Assessing the impact of network depth on the analysis of PPI networks: A case study

Recent years have seen a growing interest in the incorporation of protein-protein interaction (PPI) networks to support functional genomic research. Often a default depth is assumed by network inference software. This case study considers the impact of network depth on the analysis of PPI networks using seven proteins known to be relevant to heart failure as inputs into the analysis. This paper analyses how the characteristics of a PPI network vary according to the level examined, suggesting that the investigation of network topology is an essential first step in PPI analysis. The classification of nodes, in terms of degree and betweenness centrality, within the network is also considered. The effect of network depth is also proved to be significant in the identification of potentially essential proteins with large connectivity and/or high betweenness centrality values.