From Gene Expression to Disease Phenotypes: Network-Based Approaches to Study Complex Human Diseases

Gene expression is a fundamental biological process under tight regulation at all levels in normal cells. Its dysregulation can cause abnormal cell behaviors and result in diseases, and thus gene expression profiling and analysis have been widely used to provide the first clue about the molecular mechanisms of human diseases. Because genes and their products interact with and regulate one another, it is essential to analyze gene expression data and understand the genetics of disease in a biological network context. In this chapter, we first introduce the state-of-the-art gene expression analysis (GEA) with network integration and the joint analysis of mRNA and miRNA expression to understand disease regulatory mechanisms and then discuss how disease genes are predicted by incorporating knowledge of gene regulation and characterized in biological networks.