Fig. 3. Angiogenic and inflammatory pathways are differentially expressed in FB and PC co-expression network modules with AD.

Volcano and violin plots showing genes differentially expressed in AD relative to NDC donor cortical tissue in FB (A, B) and PC (C, D). In FB, PDE7A (logFC=1.33, padj=0.007), TRPM3 (logFC=1.44, padj=0.09), ROBO1 (logFC=1.35, padj=0.09) are significantly upregulated, whereas BCL2L1 (logFC = −0.35, padj=0.04), SPTBN1 (logFC = −1.34, padj=0.0001) and LAMC1 (logFC = −0.84, padj=0.01) are downregulated. In PC, TCF4 (logFC=1.27, padj=0.01), ARHGAP29 (logFC=1.47, padj=0.004), PLOD2 (logFC=0.91, padj=0.003) are significantly upregulated, whereas RASAL2 (logFC = −1.15, padj=0.005), EGFR (logFC = −0.76, padj=0.07) and CFLAR (logFC = −0.38, padj=0.03) are downregulated. Statistical significance was determined using a likelihood ratio test with a mixed-effects model and a zero-inflated negative binomial distribution (two-sided). For demonstration purposes, the TRPM3, EGFR, PLOD2, LAMC1 and BCL2L1 violin plots describe expression only for nuclei in which the respective genes are expressed, although the statistical analysis was performed on all nuclei. E Gene co-expression module hierarchy for FB and (F) PC. Modules that belong to the same branch are related, i.e., larger (“parent”) modules are closer to the centre of the plot and are further divided into subset (“children”) modules. “Children” modules are subsets of the “parent” ones and have higher numbers as names than their “parents”. Modules that show a significant overrepresentation of DEG (as shown in the volcano plots of Fig. 3A–C) by means of a one-sided Fisher’s exact test are labelled and represented as coloured points in the graph (red, for modules showing an overrepresentation of upregulated DEG; blue, showing an overrepresentation of downregulated DEG). Module number font size corresponds to the significance of the overrepresentation of DEG in the module. In the boxes, the top (maximum 5) hub genes (genes with the higher number of significant correlations within the module) are described. G Circular heatmap of odds ratios from the functional enrichment analyses for the FB and (H) PC modules that show a significant DEG overrepresentation (significant modules that show redundant functional enrichment terms were omitted from this heatmap). The adjusted p values of the significance of the overrepresentation are provided in Supplementary file 5. The inner two tracks of the circular heatmap represent the significance (−log₁₀(padj), one-sided) of the overrepresentation of down- (innermost track) and up-regulated DEG (second innermost track). The DGE and co-expression analyses were performed on 9’594 PC and 20’885 FB nuclei from 57 independent samples. Source data are provided as a Source data file.