Chapter 5
Construction of Phenotype-Specific Gene Network by Synergy Analysis

5.1.		Introduction
5.2.		Experimental Design
5.3.		Materials
5.3.1.		Cell Culture and Reagents
5.3.2.		Fatty Acid Salt Treatment
5.4		Methods
5.4.1		Cytotoxicity Measurement
5.4.2		Gene Expression Profiling
5.4.3		Metabolites Measurements
5.4.4		Gene Selection Based on Trends of Metabolites
5.4.5		Calculation of the Synergy Scores of Gene Pairs
5.4.6.		Permutation Test to Evaluate the Significance of the Synergy
5.4.7		Characterization of the Network Topology
5.5		Data Acquisition, Anticipated Results, and Interpretation
5.6		Discussion and Commentary
5.7		Troubleshooting Table
5.8		Application Notes
5.8.1		Topological Characteristic of the Synergy Network
5.8.2		Hub Genes in the Network
5.9		Summary Points
		Acknowledgements
		References

Chapter 6
Genome Scale Analysis of Metabolic Networks

6.1.		Introduction
6.2.		Materials and Methods
6.2.1.		Flux Analysis Theory
6.2.2		Model Development
6.2.3.		Objective Function
6.2.3.1		Objective Function Choices
6.2.3.2		Objective Function Determination/Evaluation
6.2.3.3		Caveats
6.2.4		Optimization
6.3		Data Acquisition, Anticipate Results and Interpretation
6.3.1		Feasible Solution Determined
6.3.2		No Feasible Solution Determined
6.4		Discussion and Commentary
6.5		Summary Points
6.6		Acknowledgements
6.7		References

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