BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species.
Identifieur interne : 002B91 ( Main/Exploration ); précédent : 002B90; suivant : 002B92BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species.
Auteurs : Rohan V. Patel [Canada] ; Hardeep K. Nahal ; Robert Breit ; Nicholas J. ProvartSource :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2012.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Arabidopsis (génétique), Bases de données génétiques (MeSH), Famille multigénique (MeSH), Feuilles de plante (génétique), Fleurs (génétique), Hordeum (génétique), Internet (MeSH), Logiciel (MeSH), Magnoliopsida (génétique), Medicago truncatula (génétique), Mémorisation et recherche des informations (MeSH), Oryza (génétique), Populus (génétique), Racines de plante (génétique), Régulation de l'expression des gènes végétaux (MeSH), Similitude de séquences (MeSH), Soja (génétique), Spécificité d'organe (MeSH), Transcriptome (MeSH), Xylème (génétique), Zea mays (génétique).
- MESH :
- génétique : Arabidopsis, Feuilles de plante, Fleurs, Hordeum, Magnoliopsida, Medicago truncatula, Oryza, Populus, Racines de plante, Soja, Xylème, Zea mays.
- Analyse de profil d'expression de gènes, Bases de données génétiques, Famille multigénique, Internet, Logiciel, Mémorisation et recherche des informations, Régulation de l'expression des gènes végétaux, Similitude de séquences, Spécificité d'organe, Transcriptome.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Databases, Genetic (MeSH), Flowers (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Hordeum (genetics), Information Storage and Retrieval (MeSH), Internet (MeSH), Magnoliopsida (genetics), Medicago truncatula (genetics), Multigene Family (MeSH), Organ Specificity (MeSH), Oryza (genetics), Plant Leaves (genetics), Plant Roots (genetics), Populus (genetics), Sequence Homology (MeSH), Software (MeSH), Soybeans (genetics), Transcriptome (MeSH), Xylem (genetics), Zea mays (genetics).
- MESH :
- genetics : Arabidopsis, Flowers, Hordeum, Magnoliopsida, Medicago truncatula, Oryza, Plant Leaves, Plant Roots, Populus, Soybeans, Xylem, Zea mays.
- Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Plant, Information Storage and Retrieval, Internet, Multigene Family, Organ Specificity, Sequence Homology, Software, Transcriptome.
Abstract
Large numbers of sequences are now readily available for many plant species, allowing easy identification of homologous genes. However, orthologous gene identification across multiple species is made difficult by evolutionary events such as whole-genome or segmental duplications. Several developmental atlases of gene expression have been produced in the past couple of years, and it may be possible to use these transcript abundance data to refine ortholog predictions. In this study, clusters of homologous genes between seven plant species - Arabidopsis, soybean, Medicago truncatula, poplar, barley, maize and rice - were identified. Following this, a pipeline to rank homologs within gene clusters by both sequence and expression profile similarity was devised by determining equivalent tissues between species, with the best expression profile match being termed the 'expressolog'. Five electronic fluorescent pictograph (eFP) browsers were produced as part of this effort, to aid in visualization of gene expression data and to complement existing eFP browsers at the Bio-Array Resource (BAR). Within the eFP browser framework, these expression profile similarity rankings were incorporated into an Expressolog Tree Viewer to allow cross-species homolog browsing by both sequence and expression pattern similarity. Global analyses showed that orthologs with the highest sequence similarity do not necessarily exhibit the highest expression pattern similarity. Other orthologs may show different expression patterns, indicating that such genes may require re-annotation or more specific annotation. Ultimately, it is envisaged that this pipeline will aid in improvement of the functional annotation of genes and translational plant research.
