Fig. 3

Identification of relevant modules of breast cancer clinical traits and construction of the PPI network. (a) Visualization of the gene network with a heatmap. The heatmap depicts the TOM among all genes in the analysis. A light colour represents low overlap, and progressively darker reds indicate higher overlap. Blocks of darker colours along the diagonal are the modules. The gene dendrogram and module assignment are also shown along the left and upper sides. (b) The eigengene dendrogram and heatmap identify groups of correlated eigengenes termed meta-modules. As a result, the dendrogram shows that yellow, pink and green-yellow modules are highly related to breast cancer clinical stage. (c) Heatmap of the correlation between module eigengenes and clinical traits of breast cancer. The yellow gene module was shown to exhibit the strongest correlation with the clinical stage (clinical stage, T stage, N stage, metastatic risk). (d) PPI network of genes in the yellow module for clinical stage. The nodes other than the pale blue nodes represent the hub genes with the highest prediction scores calculated with the stress algorithm