Construction and analysis of gene networks for Arabidopsis

Constructing gene network and analyzing its structure is a basic but important way to discover and understand unknown physiological mechanisms of Arabidopsis subject to external stimuli on both the cellular and molecular levels. Mutual information networks are identified based on gene expression profiles of Arabidopsis in normal condition and subject to stimuli. The comparison and analysis of these network structures show that four network statistics, average degree, average clustering coefficient, modularity, the proportion of non-isolated nodes can distinguish the two types of networks corresponding to normal condition and those subject to different stimuli. A new method is proposed to classify these networks in multidimensional parameter space. Our studies can help better understanding of physiological mechanisms of genome response to stimuli.