Fig. 8: Molecular validation of VGF.
From: Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease

a Consensus subnetwork within a path length of 2 of VGF. The consensus subnetworks around VGF, two steps away from VGF, across all three networks are depicted. The blue and red nodes are genes and proteins, respectively. The blue edges originate from the gene-only network, the red edges from the protein only network, and the purple edges from the multiscale network. VGF and its known partners are in bold in the plot. b Density plot of the distribution of differential expression nominal p values for genes downstream and not downstream (causally independent of the expression levels) of VGF in the gene-only network for mouse DE genes (5xFAD, AAV5-GFP versus 5xFAD, AAV5-VGF brains). The x-axis is the −log 10(p value) for differential expression, and the y-axis represents the densities at the different −log10(p value). The red and blue curves are for genes downstream and not downstream of VGF in the network, respectively. c Summary of DE results of VGF network genes in the 5xFAD, AAV5-GFP versus 5xFAD, AAV5-VGF brains overlaid on the VGF gene-only subnetwork. The nodes are colored by log fold change from green (negative) to orange (positive). The size of the node represents the DE FDR. Gray genes names are not significantly DE and white nodes have no orthologous genes in mice.