Detecting Perturbation in Co-Expression Modules Associated with Different Stages of HIV-1 Progression: A Multi-objective Evolutionary Approach

Investigating co-regulation pattern of a group (or cluster) of genes is widely used to explore the topological and biological properties of co-expression network in a specific phenotype condition. Recent approaches go one step beyond and look for change in co-expression patterns in a pair of phenotype conditions during a disease progression. Here we develop a novel multi-objective framework to identify co-expressed modules undergoing topological changes in two phenotype conditions during disease progression. The proposed method is demonstrated on a microarray dataset of HIV disease progression. We identify co-expression modules during propagation of HIV infection from acute to chronic stage and from acute to non-progressive stage. We also perform a comparative study to explore topological properties of the identified modules in each pair of stages. The identified modules are also enriched with significant TFs like ZNF 771, ZNF 317, FOXJ3, SMARCC1 etc. TFs in the ZNF family are coming out as common regulators of genes involved in two categories of modules.