Understanding Protein-Protein Interaction Networks from Conserved Patterns to Conserved Controllability

Conserved patterns in protein-protein interaction (PPI) networks are of great importance for understanding the evolutions and functions in multiple species. By identifying important genes (driver nodes), network controllability-based on the minimum dominating set (MDS) provides a new way to study PPI networks, which motivates us to shift the focus from conserved patterns to conserved controllability. In this paper, we study the controllability by taking network structures into account, which emphasises that a driver node can control a non-driver node if they belong to a specific structure, and further extend the controllability to multiple species for conserved controllability. We find that driver nodes are more likely to be tumour suppressor/drug targets and essential genes. The results over five species indicate that driver nodes across multiple species tend to be conserved, i.e., the homologous proteins of driver nodes in one species tend to be driver nodes in another species, and this tendency strengthens for the homologous protein pairs with stronger homologies. In addition, an interesting finding can be observed for conserved controllability, i.e., the five species can be classified into two groups, and within groups the conservation is stronger from low species to high species, which is just contrary to the species across the two groups.