Fig. 5

A deeper look into astrocytic gene regulation in HD. a Differential gene correlation analysis of the top 5% of genes in astrocytic nuclei by mean normalized expression (856 genes). Pearson correlation coefficients are shown and empirical p-values were calculated by a permutation test (100 permutations) in DGCA package in R. Top gene-pairs that are significantly differentially correlated between HD and control astrocytes are labeled. b Scatterplot of normalized expression of GFAP and MT1G (A representative metallothionein gene) in Control (left panel) and HD (Right panel) astrocytic nuclei. Pearson correlation coefficients are shown and are significantly different between control and HD. c Hierarchy structure representing the astrocytic gene modules/networks (labeled here as c1_3, c1_5, … etc) as the output using Multiscale Embedded Gene Co-Expression Network Analysis (MEGENA). Clusters on the same line are more related to each other than clusters on different lines. d Representative gene modules/networks, illustrating modules 9, 16, and 26. Hub genes are shown as triangles, genes as nodes, different colors represent different networks in the same graph (Left panel – Mod9). e Gene Ontology term enrichment analysis showing representative “Molecular Function” gene ontologies enriched in astrocytic gene modules. f Gene set variation analysis showing enrichment scores of modules in different astrocytic clusters, condition is shown as colored bars on the top