Integration of genome-wide expression and methylation data: relevance to aging and Alzheimer's disease

The progressive and latent nature of neurodegenerative diseases, such as Alzheimer's disease (AD) indicates the role of epigenetic modification in disease susceptibility. Previous studies from our lab show that developmental exposure to lead (Pb) perturbs the expression of AD-associated proteins. In order to better understand the role of DNA methylation as an epigenetic modifications mechanism in gene expression regulation, an integrative study of global gene expression and methylation profiles is essential. Given the different formats of gene expression and methylation data, combining these data for integrative analysis can be challenging. In this paper we describe a method to integrate and analyze gene expression and methylation arrays. Methylation array raw data contain the signal intensities of each probe of CpG sites, whereas gene expression data measure the signal intensity values of genes. In order to combine these data, methylation data of CpG sites have to be associated with genes.