For this network, there are two alternative Tree of Complexes representations: functional group E can be connected to either D or C. The representation that maximizes the number of leaves is shown in Figure 3(b). One can clearly see the interplay between the activators and inhibitors. Proteins p105 and NF-κB participate in the same functional groups and thus follow the same path in the tree. The same is true for the pair of proteins IkBα and IkBβ. The Tree of Complexes captures this by grouping p105 and NF-κB, and IkBα and IkBβ.