FIGURE 3.

(A) Scatter plot comparing the t-statistics of differential gene expression associated with the AD effect in MayoClinic and Nativio samples. Points (genes) are colored according to the FDR of the random permutation test on the product of the t-statistics (section “Materials and Methods”). Labeled genes are those significantly differentially expressed (FDR < 0.05) in both datasets and significant in that permutation test (FDR < 0.05). Light gray dashed zero and identity lines, light gray solid contour density lines. (B) Volcano plots, relating log₂ fold-changes (log₂FC) and B-statistics, of differential gene expression associated with the of AD and Neuronal proportion effects in MayoClinic and Nativio samples. Genes highlighted in orange are those manually selected as candidates for AD-specific alterations already represented in Figure 2, those labeled in panel (A) are here highlighted in purple (“Common”), and those here labeled in purple are presented in panel (C). (C) Expression of manually selected “Common” genes in MayoClinic and Nativio samples. Colored solid lines represent linear regressions.