To improve the clustering results, PPI networks were weighted based on topological properties such as shortest path length [2], [3], clustering coefficients [4], node degree, or the degree of experimental validity [5].
Some approaches for identifying disease genes based on topological properties have been shown effective in protein-protein interaction network [ 11, 29- 31].
Analysis of the EDI distribution, based on topological properties, revealed that genes interacted with as few partners as possible (the 'economical' principle).
In other words, the formation of such protein complexes was mainly based on topological properties rather than functional similarities of their protein elements.
Briefly, the networks are based only on calculated gene gene pairwise correlations, with the modules in these networks identified based on topological properties in an approach that avoids hard thresholding on the correlations.
While approaches for identifying disease genes based on topological properties have been shown to be effective [ 21, 33, 34], incorporating the effects of function may lead to further performance improvements, as this better highlights the purely topological features that make disease genes distinct from other genes.
Functional modules, highly connected subgraphs, were identified using a modularity measure based solely on topological properties, allowing modules to overlap.
This suggests that these two disorders are somehow related based on topological and ontological properties of the proteins that are directly associated with those disorders.
Approaches based on topological or abstract spectral properties do not necessarily take into account functional properties of the system to be simplified.
We concluded that materials design based on topological interlocking leads to an excellent combination of mechanical and sound absorption properties.
The protein interaction networks (PINs) of curcumin were constructed by Cytoscape, and the properties of the scale-free, small-world network and module were analyzed based on topological parameters.
