• KSBB Journal
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• v.24 no.3
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• pp.287-290
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• 2009

Metabolic network is composed of more than thousands of metabolic reactions. Therefore, understanding of metabolic behavior of microorganisms is required to engineer metabolism of microorganisms. In this paper, we employed ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks) to quantify relationships among metabolic subpathways. The results showed that ARACNE analysis can give new insight into the study of bacterial metabolism.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.12-16
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• 2007

DNA repair means a collection of processes that a cell identifies and corrects damage to genome sequence. The DNA repair processes are important because a genome would not be able to maintain its essential cellular functions without the processes. In this research, we make some gene regulatory networks of DNA repair in S. cerevisiae to know how each gene interacts with others. Two approaches are adapted to make the networks; Bayesian Network and ARACNE. After construction of gene regulatory networks based on the two approaches, the two networks are compared to each other to predict which genes have important roles in the DNA repair processes by finding conserved interactions and looking for hubs. In addition, each interaction between genes in the networks is validated with interaction information in S. cerevisiae genome database to support the meaning of predicted interactions in the networks.

• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.71-74
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• 2007

Cell phenotypes are determined by groups of functionally related genes. Microarray profiling of gene expression provides us response of cellular state to its perturbation. Several methods for uncovering a cellular network show reliable network reconstruction. In this study, we present reconstruction of genetic regulatory network of inflammation bowel disease in human peripheral blood mononuclear cell. The microarray based on Affymetrix Gene Chip Human Genome U133 Array Set HG-U133A is processed and applied network reconstruction algorithm, ARACNe. As a result, we will show that inferred network composed of 450 nodes and 2017 edges is roughly scale-free network and hierarchical organization. The major hub, CCNL2 (cyclin A2), in inferred network is shown to be associated with inflammatory function as well as apoptotic function.

• Journal of Microbiology and Biotechnology
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• v.19 no.11
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• pp.1301-1305
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• 2009

The evolution of living organisms occurs via a combination of highly complicated processes that involve modification of various features such as appearance, metabolism and sensing systems. To understand the evolution of life, it is necessary to understand how each biological feature has been optimized in response to new environmental conditions and interrelated with other features through evolution. To accomplish this, we constructed contents-based trees for a two-component system (TCS) and metabolic network to determine how the environmental communication mechanism and the intracellular metabolism have evolved, respectively. We then conducted a comparative analysis of the two trees using ARACNE to evaluate the evolutionary and functional relationship between TCS and metabolism. The results showed that such integrated analysis can give new insight into the study of bacterial evolution.