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. 2012 Dec;33(6):1450-1453.
doi: 10.1016/j.neuro.2012.06.008. Epub 2012 Jun 25.

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

Hany Alashwal  1 , Remi Dosunmu  2 , Nasser H Zawia  3
Affiliations

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

Hany Alashwal et al. Neurotoxicology. 2012 Dec.

Abstract

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.

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Figures

Figure 1
Figure 1. Differential Gene Expression and Methylation Correlation
A scatter plot of differential gene expression of control PND20 and developmentally-exposed PND700 (E700 - C20) vs the differential methylation of control PND20 and developmentally-exposed PND700 (E700 - C20). Methylation signal intensity data were linearly transformed.
Figure 2
Figure 2. Gene Expression and Methylation Profile
A circular representation of the genes with ≥2 fold change (563 genes) in gene expression of control PND20 and developmentally-exposed PND700. The tracks from the outside represent: (1) Genes, (2) Chromosomes, (3) Gene Expression of Control PND20, (4) Methylation of Control PND20, (5) Gene Expression of developmentally-exposedPND700, (6) Methylation of developmentally-exposed PND700.
Figure 3
Figure 3. Significant Genes Differential Profile
A line plot of the differential gene expression and methylation of significant genes (50 genes). Differential gene expression of control PND20 and developmentally-exposed PND700 (E700 - C20) vs the differential methylation of control PND20 and developmentally-exposed PND700 (E700 - C20). Methylation data were linearly transferred and log2 was applied to gene expression and methylation signal intensity values.
See this image and copyright information in PMC

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