Identifying hubs in protein interaction networks.
BACKGROUND
In 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.


METHODS
In 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.


CONCLUSIONS
We 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.
Vallabhajosyula
Ravishankar R
RR
Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA.
Chakravarti
Deboki
D
Lutfeali
Samina
S
Ray
Animesh
A
Raval
Alpan
A
D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D040081:Protein Array Analysis; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D011499:Protein Processing, Post-Translational; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction
D012333:RNA, Messenger