SCIENCE@home

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA]

M. Mutwil,S. Klie,Takayuki Tohge,F. Giorgi,Olivia Wilkins,M. Campbell,A. Fernie,B. Usadel,Z. Nikoloski,S. Persson

Published 2011 in The Plant Cell

ABSTRACT

Genes that are similarly expressed, or coexpressed, are often involved in related biological processes. Such coexpressed relationships also appear to be conserved across species. The PlaNet platform enables comparative analysis of genome-wide coexpression networks across seven plant species, thus enabling prediction of gene function and elucidation of the identity of functional homologs. 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.

PUBLICATION RECORD

CITATION MAP

EXTRACTION MAP

CLAIMS

  • No claims are published for this paper.

CONCEPTS

  • No concepts are published for this paper.

REFERENCES

Showing 1-69 of 69 references · Page 1 of 1

CITED BY

Showing 1-100 of 298 citing papers · Page 1 of 3

123
Next