Identifying Hubs in Protein Interaction Networks

Abstract

BackgroundIn spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines “hub” proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust.MethodologyIn this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction.ConclusionsWe find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks.

Domain distribution and intrinsic disorder in hubs in the human protein–protein interaction network

“…2,18 Hence, we used this criterion to identify hubs in our dataset. Further, we defined non-hubs as proteins with one interaction and ignored those with two to four interactions to minimize the effect of potential hubs with unknown interactions.…”

Construction and Application of a Protein Interaction Map for White Spot Syndrome Virus (WSSV)

“…Proteins with a large number of interactions (usually called hubs) are likely to be more essential than proteins with a few links (42). However, there are many criteria to specify hub proteins (43). In this study, we defined the top 8 proteins with the highest number of interactions shown in Fig.…”

Comparative transcriptomics of hepatic differentiation of human pluripotent stem cells and adult human liver tissue

“…As expected, some differences in the transcription profiles between the hPSC-HEP and liver tissue samples were observed. Moreover, hub proteins [proteins with high level of interactivity that usually are essential and play central role in protein interaction networks (53)], which appear to be involved in the different hepatocyte developmental stages, were identified.…”