Proteins have important functions in cell biology such as transferring signals, con-
trolling the functions of enzymes and regulating activities in the cell. Proteins interact
with other proteins in the cell to form protein-protein interaction (PPI) networks to
perform important tasks in the cell such as cell cycle control, protein folding, transla-
tion and transcription. A protein may also modify another protein by interacting with
it in a PPI network. Understanding the role of interactions of proteins is believed
to provide molecular indications of health and disease states which can be used to
provide new drugs and therapies.
PPI networks can be modeled by graphs where nodes represent proteins and
edges show the interactions between them. These networks act as an interface be-
tween the genome and the metabolism as shown in Figure 10.1. They perform the
functions under the control of the genes which results in biochemical reactions gov-
erning metabolism. Using technologies such as mass spectrometry provided large
volumes of data of PPI networks; however, the size of data and the fact that it con-
tains signiﬁcant noise make the analysis difﬁcult.
There are many public PPI databases such as Munich Information center for Pro-
tein Sequences (MIPS) , Yeast Proteomics Database (YPD) , Database of In-
teracting Proteins (DIP)  and Human Reference Protein Database (HRPD) 
which contain data about PPI networks of various organisms. Recent studies have
shown that disease genes share common topological properties [28, 14]. Assessment
of the relationship between PPI network topology and biological function of PPI
networks and disease is a challenging and active research area.