last="Naznin">Hushna Ara Naznin</name></author><author><name sortKey="Hyakumachi, Mitsuro" sort="Hyakumachi, Mitsuro" uniqKey="Hyakumachi M" first="Mitsuro" last="Hyakumachi">Mitsuro Hyakumachi</name></author><author><name sortKey="Sakurai, Tetsuya" sort="Sakurai, Tetsuya" uniqKey="Sakurai T" first="Tetsuya" last="Sakurai">Tetsuya Sakurai</name></author><author><name sortKey="Tokizawa, Mututomo" sort="Tokizawa, Mututomo" uniqKey="Tokizawa M" first="Mututomo" last="Tokizawa">Mututomo Tokizawa</name></author><author><name sortKey="Koyama, Hiroyuki" sort="Koyama, Hiroyuki" uniqKey="Koyama H" first="Hiroyuki" last="Koyama">Hiroyuki Koyama</name></author><author><name sortKey="Sato, Naoki" sort="Sato, Naoki" uniqKey="Sato N" first="Naoki" last="Sato">Naoki Sato</name></author><author><name sortKey="Nishiyama, Tomoaki" sort="Nishiyama, Tomoaki" uniqKey="Nishiyama T" first="Tomoaki" last="Nishiyama">Tomoaki Nishiyama</name></author><author><name sortKey="Hasebe, Mitsuyasu" sort="Hasebe, Mitsuyasu" uniqKey="Hasebe M" first="Mitsuyasu" last="Hasebe">Mitsuyasu Hasebe</name></author><author><name sortKey="Zimmer, Andreas D" sort="Zimmer, Andreas D" uniqKey="Zimmer A" first="Andreas D" last="Zimmer">Andreas D. 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Kanazawa City, Ishikawa 920-0934, Japan, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki City, Aichi 444-8585 Japan, Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D79104 Freiburg, Germany, Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 9, 35043 Marburg, Germany and Graduate School of Environmental Life Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522 Japan.</nlm:affiliation><orgName type="university">Université de Gifu</orgName><country>Japon</country><placeName><settlement type="city">Gifu (ville)</settlement><region type="province">Région du Chūbu</region><region type="prefecture">Préfecture de Gifu</region></placeName></affiliation></author><author><name sortKey="Naznin, Hushna Ara" sort="Naznin, Hushna Ara" uniqKey="Naznin H" first="Hushna Ara" last="Naznin">Hushna Ara Naznin</name></author><author><name sortKey="Hyakumachi, Mitsuro" sort="Hyakumachi, Mitsuro" uniqKey="Hyakumachi M" first="Mitsuro" last="Hyakumachi">Mitsuro Hyakumachi</name></author><author><name sortKey="Sakurai, Tetsuya" sort="Sakurai, Tetsuya" uniqKey="Sakurai T" first="Tetsuya" last="Sakurai">Tetsuya Sakurai</name></author><author><name sortKey="Tokizawa, Mututomo" sort="Tokizawa, Mututomo" uniqKey="Tokizawa M" first="Mututomo" last="Tokizawa">Mututomo Tokizawa</name></author><author><name sortKey="Koyama, Hiroyuki" sort="Koyama, Hiroyuki" uniqKey="Koyama H" first="Hiroyuki" last="Koyama">Hiroyuki Koyama</name></author><author><name sortKey="Sato, Naoki" sort="Sato, Naoki" uniqKey="Sato N" first="Naoki" last="Sato">Naoki Sato</name></author><author><name sortKey="Nishiyama, Tomoaki" sort="Nishiyama, Tomoaki" uniqKey="Nishiyama T" first="Tomoaki" last="Nishiyama">Tomoaki Nishiyama</name></author><author><name sortKey="Hasebe, Mitsuyasu" sort="Hasebe, Mitsuyasu" uniqKey="Hasebe M" first="Mitsuyasu" last="Hasebe">Mitsuyasu Hasebe</name></author><author><name sortKey="Zimmer, Andreas D" sort="Zimmer, Andreas D" uniqKey="Zimmer A" first="Andreas D" last="Zimmer">Andreas D. Zimmer</name></author><author><name sortKey="Lang, Daniel" sort="Lang, Daniel" uniqKey="Lang D" first="Daniel" last="Lang">Daniel Lang</name></author><author><name sortKey="Reski, Ralf" sort="Reski, Ralf" uniqKey="Reski R" first="Ralf" last="Reski">Ralf Reski</name></author><author><name sortKey="Rensing, Stefan A" sort="Rensing, Stefan A" uniqKey="Rensing S" first="Stefan A" last="Rensing">Stefan A. Rensing</name></author><author><name sortKey="Obokata, Junichi" sort="Obokata, Junichi" uniqKey="Obokata J" first="Junichi" last="Obokata">Junichi Obokata</name></author><author><name sortKey="Yamamoto, Yoshiharu Y" sort="Yamamoto, Yoshiharu Y" uniqKey="Yamamoto Y" first="Yoshiharu Y" last="Yamamoto">Yoshiharu Y. Yamamoto</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Bryopsida (genetics)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Internet (MeSH)</term><term>Oryza (genetics)</term><term>Promoter Regions, Genetic (MeSH)</term><term>Regulatory Elements, Transcriptional (MeSH)</term><term>Transcription Initiation Site (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (génétique)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Bryopsida (génétique)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Internet (MeSH)</term><term>Oryza (génétique)</term><term>Régions promotrices (génétique) (MeSH)</term><term>Site d'initiation de la transcription (MeSH)</term><term>Éléments de régulation transcriptionnelle (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Bryopsida</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Bryopsida</term><term>Oryza</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Nucleic Acid</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Internet</term><term>Promoter Regions, Genetic</term><term>Regulatory Elements, Transcriptional</term><term>Transcription Initiation Site</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données d'acides nucléiques</term><term>Gènes de plante</term><term>Génome végétal</term><term>Internet</term><term>Régions promotrices (génétique)</term><term>Site d'initiation de la transcription</term><term>Éléments de régulation transcriptionnelle</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27,000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24194597</PMID><DateCompleted><Year>2014</Year><Month>03</Month><Day>17</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>42</Volume><Issue>Database issue</Issue><PubDate><Year>2014</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res</ISOAbbreviation></Journal><ArticleTitle>ppdb: plant promoter database version 3.0.