HIERARCHICAL AND TOPOLOGICAL STUDY OF THE PROTEIN–PROTEIN INTERACTION NETWORKS

Po-Han Lee, Chien-Hung Huang, Jywe-Fei Fang, Hsiang-Chuan Liu and Ka-Lok Ng ()
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Po-Han Lee: The Affiliated Senior High School of National Taiwan Normal University, 143, Hsin-Yi Road, Sec 3, Taipei, Taiwan 106, ROC
Chien-Hung Huang: Department of Computer Science and Information Engineering, National Formosa University, 64, Wen-Hwa Road, Hu-wei, Yun-Lin, Taiwan 632, ROC
Jywe-Fei Fang: Department of Digital Content and Technology, National Taichung Teachers College, 140, Min Sheng Road, Taichung, Taiwan 403, ROC
Hsiang-Chuan Liu: Department of Biotechnology and Bioinformatics, Asia University, No.500, Lioufeng Road, Wufeng Shiang, Taichung, Taiwan 413, ROC
Ka-Lok Ng: Department of Biotechnology and Bioinformatics, Asia University, No.500, Lioufeng Road, Wufeng Shiang, Taichung, Taiwan 413, ROC

Advances in Complex Systems (ACS), 2005, vol. 08, issue 04, 383-397

Abstract: We employ the random graph theory approach to analyze the protein–protein interaction database DIP. Several global topological parameters are used to characterize the protein–protein interaction networks (PINs) for seven organisms. We find that the seven PINs are well approximated by the scale-free networks, that is, the node degree cumulative distributionPcum(k)scales with the node degreek (Pcum(k) ~ k-α). We also find that the logarithm of theaverageclustering coefficientCave(k)scales withk (Cave(k) ~ k-β), forE. coliandS. cerevisiae. In particular, we determine that theE. coliand theS. cerevisiaePINs are better represented by the stochastic and deterministic hierarchical network models, respectively. The current fruit fly protein–protein interaction dataset does not have convincing evidence in favor of the hierarchical network model. These findings lead us to conclude that, in contrast to scale-free structure, hierarchical structure model applies for certain species' PINs only.We also demonstrate that PINs are robust when subject to random perturbation where up to 50% of the nodes are rewired. Average node degree correlation study supports the fact that nodes of low connectivity are correlated, whereas nodes of high connectivity are not directly linked.

Keywords: Protein–Protein interaction networks; biological networks; scale-free networks; hierarchical networks (search for similar items in EconPapers)
Date: 2005
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DOI: 10.1142/S0219525905000531

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