Differential eigengene network analysis in human and chimp brain samples. A. Hierarchical clustering dendrogram of genes for identifying consensus modules (see text). Branches of the dendrogram, cut at the red line, correspond to consensus modules. Genes in each module are assigned the same color, shown in the color band below the dendrogram. Genes not assigned to any of the modules are colored grey. B., C. Clustering dendrograms of consensus module eigengenes for identifying meta-modules. The same three meta-modules (major branches) are evident in both dendrograms. D. Heatmap of eigengene adjacencies in the consensus eigengene network in human samples. Each row and column corresponds to one eigengene (labeled by consensus module color). Within the heatmap, red indicates high adjacency (positive correlation) and green low adjacency (negative correlation) as shown by the color legend. G. Corresponding plot for the chimp samples. E. Preservation measure for each consensus eigengene. Each colored bar corresponds to the eigengene of the corresponding color. The height of the bar (y-axis) gives the eigengene preservation measure (16). D denotes the overall preservation of the eigengene networks, Eq. (17). F. Heatmap of adjacencies in the preservation network Preservhuman,chimp, Eq. (15). Each row and column corresponds to a consensus module; saturation of the red color encodes adjacency according to the color legend. H. Characterizing consensus modules by differential expression of their corresponding eigengenes in the various brain areas from which samples were taken. Red means over-expression, green under-expression; numbers in each cell give the corresponding t-test p-value. Each column corresponds to an eigengene and each row corresponds to a brain area. Caudacc, caudate nucleus and anterior cingulate cortex; cerebcort, cerebellum and cortex; caudate, caudate nucleus.
Langfelder and Horvath BMC Systems Biology 2007 1:54 doi:10.1186/1752-0509-1-54