Figure 4

Network and pathway analyses reveal common pathways and hubs in neurodegeneration. (A) EnrichmentMap [42] network for overlapping enriched Gene Ontology gene sets identified by GSEA. Each node represents a significantly enriched gene set (FDR q-value ≤ 0.05), and more significant nodes are proportionally larger. Red nodes denote gene sets enriched in neurodegenerative disease tissue, while blue nodes denote those enriched in control tissue. Green lines appear between any gene sets with > 50% overlap, and are proportionally thicker given greater overlap. See Additional file 2: Figure S3 for full annotations of nodes. (B and C) MetaCore analyses generated, inputting all 243 CNM genes. (B) Network generated using only direct interactions between CNM genes. Smaller red and blue circles denote up-regulated and down-regulated genes respectively. Refer to MetaCore website for detailed network symbol legend. (C) MetaCore “Interactions by Protein Function” analysis identification of proteins, not necessarily within the CNM or differentially expressed at all, that are highly functionally connected with proteins corresponding to genes in the CNM. Z-score, standardized connectivity ratio (higher ratios denote greater connectivity).