FIGURE 2.

(A,B) Volcano plots, relating log₂ fold-changes (log₂FC) and B-statistics, of differential gene expression associated with the (A) AD and (B) Neuronal proportion effects in MayoClinic samples. Highlighted with larger colored dots are disease-associated genes from DisgeNet (Piñero et al., 2019) (light blue), genes reported by Kelley et al. (2018) as undergoing cell-type-specific changes in AD (pink), manually selected gene candidates for AD-specific alterations (orange), and genes included in the CIBERSORTx-derived expression signature for the major brain cell types (dark gray). Amongst all these, labeled are genes of particular interest, with individual expression profiles plotted in panels (C,D). The other labeled genes are the top 10 differentially expressed genes. (C) Expression of manually selected gene candidates for AD-specific alterations (labeled in orange in panels (A,B) in Control and AD samples – scatterplots against neuronal proportion on the left, boxplots of distribution by condition on the right. (D) Same as (C) for selected DisgeNet genes (labeled in light blue in panels A,B). Colored solid lines in panels C,D) represent linear regressions. T-tests, for which p-values are indicated, were used to compare gene expression mean differences between Control and AD samples.