Topological overlap matrix plots for the yeast gene co-expression network. A. GTOM0 plot. B. GTOM1 plot. C. GTOM2 plot. D. GTOM3 plot. The color bar on the top of each heatmap shows the module assignment obtained from GTOM1. The color bar on the left of each heatmap shows the functional category of the corresponding genes. Dark red indicates the membership to the class 'protein biosynthesis'. Modules are more pronounced in the GTOM2 and GTOM3 plots (larger contrast between the diagonal blocks and off-diagonal blocks). Smaller modules (as diagonal blocks of red) are more visible in GTOM0 and GTOM1 plots whereas larger modules are more respected in GTOM2 and GTOM3 plots. However, GTOM3 leads to excessively large modules and thus the specificity of the modules is compromised. Protein biosynthesis genes are grouped together in the GTOM2 and GTOM3 plots.