DOI: 10.1111/j.1365-313X.2012.05055.x
PubMed: 22607031
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Provart</name></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Databases, Genetic (MeSH)</term><term>Flowers (genetics)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Hordeum (genetics)</term><term>Information Storage and Retrieval (MeSH)</term><term>Internet (MeSH)</term><term>Magnoliopsida (genetics)</term><term>Medicago truncatula (genetics)</term><term>Multigene Family (MeSH)</term><term>Organ Specificity (MeSH)</term><term>Oryza (genetics)</term><term>Plant Leaves (genetics)</term><term>Plant Roots (genetics)</term><term>Populus (genetics)</term><term>Sequence Homology (MeSH)</term><term>Software (MeSH)</term><term>Soybeans (genetics)</term><term>Transcriptome (MeSH)</term><term>Xylem (genetics)</term><term>Zea mays (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Arabidopsis (génétique)</term><term>Bases de données génétiques (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Feuilles de plante (génétique)</term><term>Fleurs (génétique)</term><term>Hordeum (génétique)</term><term>Internet (MeSH)</term><term>Logiciel (MeSH)</term><term>Magnoliopsida (génétique)</term><term>Medicago truncatula (génétique)</term><term>Mémorisation et recherche des informations (MeSH)</term><term>Oryza (génétique)</term><term>Populus (génétique)</term><term>Racines de plante (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Similitude de séquences (MeSH)</term><term>Soja (génétique)</term><term>Spécificité d'organe (MeSH)</term><term>Transcriptome (MeSH)</term><term>Xylème (génétique)</term><term>Zea mays (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Flowers</term><term>Hordeum</term><term>Magnoliopsida</term><term>Medicago truncatula</term><term>Oryza</term><term>Plant Leaves</term><term>Plant Roots</term><term>Populus</term><term>Soybeans</term><term>Xylem</term><term>Zea mays</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Feuilles de plante</term><term>Fleurs</term><term>Hordeum</term><term>Magnoliopsida</term><term>Medicago truncatula</term><term>Oryza</term><term>Populus</term><term>Racines de plante</term><term>Soja</term><term>Xylème</term><term>Zea mays</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Information Storage and Retrieval</term><term>Internet</term><term>Multigene Family</term><term>Organ Specificity</term><term>Sequence Homology</term><term>Software</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Bases de données génétiques</term><term>Famille multigénique</term><term>Internet</term><term>Logiciel</term><term>Mémorisation et recherche des informations</term><term>Régulation de l'expression des gènes végétaux</term><term>Similitude de séquences</term><term>Spécificité d'organe</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Large numbers of sequences are now readily available for many plant species, allowing easy identification of homologous genes. 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Within the eFP browser framework, these expression profile similarity rankings were incorporated into an Expressolog Tree Viewer to allow cross-species homolog browsing by both sequence and expression pattern similarity. Global analyses showed that orthologs with the highest sequence similarity do not necessarily exhibit the highest expression pattern similarity. Other orthologs may show different expression patterns, indicating that such genes may require re-annotation or more specific annotation. 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However, orthologous gene identification across multiple species is made difficult by evolutionary events such as whole-genome or segmental duplications. Several developmental atlases of gene expression have been produced in the past couple of years, and it may be possible to use these transcript abundance data to refine ortholog predictions. In this study, clusters of homologous genes between seven plant species - Arabidopsis, soybean, Medicago truncatula, poplar, barley, maize and rice - were identified. Following this, a pipeline to rank homologs within gene clusters by both sequence and expression profile similarity was devised by determining equivalent tissues between species, with the best expression profile match being termed the 'expressolog'. Five electronic fluorescent pictograph (eFP) browsers were produced as part of this effort, to aid in visualization of gene expression data and to complement existing eFP browsers at the Bio-Array Resource (BAR). Within the eFP browser framework, these expression profile similarity rankings were incorporated into an Expressolog Tree Viewer to allow cross-species homolog browsing by both sequence and expression pattern similarity. Global analyses showed that orthologs with the highest sequence similarity do not necessarily exhibit the highest expression pattern similarity. Other orthologs may show different expression patterns, indicating that such genes may require re-annotation or more specific annotation. Ultimately, it is envisaged that this pipeline will aid in improvement of the functional annotation of genes and translational plant research.</AbstractText><CopyrightInformation>© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Patel</LastName><ForeName>Rohan V</ForeName><Initials>RV</Initials><AffiliationInfo><Affiliation>Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nahal</LastName><ForeName>Hardeep K</ForeName><Initials>HK</Initials></Author><Author ValidYN="Y"><LastName>Breit</LastName><ForeName>Robert</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Provart</LastName><ForeName>Nicholas J</ForeName><Initials>NJ</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>2012</Year><Month>07</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</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="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035264" MajorTopicYN="N">Flowers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, 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MajorTopicYN="N">Soybeans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D052584" MajorTopicYN="N">Xylem</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003313" MajorTopicYN="N">Zea mays</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>5</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>5</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>9</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22607031</ArticleId><ArticleId IdType="doi">10.1111/j.1365-313X.2012.05055.x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country><region><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><noCountry><name sortKey="Breit, Robert" sort="Breit, Robert" uniqKey="Breit R" first="Robert" last="Breit">Robert Breit</name><name sortKey="Nahal, Hardeep K" sort="Nahal, Hardeep K" uniqKey="Nahal H" first="Hardeep K" last="Nahal">Hardeep K. Nahal</name><name sortKey="Provart, Nicholas J" sort="Provart, Nicholas J" uniqKey="Provart N" first="Nicholas J" last="Provart">Nicholas J. Provart</name></noCountry><country name="Canada"><region name="Ontario"><name sortKey="Patel, Rohan V" sort="Patel, Rohan V" uniqKey="Patel R" first="Rohan V" last="Patel">Rohan V. Patel</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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