Fig. 2.

Network analysis of the HDID-1 and HS/Npt transcriptome and functional annotation of gene modules. The dendrogram of the gene network was constructed using all brain regional data from HDID-1 and HS/Npt mice (N = 12 mice/genotype/brain region; 12 mice × 2 genotypes × 7 brain regions − 2 outlier samples = 166 samples total) (a). The x-axis corresponds to genes detected across all regions, and the y-axis represents the coexpression distance in arbitrary units (a.u.) between genes, determined by the extent of topological overlap. Dynamic tree cutting identified modules, generally dividing them at significant branch points in the dendrogram. Genes in the 44 modules are color-coded, and those not assigned to a module are labeled gray. Heatmap plots of the false discovery rate (FDR)-corrected hypergeometric p values from the over-representation (enrichment) analysis for the differentially expressed genes (DEGs) and cell type-specific genes (b). Each row in the heatmap corresponds to one module (labeled by color on the left), and each column corresponds to the category being tested for over-representation. The scale bar on the right represents hypergeometric p values used to assess statistical significance of over-representation (red = high statistical significance). P values were adjusted using FDR correction. Rows for the DEGs were arranged by hierarchical clustering, and the same row order was maintained for the cell type panel. R was used for analyses and graphical representations