Fig. 2: Characterization of AD traits, and brain gene and protein expression.
From: Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease
a Canonical correlation heatmap of disease traits. The intensity of the red color indicates the strength of correlation between traits; the canonical correlation is indicated in each box. The x- and y-axis represent the traits: clinical dementia rating (CDR), Braak score (bbscore), clinical neuropathology (PATH.Dx), neuropathology category (NP.1), CERAD neuropath criteria (CERJ), and mean neocortical plaque density (number of plaques/mm2, PlaqueMean). b, e Breakdown of DE genes (b) and proteins (e). This figure shows the UpsetR plot (“Methods”) of the DE genes or proteins overlapping across tests. The bars represent the size of the DE sets and the points represent the category to which each set belongs. c, f PlaqueMean DE genes (c) and proteins (f). The x-axis is the mean normalized count for each gene or protein and the y-axis is their log fold change. Blue and red genes and proteins correspond to FDR ≥ 0.05 and FDR < 0.05, respectively. The strongest DE genes are highlighted on the plot. d GO term enrichment across all signatures. The heatmap depicted represents the −log 10(FDR) of the top 5 most significant GO terms associated with signatures across all traits. Rows are GO terms and columns signatures. g MsigDB pathway enrichment for all signatures. The barplot represents the union of the top 10 significant MsigDB categories associated to signatures for all traits; x- and y-axis are MsigDB terms and the −log 10(FDR), respectively. Colors represent the individual traits.
