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A systems approach to morphogenesis in Arabidopsis thaliana: I. AGNS database

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Abstract

In systems biology, study of a complex and multicomponent system, such as morphogenesis, comprises accumulation of data on morphogenetic processes in databases, classification and logical analysis of this information, and computer simulation of the processes in question using the data accumulated and the results of their analysis. This paper describes realization of the first steps in a systems study of morphogenesis (annotating research papers, compiling information in a database, data systematization, and their logical analysis) by the example of Arabidopsis thaliana, a model object in plant molecular biology. The database AGNS (Arabidopsis GeneNet Supplementary; http://wwwmgs.bionet.nsc.ru/agns) contains the experimentally confirmed information from published papers on specific features of gene expression and phenotypes of wild-type, mutant, and transgenic A. thaliana plants. AGNS queries and logical data analysis with the aid of specially developed software makes it possible to model various morphogenetic processes from gene expression to functioning of gene networks and their contribution to the development of certain traits.

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia

    N. A. Omelyanchuk, V. V. Mironova, E. M. Zalevsky, I. S. Shamov, A. S. Poplavsky, N. L. Podkolodny, S. V. Nikolaev & N. A. Kolchanov

  2. Ershov Institute of Informatics Systems, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia

    D. K. Ponomaryov

  3. Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92607, USA

    E. D. Mjolsness

  4. California Institute of Technology, Pasadena, CA, 91125, USA

    E. M. Meyerowitz

Authors
  1. N. A. Omelyanchuk
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  2. V. V. Mironova
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  3. E. M. Zalevsky
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  4. I. S. Shamov
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  5. A. S. Poplavsky
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  6. N. L. Podkolodny
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  7. D. K. Ponomaryov
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  8. S. V. Nikolaev
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  9. E. D. Mjolsness
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  10. E. M. Meyerowitz
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  11. N. A. Kolchanov
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Corresponding author

Correspondence to N. A. Omelyanchuk.

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Omelyanchuk, N.A., Mironova, V.V., Zalevsky, E.M. et al. A systems approach to morphogenesis in Arabidopsis thaliana: I. AGNS database. BIOPHYSICS 51 (Suppl 1), 75–82 (2006). https://doi.org/10.1134/S0006350906070165

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  • DOI: https://doi.org/10.1134/S0006350906070165

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