PoplarV1, Main, Exploration, bibRecord, 002D55

PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.

Identifieur interne : 002D55 ( Main/Exploration ); précédent : 002D54; suivant : 002D56

PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.

Auteurs : Marek Mutwil [Allemagne] ; Sebastian Klie ; Takayuki Tohge ; Federico M. Giorgi ; Olivia Wilkins ; Malcolm M. Campbell ; Alisdair R. Fernie ; Björn Usadel ; Zoran Nikoloski ; Staffan Persson

Source :

The Plant cell [ 1532-298X ] ; 2011.

RBID : pubmed:21441431

Descripteurs français

English descriptors

KwdEn :
- Acyltransferases (genetics), Arabidopsis (genetics), Cluster Analysis (MeSH), Gene Expression Profiling (MeSH), Genome, Plant (MeSH), Hordeum (genetics), Medicago (genetics), Oligonucleotide Array Sequence Analysis (MeSH), Oryza (genetics), Phenotype (MeSH), Populus (genetics), Sequence Analysis (MeSH), Sequence Homology (MeSH), Software (MeSH), Soybeans (genetics), Transcription, Genetic (MeSH), Triticum (genetics).
MESH :
- chemical , genetics : Acyltransferases.
- genetics : Arabidopsis, Hordeum, Medicago, Oryza, Populus, Soybeans, Triticum.
- Cluster Analysis, Gene Expression Profiling, Genome, Plant, Oligonucleotide Array Sequence Analysis, Phenotype, Sequence Analysis, Sequence Homology, Software, Transcription, Genetic.

Abstract

The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species.

DOI: 10.1105/tpc.111.083667
PubMed: 21441431
PubMed Central: PMC3082271

Affiliations:

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Le document en format XML

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<term>Sequence Homology (MeSH)</term>
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<term>Analyse de séquence (MeSH)</term>
<term>Arabidopsis (génétique)</term>
<term>Génome végétal (MeSH)</term>
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<term>Oryza (génétique)</term>
<term>Phénotype (MeSH)</term>
<term>Populus (génétique)</term>
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<term>Soja (génétique)</term>
<term>Séquençage par oligonucléotides en batterie (MeSH)</term>
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<front><div type="abstract" xml:lang="en">The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species.</div>
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<Abstract><AbstractText>The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species.</AbstractText>
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PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.

PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.

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