ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.
Identifieur interne : 001A20 ( Main/Exploration ); précédent : 001A19; suivant : 001A21ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.
Auteurs : Yuichi Aoki [Japon] ; Yasunobu Okamura [Japon] ; Shu Tadaka [Japon] ; Kengo Kinoshita [Japon] ; Takeshi Obayashi [Japon]Source :
- Plant & cell physiology [ 1471-9053 ] ; 2016.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Analyse de séquence d'ARN (MeSH), Arabidopsis (génétique), Bases de données génétiques (MeSH), Lycopersicon esculentum (génétique), Oryza (génétique), Reproductibilité des résultats (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Soja (génétique), Spécificité d'espèce (MeSH), Séquençage par oligonucléotides en batterie (MeSH), Zea mays (génétique).
- MESH :
- génétique : Arabidopsis, Lycopersicon esculentum, Oryza, Soja, Zea mays.
- Analyse de profil d'expression de gènes, Analyse de regroupements, Analyse de séquence d'ARN, Bases de données génétiques, Reproductibilité des résultats, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique, Spécificité d'espèce, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Cluster Analysis (MeSH), Databases, Genetic (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Lycopersicon esculentum (genetics), Oligonucleotide Array Sequence Analysis (MeSH), Oryza (genetics), Reproducibility of Results (MeSH), Sequence Analysis, RNA (MeSH), Soybeans (genetics), Species Specificity (MeSH), Zea mays (genetics).
- MESH :
- genetics : Arabidopsis, Lycopersicon esculentum, Oryza, Soybeans, Zea mays.
- Cluster Analysis, Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Regulatory Networks, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, Sequence Analysis, RNA, Species Specificity.
Abstract
ATTED-II (http://atted.jp) is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can efficiently find functional gene relationships and design experiments to identify gene functions by reverse genetics and general molecular biology techniques. Here, we report updates to ATTED-II (version 8.0), including new and updated coexpression data and analysis tools. ATTED-II now includes eight microarray- and six RNA sequencing-based coexpression data sets for seven dicot species (Arabidopsis, field mustard, soybean, barrel medick, poplar, tomato and grape) and two monocot species (rice and maize). Stand-alone coexpression analyses tend to have low reliability. Therefore, examining evolutionarily conserved coexpression is a more effective approach from the viewpoints of reliability and evolutionary importance. In contrast, the reliability of species-specific coexpression data remains poor. Our assessment scores for individual coexpression data sets indicated that the quality of the new coexpression data sets in ATTED-II is higher than for any previous coexpression data set. In addition, five species (Arabidopsis, soybean, tomato, rice and maize) in ATTED-II are now supported by both microarray- and RNA sequencing-based coexpression data, which has increased the reliability. Consequently, ATTED-II can now provide lineage-specific coexpression information. As an example of the use of ATTED-II to explore lineage-specific coexpression, we demonstrate monocot- and dicot-specific coexpression of cell wall genes. With the expanded coexpression data for multilevel evaluation, ATTED-II provides new opportunities to investigate lineage-specific evolution in plants.
DOI: 10.1093/pcp/pcv165
PubMed: 26546318
PubMed Central: PMC4722172
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Cancer, Tohoku University, Sendai, 980-8575 Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573 Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575 Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai</wicri:regionArea><orgName type="university">Université du Tōhoku</orgName><placeName><settlement type="city">Sendai</settlement><region type="province">Région de Tōhoku</region></placeName></affiliation></author><author><name sortKey="Obayashi, Takeshi" sort="Obayashi, Takeshi" uniqKey="Obayashi T" first="Takeshi" last="Obayashi">Takeshi Obayashi</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan obayashi@ecei.tohoku.ac.jp.</nlm:affiliation><country wicri:rule="url">Japon</country><wicri:regionArea>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama</wicri:regionArea><orgName type="university">Université du Tōhoku</orgName><placeName><settlement type="city">Sendai</settlement><region type="province">Région de Tōhoku</region></placeName></affiliation></author></analytic><series><title level="j">Plant & cell physiology</title><idno type="eISSN">1471-9053</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Cluster Analysis (MeSH)</term><term>Databases, Genetic (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Lycopersicon esculentum (genetics)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Oryza (genetics)</term><term>Reproducibility of Results (MeSH)</term><term>Sequence Analysis, RNA (MeSH)</term><term>Soybeans (genetics)</term><term>Species Specificity (MeSH)</term><term>Zea mays (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Arabidopsis (génétique)</term><term>Bases de données génétiques (MeSH)</term><term>Lycopersicon esculentum (génétique)</term><term>Oryza (génétique)</term><term>Reproductibilité des résultats (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Soja (génétique)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term><term>Zea mays (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Lycopersicon esculentum</term><term>Oryza</term><term>Soybeans</term><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Lycopersicon esculentum</term><term>Oryza</term><term>Soja</term><term>Zea mays</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Databases, Genetic</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Oligonucleotide Array Sequence Analysis</term><term>Reproducibility of Results</term><term>Sequence Analysis, RNA</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ARN</term><term>Bases de données génétiques</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term><term>Spécificité d'espèce</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">ATTED-II (http://atted.jp) is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can efficiently find functional gene relationships and design experiments to identify gene functions by reverse genetics and general molecular biology techniques. Here, we report updates to ATTED-II (version 8.0), including new and updated coexpression data and analysis tools. ATTED-II now includes eight microarray- and six RNA sequencing-based coexpression data sets for seven dicot species (Arabidopsis, field mustard, soybean, barrel medick, poplar, tomato and grape) and two monocot species (rice and maize). Stand-alone coexpression analyses tend to have low reliability. Therefore, examining evolutionarily conserved coexpression is a more effective approach from the viewpoints of reliability and evolutionary importance. In contrast, the reliability of species-specific coexpression data remains poor. Our assessment scores for individual coexpression data sets indicated that the quality of the new coexpression data sets in ATTED-II is higher than for any previous coexpression data set. In addition, five species (Arabidopsis, soybean, tomato, rice and maize) in ATTED-II are now supported by both microarray- and RNA sequencing-based coexpression data, which has increased the reliability. Consequently, ATTED-II can now provide lineage-specific coexpression information. As an example of the use of ATTED-II to explore lineage-specific coexpression, we demonstrate monocot- and dicot-specific coexpression of cell wall genes. With the expanded coexpression data for multilevel evaluation, ATTED-II provides new opportunities to investigate lineage-specific evolution in plants.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26546318</PMID><DateCompleted><Year>2017</Year><Month>11</Month><Day>27</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1471-9053</ISSN><JournalIssue CitedMedium="Internet"><Volume>57</Volume><Issue>1</Issue><PubDate><Year>2016</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Plant & cell physiology</Title><ISOAbbreviation>Plant Cell Physiol</ISOAbbreviation></Journal><ArticleTitle>ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.</ArticleTitle><Pagination><MedlinePgn>e5</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/pcp/pcv165</ELocationID><Abstract><AbstractText>ATTED-II (http://atted.jp) is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can efficiently find functional gene relationships and design experiments to identify gene functions by reverse genetics and general molecular biology techniques. Here, we report updates to ATTED-II (version 8.0), including new and updated coexpression data and analysis tools. ATTED-II now includes eight microarray- and six RNA sequencing-based coexpression data sets for seven dicot species (Arabidopsis, field mustard, soybean, barrel medick, poplar, tomato and grape) and two monocot species (rice and maize). Stand-alone coexpression analyses tend to have low reliability. Therefore, examining evolutionarily conserved coexpression is a more effective approach from the viewpoints of reliability and evolutionary importance. In contrast, the reliability of species-specific coexpression data remains poor. Our assessment scores for individual coexpression data sets indicated that the quality of the new coexpression data sets in ATTED-II is higher than for any previous coexpression data set. In addition, five species (Arabidopsis, soybean, tomato, rice and maize) in ATTED-II are now supported by both microarray- and RNA sequencing-based coexpression data, which has increased the reliability. Consequently, ATTED-II can now provide lineage-specific coexpression information. As an example of the use of ATTED-II to explore lineage-specific coexpression, we demonstrate monocot- and dicot-specific coexpression of cell wall genes. With the expanded coexpression data for multilevel evaluation, ATTED-II provides new opportunities to investigate lineage-specific evolution in plants.</AbstractText><CopyrightInformation>© The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Aoki</LastName><ForeName>Yuichi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Okamura</LastName><ForeName>Yasunobu</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tadaka</LastName><ForeName>Shu</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kinoshita</LastName><ForeName>Kengo</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575 Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573 Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Obayashi</LastName><ForeName>Takeshi</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan obayashi@ecei.tohoku.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><ArticleDate DateType="Electronic"><Year>2015</Year><Month>11</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>Japan</Country><MedlineTA>Plant Cell Physiol</MedlineTA><NlmUniqueID>9430925</NlmUniqueID><ISSNLinking>0032-0781</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018551" MajorTopicYN="N">Lycopersicon esculentum</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of 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network</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>09</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>10</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>11</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26546318</ArticleId><ArticleId IdType="pii">pcv165</ArticleId><ArticleId IdType="doi">10.1093/pcp/pcv165</ArticleId><ArticleId IdType="pmc">PMC4722172</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>PLoS One. 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sort="Okamura, Yasunobu" uniqKey="Okamura Y" first="Yasunobu" last="Okamura">Yasunobu Okamura</name><name sortKey="Tadaka, Shu" sort="Tadaka, Shu" uniqKey="Tadaka S" first="Shu" last="Tadaka">Shu Tadaka</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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