In bio-systems, genes, proteins and compounds are related to each other, thus forming complex networks. Although each organism has its individual network, some organisms contain common sub-networks based on function. Given a certain sub-network, the distribution of organisms common to it represents the diversity of its function.
We extracted such "common" sub-networks, defined as "phylogenetic ... [Show full abstract] network modules," using phylogenetic profiles and cluster analysis. The enzymes in the same "phylogenetic network module" have similar phylogenetic profiles and related functions. These modules are shown to be phylogenetic building blocks. Furthermore, the network of the modules illustrated hierarchical feature as well as the network of enzymes involved in the metabolism.
We conclude that phylogenetic network modules are evolutionary conserved functional units in the metabolic network. We claim that our concept of phylogenetic modules provides a more accurate understanding of the evolution of biological networks.