Overview of eigengene networks. A. Flowchart of the construction and analysis of an eigengene network based on a single data set. B. Analogous flowchart for constructing and analyzing consensus eigengene networks based on multiple data sets. C.–E. Illustrating the notion of eigengene as a representative of an entire gene co-expression module. C. Expression levels (y-axis) of module genes (grey lines) and the eigengene (black line) across microarray samples (x-axis). The plot shows that an eigengene is highly correlated with the expression profiles of the genes in the module. D. Heatmap of the gene expressions (rows correspond to genes, columns to samples, red denotes over-expression, green under-expression). E. Expression levels (y-axis) of the corresponding eigengene across the samples (x-axis). Whenever the module gene expression are high (red), the module eigengene are high and similarly for low (green) gene expressions.