Cell type-specific profiling of our co-expression networks revealed significant enrichment of neuronal or glial marker genes within specific modules. The genes in the neuronal and glial specific modules showed interesting and opposing patterns of expression. Genes from the neuronal expression associated modules were downregulated in AD, while those from the glial modules were upregulated in AD. We speculate that the opposing patterns of expression reflect cytological changes occurring in the brains of AD as a result of prolonged alcohol consumption, which is known to have strong neurotoxic effects [63]. We could not differentiate whether these changes are the result of a global downregulation of expression in neurons or the result of a progressive loss of neuronal cell mass. A previous study on the amygdala of chronic alcoholics reported downregulation of neuronal gene expression, coupled with the upregulation of glial cell expression[40]. We would like to point out that using cell deconvolution to estimate cell-specific gene expression relies on computational algorithms; thus, it is conceivable that these approaches will be inherently noisier than a direct estimation of cell proportions.
