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  Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response

Nikiforova, V. J., Daub, C. O., Hesse, H., Willmitzer, L., & Hoefgen, R. (2005). Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. Journal of Experimental Botany, 56(417), 1887-1896. doi:10.1093/jxb/eri179.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2B5F-1 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2B60-C
Genre: Journal Article

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 Creators:
Nikiforova, V. J.1, Author
Daub, C. O.2, Author              
Hesse, H.3, Author              
Willmitzer, L.4, Author              
Hoefgen, R.3, Author              
Affiliations:
1External Organizations, ou_persistent22              
2BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
3Amino Acid and Sulfur Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753337              
4Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              

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Free keywords: auxin causality metabolome network network topology plait concept scale-free network sulphur metabolism systems biology transcriptome arabidopsis-thaliana escherichia-coli transcriptional regulation vascular development mutual information auxin expression calcium calmodulin pathways
 Abstract: The systematic accumulation of gene expression data, although revolutionary, is insufficient in itself for an understanding of system-level physiology. In the post-genomic era, the next cognitive step is linking genes to biological processes and assembling a mosaic of data into global models of biosystem function. A dynamic network of informational flows in Arabidopsis plants perturbed by sulphur depletion is presented here. With the use of an original protocol, the first blosystem response network was reconstructed from a time series of transcript and metabolite profiles, which, on the one hand, integrates complex metabolic and transcript data and, on the other hand, possesses a causal relationship. Using the informational fluxes within this reconstruction, it was possible to link system perturbation to response endpoints. Robustness and stress tolerance, as consequences of scale-free network topology, and hubs, as potential controllers of homeostasis maintenance, were revealed. Communication paths of propagating system excitement directed to physiological endpoints, such as anthocyanin accumulation and enforced root formation were dissected from the network. An auxin regulatory circuit involved in the control of a hypo-sulphur stress response was uncovered.

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Language(s): eng - English
 Dates: 2005-05-252005
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000230309700018
DOI: 10.1093/jxb/eri179
ISSN: 0022-0957 (Print) 0022-0957 (Linking)
URI: ://000230309700018 http://jxb.oxfordjournals.org/content/56/417/1887.full.pdf
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Title: Journal of Experimental Botany
Source Genre: Journal
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Pages: - Volume / Issue: 56 (417) Sequence Number: - Start / End Page: 1887 - 1896 Identifier: -