Figure 3

Differential eigengene network analysis across four tissues in female mice. 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. Biological significance of the found modules was assessed by functional enrichment analysis, presented in the main text and in Additional File 4. B.–E. Clustering dendrograms of consensus module eigengenes for identifying meta-modules. F.–U. Matrix of plots showing the consensus eigengene networks in the four tissues. Each row and column corresponds to one tissue as indicated on the diagonal plots. The diagonal plots F., K., P., U. show the 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 hight adjacency (positive correlation) and green low adjacency (negative correlation) as shown by the color legend. Each of the upper triangle plots (G., H., I., L., M., Q.) shows a barplot of of preservation of relationships of consensus eigengenes, Eq. (16) between the two tissues (corresponding row and column) as well as the overall network preservation measure D for that pair of tissues, Eq. (17). The lower triangle plots (J., N., O., R., S., T.) show the adjacency heatmaps for the pairwise preservation networks of the tissues corresponding to the row and column, Eq. (15). In the heatmap, each row and column corresponds to a consensus module; saturation of the red color encodes adjacency according to the color legend.