Minimum dominating sets in cell cycle specific protein interaction networks

Recently, scientists start to examine the dynamics of biological networks from a control theory perspective. Based on the determination of minimum dominating sets (MDSets), this paper investigated the properties associated with MDSet proteins in the context of the analysis of protein interaction networks specific to the yeast cell cycle. Statistically significant differences between MDSet and non-MDSet proteins were observed in terms of topological features, Gene Ontology-driven semantic similarities, and the number of protein domains associated with each protein. However, unlike previous studies, MDSet proteins were found to be enriched with essential genes. Furthermore, we constructed and analyzed a PPI network specific to the human cell cycle and highlighted that the distinction between MDSet and non-MDSet proteins is far more complex than that observed in yeast. The system used to determine a minimum dominating set in a protein interaction network was implemented as a user-friendly Java-based plugin for Cytoscape.