Differential eigengene network analysis across female and male mouse liver tissues. 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. D.–G. Matrix of plots showing the consensus eigengene networks. The diagonal plots D., G. show heatmap plots of eigengene adjacencies in each eigengene network. Each row and column corresponds to one eigengene (labeled by consensus module color). Within each heatmap, red indicates high adjacency (positive correlation) and green low adjacency (negative correlation) as shown by the color legend. E. Barplot of preservation of relationships of consensus eigengenes between the two data sets, Eq. (16), as well as the overall network preservation measure D, Eq. (17). Each colored bar corresponds to the eigengene of the corresponding color. The height of the bar (y-axis) gives the eigengene preservation measure (16). F. Adjacency heatmap for the preservation network between female and male consensus eigengene networks, Eq. (15). Each row and column corresponds to a consensus module; saturation of the red color encodes adjacency according to the color legend. H., I. Consensus module significance for clinical traits, given by the correlation of the corresponding module eigengene (row) with the clinical trait (column). Shown are correlations and p-values; cell color encodes correlation (red, positive correlation, green, negative correlation according to the color legend).
Langfelder and Horvath BMC Systems Biology 2007 1:54 doi:10.1186/1752-0509-1-54