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  PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

Mutwil, M., Klie, S., Tohge, T., Giorgi, F. M., Wilkins, O., Campbell, M. M., et al. (2011). PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species. The Plant Cell, 23(3), 895-910. doi:10.1105/tpc.111.083667.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-213A-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-7B19-E
Genre: Journal Article

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 Creators:
Mutwil, M.1, 2, Author              
Klie, S.3, Author              
Tohge, T.4, Author              
Giorgi, F. M.5, Author              
Wilkins, O.6, Author
Campbell, M. M.6, Author
Fernie, A. R.4, Author              
Usadel, B.5, Author              
Nikoloski, Z.7, Author              
Persson, S.1, Author              
Affiliations:
1Plant Cell Walls - Persson, Max Planck Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753318              
2Regulatory Networks, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753332              
3Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              
4Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753339              
5Integrative Carbon Biology, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753329              
6External Organizations, ou_persistent22              
7Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753310              

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Free keywords: iii polyketide synthases glycine-max l. arabidopsis-thaliana medicago-truncatula gene-coexpression phenylpropanoid biosynthesis isoflavonoid biosynthesis transcription factor functional genomics pollen development
 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.

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Language(s): eng - English
 Dates: 2011-03-252011
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: ISI:000289884200010
DOI: 10.1105/tpc.111.083667
ISSN: 1040-4651
URI: ://000289884200010http://www.plantcell.org/content/23/3/895.full.pdf
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Title: The Plant Cell
  Abbreviation : Plant C
Source Genre: Journal
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Publ. Info: Rockville : American Society of Plant Physiologists
Pages: - Volume / Issue: 23 (3) Sequence Number: - Start / End Page: 895 - 910 Identifier: Other: 1532-298X
CoNE: https://pure.mpg.de/cone/journals/resource/1532-298X