Systems Biology (Methods in Molecular Biology)

The network structure analysis revealed that the functioning

and regulation of a network are governed by a certain set of orga-

nizing principles [5]. To understand the mechanisms of these orga-

nizing principles, the mechanistic dynamical models are used to

analyze the systems. The dynamical properties of a network charac-

terize the temporal behavior of a network under certain conditions,

so as to understand the nature of regulation of interacting compo-

nents in response to perturbations that affect the functionality of

the cells, and ultimately their consequences on the cellular

phenotype.

2.4 Selection of a
Mathematical
Modeling Formalism

Recent advances in omics technology and the availability of data-

bases with information about interactions among proteins, genes,

and miRNA, make it possible to model cellular processes as bio-

chemical networks [20, 21, 23, 24, 39]. These networks provide

useful information, such as the identification regulatory motifs and

hub nodes, but their utility is confined to a static analysis that does

not help explain “cause and effect” relationships, which are ubiqui-

tous in biological systems [40]. Moreover, it is impossible to char-

acterize complex network structures, like feedback/feedforward

loops and cross-talk in network modules, which induce counter-

intuitive behavior in systems dynamics, from the network connec-

tivity only. Nevertheless, networks are an important step toward

understanding system and provide a foundation for the develop-

ment of dynamical models [6]. The dynamical analysis helps in

understanding the functioning of a system and supports the

Nodes

Interactions

A

B

Functional

module

Fig. 6Illustration of network topological properties: The circles represent

‘Nodes’ and the lines/edges between them portray the ‘Interactions’ of the

network. The node ‘A’ act as a bridge between upper and lower part of the

network therefore it stands out as a high BC node. The node ‘B’ has large

number of edges so it gets high value of node degree. The sub-network high-

lighted by red rectangle termed as ‘Functional module’ means the constituent

nodes take part in a similar cellular function

256 Faiz M. Khan et al.