Multiobjective Approach to Detection of Differentially Coexpressed Modules

Microarray-based coexpression network analysis serves as a valuable tool for understanding gene co-regulation patterns, especially in the context of disease progression. This chapter focuses on the stages of HIV infection, where past studies have unveiled distinct gene regulation patterns. However, comprehending dynamic changes in gene coexpression poses a challenge. DiffCoMO, a multiobjective framework designed to identify differentially coexpressed modules, is presented here. Unlike traditional methods, DiffCoMO employs three objective functions, enhancing precision and robustness in revealing modules with significant coexpression changes under various conditions. While traditional coexpression analysis assesses gene coexpression levels under a single condition, DiffCoMO, through differential coexpression analysis, explores how coexpression varies across multiple experimental scenarios. The framework’s application in HIV progression studies demonstrates its effectiveness in understanding the topological features of coexpression modules throughout different infection stages. By integrating multiple objectives, DiffCoMO offers a thorough exploration of dynamic coexpression changes, proving to be a robust tool for unraveling intricate gene regulatory patterns in the evolving landscape of HIV infection.