Fig. 6. Regression analysis of gene expression in EC as a function of pTau tissue density suggests increased apoptosis.

A Volcano plot showing genes with a significant positive (red) of negative (blue) correlation with tissue pTau density in EC. B Regression plots of individual genes associated to apoptosis, CCN2 (logFC= 0.80, padj=0.003), ANGPT2 (logFC= 1.73, padj=0.07), RGCC (logFC=0.41, padj=0.03), BTG1 (logFC=0.11, padj=0.02). For each gene, two plots are presented, the plot in the upper row show the scatter plot of the regression between the average expression value and the pTau density in each sample, whereas the plot in the lower row shows the regression between the percentage of non-zero counts across the nuclei in each sample and the pTau density in each sample. The DGE analysis was performed using a likelihood ratio test with a mixed-effects model and a zero-inflated negative binomial distribution (two-sided). It takes into account both the distribution of the non-zero normalised counts (corresponding to the plot in the upper row) and the abundance of non-zero nuclei in the samples (corresponding to the lower row). pTau in the horizontal axis is presented as scaled IHC binding values. The best-fit linear regression lines and 95% confidence intervals are shown (C) Dot plots of the functional enrichment analysis on the DEG that are positively and negatively associated to pTau (dot size, functional enrichment gene set size; colour, FDR, one-sided overrepresentation Fisher’s exact test). Source data are provided as a Source data file.