False hubs in a yeast protein-protein interaction network

Abstract

Protein-protein interaction (PPI) networks provide a well-established framework for elucidating structural properties. In contrast, much greater effort is required to identify useful and/or hidden information using the approach because of the complexity of the networks. Accordingly, an appropriate methodology that allows characterization of a simple, but core, sub-network of a complex network would be a potentially valuable alternative approach. Here, we employed k-core decomposition as a useful tool for obtaining core sub-networks from the complex PPI network in yeast. To apply a k-core value to the complex yeast PPI network, we constructed cytoplasmic and nuclear core sub-networks. We measured the lethality of proteins and the ratio of hub to non-hub core sub-network proteins at each k-core value step. With increasing k-core value, the values of the two parameters gradually increased. Application of 6- and 7-core values to cytoplasmic and nuclear PPI networks yielded modular, structured core sub-networks that were functionally specialized. We also elucidated a false hub: a structural hub exhibiting no functional roles or lethal properties in the network. By employing k-core decomposition to cytoplasmic and nuclear PPI networks in yeast, we obtained useful and/or hidden information during the core sub-network construction process, indicating that k-core decomposition is a useful tool for structural and informational network studies. Notably, we found false hub proteins that might provide insight into protein networks and clues to understanding network evolution.