title: PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.
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.
authors: Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany.
authors: Marek
authors: M
authors: Mutwil
authors: Sebastian
authors: S
authors: Klie
authors: Takayuki
authors: T
authors: Tohge
authors: Federico M
authors: FM
authors: Giorgi
authors: Olivia
authors: O
authors: Wilkins
authors: Malcolm M
authors: MM
authors: Campbell
authors: Alisdair R
authors: AR
authors: Fernie
authors: Björn
authors: B
authors: Usadel
authors: Zoran
authors: Z
authors: Nikoloski
authors: Staffan
authors: S
authors: Persson
mesh_terms: D000217:Acyltransferases / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics; D029902:Medicago / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D010641:Phenotype; D032107:Populus / Q000235:genetics; D017421:Sequence Analysis; D017385:Sequence Homology; D012984:Software; D013025:Glycine max / Q000235:genetics; D014158:Transcription, Genetic; D014908:Triticum / Q000235:genetics
chemical_list: D000217:Acyltransferases; C020141:flavanone synthetase