The yeast Saccharomyces cerevisiae may be present in one of two haploid cell types, which are able to mate. Pheromones released by one type of cell bind to a specific receptor of the other type. This triggers the activation of a scaffold protein-bound mitogen-activated protein kinase (MAPK) cascade and subsequent activation of nuclear proteins that control subsequent cellular events. In a recent paper, Spirin et al. [13] identified a subnetwork of proteins involved in this process within a yeast protein interaction network [21]. We analyzed this subnetwork using the COD to see if our method can extract elements of temporal ordering. The subnetwork identified by Spirin et al. and its Tree of Complexes representation is given in Figure 4. In this case, the protein network is not chordal. First, the COD method identifies and connects a pair of weak siblings, MKKl and MKK2 .Then, to transform the network to a chordal graph, three additional edges are added: (SPH1, SPA2), (FUS3, KSS1), and (STE11, STE7). In this case, some functional groups will contain more than one protein complex.