Abstract
BackgroundMinimum dominating sets (MDSet) of protein interaction networks allow the control of underlying protein interaction networks through their topological placement. While essential proteins are enriched in MDSets, we hypothesize that the statistical properties of biological functions of essential genes are enhanced when we focus on essential MDSet proteins (e-MDSet).ResultsHere, we determined minimum dominating sets of proteins (MDSet) in interaction networks of E. coli, S. cerevisiae and H. sapiens, defined as subsets of proteins whereby each remaining protein can be reached by a single interaction. We compared several topological and functional parameters of essential, MDSet, and essential MDSet (e-MDSet) proteins. In particular, we observed that their topological placement allowed e-MDSet proteins to provide a positive correlation between degree and lethality, connect more protein complexes, and have a stronger impact on network resilience than essential proteins alone. In comparison to essential proteins we further found that interactions between e-MDSet proteins appeared more frequently within complexes, while interactions of e-MDSet proteins between complexes were depleted. Finally, these e-MDSet proteins classified into functional groupings that play a central role in survival and adaptability.ConclusionsThe determination of e-MDSet of an organism highlights a set of proteins that enhances the enrichment signals of biological functions of essential proteins. As a consequence, we surmise that e-MDSets may provide a new method of evaluating the core proteins of an organism.
Highlights
Minimum dominating sets (MDSet) of protein interaction networks allow the control of underlying protein interaction networks through their topological placement
We hypothesize that essential proteins that appear in MDSets as well (e-MDSet) enhance the enrichment signals of biological functions compared to essential proteins alone
Khuri and Wuchty BMC Bioinformatics (2015) 16:109 tendency to be essential when we focused on essential proteins that appeared in the corresponding MDSet as well (e-MDSet)
Summary
Minimum dominating sets (MDSet) of protein interaction networks allow the control of underlying protein interaction networks through their topological placement. The biological importance of a protein is frequently considered a question of the number of interactions a given protein is involved in [1,2,3], suggesting that high topological centrality is an indicator of a protein’s importance [4,5,6,7,8,9]. Focusing on the determination of nodes that control an entire network, Liu et al introduced a maximum matching approach to predict nodes that allowed the control of various technical, social and biological networks [15] Their approach was only applicable to directed networks, prompting Nacher and Akutsu to determine minimum dominating sets (MDSet) of nodes, defined as a set of centrally located nodes that provide control of undirected networks [16]. While highly connected proteins showed a weak enrichment of essential proteins we recovered a strong correlation between a protein’s degree and its
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