Revisiting topological properties of protein-protein interaction networks from the perspective of dataset evolution

Protein-protein interaction (PPI) networks are crucial for organisms. Many research efforts have thus been devoted to the study on the topological properties PPI networks. However, existing studies did not always report consistent results on the topological properties of PPI networks. This situation is primarily caused by the incompleteness of current PPI datasets. To solve this problem, in this paper we revisited the topological properties of PPI networks from the perspective of PPI dataset evolution. Concretely, we used twelve PPI datasets of Arabidopsis thaliana from different BioGRID database versions, and compared the topological properties of PPI networks built from the twelve datasets. Our results show that as the dataset evolves, the PPI network becomes more and more complete, all considered topological properties seemingly converge to stable values, which possibly indicate the topological nature of the complete Arabidopsis thaliana PPI network. Such findings can not be obtained from a few datasets as used in the existing works.