Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

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Analysis of Gene Logic Networks for Arabidopsis

Author(s): Yansen Su, Shudong Wang, Eryan Li, Tao Song, Hui Yu, Dazhi Meng.

Abstract:

External stimuli may activate the stress response in Arabidopsis thaliana. The molecules which play important roles in the stress response have been widely studied. However, the interactions, especially logic interactions, among these molecules, need to be studied. In this paper, logic networks are constructed based on gene expression profiles of Arabidopsis under the normal condition and four different stimuli conditions, respectively. It is found that the distribution of different types of 2-order logics in the gene logic network under the normal condition is different from the others. Furthermore, the logic networks of genes which play important roles are constructed and their dynamics are simulated. It is then observed that the number of attractors in the logic network for Arabidopsis under the normal condition is less than those under four external stimuli. It is also observed that the number of attractors with large attraction domain in the logic network for Arabidopsis under the normal condition is greater than those under four external stimuli. The results show that the distribution of different types of 2-order logics and the number of attractors clearly distinguish logic network under the normal condition from those under external stimuli conditions. Our studies will provide the theoretical basis for experimental studies on the stress response of Arabidopsis.

Keywords: Arabidopsis, gene network, high-order logic, network dynamics, network structure, systems biology, Clustering of Genes, intrinsic mechanisms, abscisic acid,

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Article Details

VOLUME: 8
ISSUE: 2
Year: 2013
Page: [244 - 252]
Pages: 9
DOI: 10.2174/1574893611308020012
Price: $58