Figure 2

Definition of coherence. The cartoon schematically depicts our definition of coherence. The complexes that are formed in either pseudocell in the lower part of the figure are compatible with the interaction network at the top. However, the two pseudocells are fundamentally different because, while in the pseudocell on the left much fewer complexes are formed (see the list of complex species on the left side of the first pseudocell), in the one on the right each protein takes part in a larger variety of complexes as depicted in the list of complexes on the right side of the second pseudocell. Thus we conclude that the pseudocell on the left is simpler and therefore more organized than the one on the right. The similarity index between two complexes is obtained from the following formula $S.I.\left(C_1,C_2\right)=\frac{{\left(|C_1\cap C_2|\right)}^2}{\left|\Delta \left(C_1,C_2\right)\right|+1}$. The Self-Similarity Index of a pseudo-cell then can be computed as $SSI\left(C\right)=\frac{{\sum }_{i=1}^{n-1}ma{x}_{j=i+1}^{n}S.I\left(C_i,C_j\right)}{n}$.