Multi-dimensional scaling plots of the yeast gene co-expression network. MDS plots using A. GTOM0, B. GTOM1, C. GTOM2, and D. GTOM3. The coloring scheme is used to reflect the 7 modules shown in Figure 2B detected by using hierarchical clustering with the GTOM1-based dissimilarity. The symbol '▲' denotes genes that belong to the functional category 'protein biosynthesis'. Genes that belong to other classes are denoted by a '○'. In general, the module assignment is preserved across the different GTOM measures. But the spatial distributions of the points vary to a large extent. Genes in the 'protein biosynthesis' class appear to be closer together.