Fig. 3
From: Human Alzheimer’s disease reactive astrocytes exhibit a loss of homeostastic gene expression
Reactive astrocytes exhibit pathologic transcriptome dysregulation. a Linear regressions of gene expression versus pseudotime were used to identify genes associated with astrocyte reactivity. Plots of gene expression as a function of pseudotime for a VIM, a reactive astrocyte gene, b SOX9, an astrocyte marker gene, and c NRXN1, a homeostatic astrocyte gene. Plots were colored by density of nuclei at each coordinate. d MA-style plot of dysregulated genes in reactive astrocytes and colored by density of genes at each coordinate. Genes’ average expression in protoplasmic astrocytes was plotted versus their pseudotime linear regression beta, a measure of effect size. Dotted blue lines represent threshold for linear regression beta used to identify significantly dysregulated genes. e MA-style plot of dysregulated genes in amyloid responsive microglia (ARMs) [50] and colored by density of genes at each coordinate. Dotted blue lines represent beta threshold used to identify significantly dysregulated genes. For d, e, plots include genes with non-zero betas (linear regression p < 0.05 after Bonferroni correction for multiple comparisons)