</ArticleTitle><Pagination><MedlinePgn>D1188-92</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkt1027</ELocationID><Abstract><AbstractText>ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27,000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hieno</LastName><ForeName>Ayaka</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193 Japan, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193 Japan, Center for Sustainable Resource Science, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 Japan, Advanced Science Research Center, Kanazawa University, Takaramachi 13-1. Kanazawa City, Ishikawa 920-0934, Japan, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki City, Aichi 444-8585 Japan, Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D79104 Freiburg, Germany, Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 9, 35043 Marburg, Germany and Graduate School of Environmental Life Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522 Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Naznin</LastName><ForeName>Hushna Ara</ForeName><Initials>HA</Initials></Author><Author ValidYN="Y"><LastName>Hyakumachi</LastName><ForeName>Mitsuro</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Sakurai</LastName><ForeName>Tetsuya</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Tokizawa</LastName><ForeName>Mututomo</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Koyama</LastName><ForeName>Hiroyuki</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Sato</LastName><ForeName>Naoki</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Nishiyama</LastName><ForeName>Tomoaki</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Hasebe</LastName><ForeName>Mitsuyasu</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Zimmer</LastName><ForeName>Andreas D</ForeName><Initials>AD</Initials></Author><Author ValidYN="Y"><LastName>Lang</LastName><ForeName>Daniel</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Reski</LastName><ForeName>Ralf</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Rensing</LastName><ForeName>Stefan A</ForeName><Initials>SA</Initials></Author><Author ValidYN="Y"><LastName>Obokata</LastName><ForeName>Junichi</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Yamamoto</LastName><ForeName>Yoshiharu Y</ForeName><Initials>YY</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>11</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019068" MajorTopicYN="N">Bryopsida</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="Y">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011401" MajorTopicYN="Y">Promoter Regions, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D050436" MajorTopicYN="N">Regulatory Elements, Transcriptional</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D024363" 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Hiroyuki" sort="Koyama, Hiroyuki" uniqKey="Koyama H" first="Hiroyuki" last="Koyama">Hiroyuki Koyama</name><name sortKey="Lang, Daniel" sort="Lang, Daniel" uniqKey="Lang D" first="Daniel" last="Lang">Daniel Lang</name><name sortKey="Naznin, Hushna Ara" sort="Naznin, Hushna Ara" uniqKey="Naznin H" first="Hushna Ara" last="Naznin">Hushna Ara Naznin</name><name sortKey="Nishiyama, Tomoaki" sort="Nishiyama, Tomoaki" uniqKey="Nishiyama T" first="Tomoaki" last="Nishiyama">Tomoaki Nishiyama</name><name sortKey="Obokata, Junichi" sort="Obokata, Junichi" uniqKey="Obokata J" first="Junichi" last="Obokata">Junichi Obokata</name><name sortKey="Rensing, Stefan A" sort="Rensing, Stefan A" uniqKey="Rensing S" first="Stefan A" last="Rensing">Stefan A. Rensing</name><name sortKey="Reski, Ralf" sort="Reski, Ralf" uniqKey="Reski R" first="Ralf" last="Reski">Ralf Reski</name><name sortKey="Sakurai, Tetsuya" sort="Sakurai, Tetsuya" uniqKey="Sakurai T" first="Tetsuya" last="Sakurai">Tetsuya Sakurai</name><name sortKey="Sato, Naoki" sort="Sato, Naoki" uniqKey="Sato N" first="Naoki" last="Sato">Naoki Sato</name><name sortKey="Tokizawa, Mututomo" sort="Tokizawa, Mututomo" uniqKey="Tokizawa M" first="Mututomo" last="Tokizawa">Mututomo Tokizawa</name><name sortKey="Yamamoto, Yoshiharu Y" sort="Yamamoto, Yoshiharu Y" uniqKey="Yamamoto Y" first="Yoshiharu Y" last="Yamamoto">Yoshiharu Y. Yamamoto</name><name sortKey="Zimmer, Andreas D" sort="Zimmer, Andreas D" uniqKey="Zimmer A" first="Andreas D" last="Zimmer">Andreas D. Zimmer</name></noCountry><country name="Japon"><region name="Région du Chūbu"><name sortKey="Hieno, Ayaka" sort="Hieno, Ayaka" uniqKey="Hieno A" first="Ayaka" last="Hieno">Ayaka Hieno</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001F39 | SxmlIndent | more
Ou
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Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:24194597
|texte= ppdb: plant promoter database version 3.0.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:24194597" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |