ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.
Identifieur interne : 002383 ( Main/Exploration ); précédent : 002382; suivant : 002384ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.
Auteurs : Takeshi Obayashi [Japon] ; Yasunobu Okamura ; Satoshi Ito ; Shu Tadaka ; Yuichi Aoki ; Matsuyuki Shirota ; Kengo KinoshitaSource :
- Plant & cell physiology [ 1471-9053 ] ; 2014.
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Abstract
ATTED-II (http://atted.jp) is a database of coexpressed genes that was originally developed to identify functionally related genes in Arabidopsis and rice. Herein, we describe an updated version of ATTED-II, which expands this resource to include additional agriculturally important plants. To improve the quality of the coexpression data for Arabidopsis and rice, we included more gene expression data from microarray and RNA sequencing studies. The RNA sequencing-based coexpression data now cover 94% of the Arabidopsis protein-encoding genes, representing a substantial increase from previously available microarray-based coexpression data (76% coverage). We also generated coexpression data for four dicots (soybean, poplar, grape and alfalfa) and one monocot (maize). As both the quantity and quality of expression data for the non-model species are generally poorer than for the model species, we verified coexpression data associated with these new species using multiple methods. First, the overall performance of the coexpression data was evaluated using gene ontology annotations and the coincidence of a genomic feature. Secondly, the reliability of each guide gene was determined by comparing coexpressed gene lists between platforms. With the expanded and newly evaluated coexpression data, ATTED-II represents an important resource for identifying functionally related genes in agriculturally important plants.
DOI: 10.1093/pcp/pct178
PubMed: 24334350
PubMed Central: PMC3894708
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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="Okamura, Yasunobu" sort="Okamura, Yasunobu" uniqKey="Okamura Y" first="Yasunobu" last="Okamura">Yasunobu Okamura</name></author><author><name sortKey="Ito, Satoshi" sort="Ito, Satoshi" uniqKey="Ito S" first="Satoshi" last="Ito">Satoshi Ito</name></author><author><name sortKey="Tadaka, Shu" sort="Tadaka, Shu" uniqKey="Tadaka S" first="Shu" last="Tadaka">Shu Tadaka</name></author><author><name sortKey="Aoki, Yuichi" sort="Aoki, Yuichi" uniqKey="Aoki Y" first="Yuichi" last="Aoki">Yuichi Aoki</name></author><author><name sortKey="Shirota, Matsuyuki" sort="Shirota, Matsuyuki" uniqKey="Shirota M" first="Matsuyuki" last="Shirota">Matsuyuki Shirota</name></author><author><name sortKey="Kinoshita, Kengo" sort="Kinoshita, Kengo" uniqKey="Kinoshita K" first="Kengo" last="Kinoshita">Kengo Kinoshita</name></author></analytic><series><title level="j">Plant & cell physiology</title><idno type="eISSN">1471-9053</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Crops, Agricultural (genetics)</term><term>Databases, Genetic (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Genes, Plant (genetics)</term><term>Reproducibility of Results (MeSH)</term><term>Species Specificity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données génétiques (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Gènes de plante (génétique)</term><term>Produits agricoles (génétique)</term><term>Reproductibilité des résultats (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Spécificité d'espèce (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Crops, Agricultural</term><term>Genes, Plant</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Gènes de plante</term><term>Produits agricoles</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Regulation, Plant</term><term>Gene Ontology</term><term>Reproducibility of Results</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données génétiques</term><term>Gene Ontology</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term><term>Spécificité d'espèce</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">ATTED-II (http://atted.jp) is a database of coexpressed genes that was originally developed to identify functionally related genes in Arabidopsis and rice. Herein, we describe an updated version of ATTED-II, which expands this resource to include additional agriculturally important plants. To improve the quality of the coexpression data for Arabidopsis and rice, we included more gene expression data from microarray and RNA sequencing studies. The RNA sequencing-based coexpression data now cover 94% of the Arabidopsis protein-encoding genes, representing a substantial increase from previously available microarray-based coexpression data (76% coverage). We also generated coexpression data for four dicots (soybean, poplar, grape and alfalfa) and one monocot (maize). As both the quantity and quality of expression data for the non-model species are generally poorer than for the model species, we verified coexpression data associated with these new species using multiple methods. First, the overall performance of the coexpression data was evaluated using gene ontology annotations and the coincidence of a genomic feature. Secondly, the reliability of each guide gene was determined by comparing coexpressed gene lists between platforms. With the expanded and newly evaluated coexpression data, ATTED-II represents an important resource for identifying functionally related genes in agriculturally important plants. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24334350</PMID><DateCompleted><Year>2014</Year><Month>09</Month><Day>08</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>55</Volume><Issue>1</Issue><PubDate><Year>2014</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Plant & cell physiology</Title><ISOAbbreviation>Plant Cell Physiol</ISOAbbreviation></Journal><ArticleTitle>ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.</ArticleTitle><Pagination><MedlinePgn>e6</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/pcp/pct178</ELocationID><Abstract><AbstractText>ATTED-II (http://atted.jp) is a database of coexpressed genes that was originally developed to identify functionally related genes in Arabidopsis and rice. Herein, we describe an updated version of ATTED-II, which expands this resource to include additional agriculturally important plants. To improve the quality of the coexpression data for Arabidopsis and rice, we included more gene expression data from microarray and RNA sequencing studies. The RNA sequencing-based coexpression data now cover 94% of the Arabidopsis protein-encoding genes, representing a substantial increase from previously available microarray-based coexpression data (76% coverage). We also generated coexpression data for four dicots (soybean, poplar, grape and alfalfa) and one monocot (maize). As both the quantity and quality of expression data for the non-model species are generally poorer than for the model species, we verified coexpression data associated with these new species using multiple methods. First, the overall performance of the coexpression data was evaluated using gene ontology annotations and the coincidence of a genomic feature. Secondly, the reliability of each guide gene was determined by comparing coexpressed gene lists between platforms. With the expanded and newly evaluated coexpression data, ATTED-II represents an important resource for identifying functionally related genes in agriculturally important plants. </AbstractText></Abstract><AuthorList CompleteYN="Y"><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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Okamura</LastName><ForeName>Yasunobu</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Ito</LastName><ForeName>Satoshi</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Tadaka</LastName><ForeName>Shu</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Aoki</LastName><ForeName>Yuichi</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Shirota</LastName><ForeName>Matsuyuki</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Kinoshita</LastName><ForeName>Kengo</ForeName><Initials>K</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>12</Month><Day>10</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="D018556" MajorTopicYN="N">Crops, Agricultural</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030541" 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sortKey="Ito, Satoshi" sort="Ito, Satoshi" uniqKey="Ito S" first="Satoshi" last="Ito">Satoshi Ito</name><name sortKey="Kinoshita, Kengo" sort="Kinoshita, Kengo" uniqKey="Kinoshita K" first="Kengo" last="Kinoshita">Kengo Kinoshita</name><name sortKey="Okamura, Yasunobu" sort="Okamura, Yasunobu" uniqKey="Okamura Y" first="Yasunobu" last="Okamura">Yasunobu Okamura</name><name sortKey="Shirota, Matsuyuki" sort="Shirota, Matsuyuki" uniqKey="Shirota M" first="Matsuyuki" last="Shirota">Matsuyuki Shirota</name><name sortKey="Tadaka, Shu" sort="Tadaka, Shu" uniqKey="Tadaka S" first="Shu" last="Tadaka">Shu Tadaka</name></noCountry><country name="Japon"><region name="Région de Tōhoku"><name sortKey="Obayashi, Takeshi" sort="Obayashi, Takeshi" uniqKey="Obayashi T" first="Takeshi" last="Obayashi">Takeshi Obayashi</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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