Technical Report CSI-0002

Centrality Metrics for Comparing Protein-Protein Interaction Networks with Synthesized NK Systems

K. A. Hawick

Archived: 2014

Abstract

Computational graph analysis metrics can be used to make quantitative comparisons between biological and regulatory networks obtained from real specimens with simulated synthetic networks that have well parameterized properties such as a scale-free structure. We compute the betweenness centrality metric for five public domain protein-protein network data sets and compare them with synthesized NK networks. We employ a node-culling procedure to progressively remove the highest connected nodes in these networks and assess the wholistic system changes as revealed by the resulting Floyd all-pairs distance and the number of component clusters in the networks as they fail and break up. We discuss the potential for this method in assigning characteristic signatures or categories to networks of this sort as well as for identifying network components that are most vulnerable to biological attack.

Keywords: betweenness centrality; node vulnerability; regulatory networks; computational biology; node culling; simulation

Full Document Text: PDF version.

Citation Information: BiBTeX database for CSI Notes.

BiBTeX reference:

@InProceedings{CSI-0002,
        Title = {Centrality Metrics for Comparing Protein-Protein Interaction Networks with Synthesized NK Systems},
        Author = {K. A. Hawick},
        Booktitle = {Proc. IASTED International Conference on Biomedical Engineering},
        Year = {2014},
        Address = {Zurich, Switzerland},
        Month = {23-25 June},
        Organization = {IASTED},
        Pages = {1-8},
        Keywords = {betweenness centrality; node vulnerability; regulatory networks; computational biology; node culling; simulation},
        Owner = {kahawick},
        Timestamp = {2014.08.17},
        Url = {http://digital.hull.ac.uk/reports/0002/csi-0002.html}
}