Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so the dynamics of the two objects are intrinsically linked. Here we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach. We then employ this unified framework to address the specific issue of the age dependence of protein interactions through the definition of three different node wiring or divergence schemes. A comparison with empirical data indicates that an age-dependent divergence move is necessary in order to reproduce the basic topological observables together with the age correlation between interacting nodes visible in empirical data. We also discuss the possibility of nontrivial joint partition and topology observables.

Influence of homology and node age on the growth of protein-protein interaction networks / A. Bottinelli, B. Bassetti, M. Gherardi, M. Cosentino Lagomarsino. - In: PHYSICAL REVIEW E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS. - ISSN 1539-3755. - 86:4(2012 Oct 31), pp. 041919.1-041919.12. [10.1103/PhysRevE.86.041919]

Influence of homology and node age on the growth of protein-protein interaction networks

B. Bassetti;M. Gherardi;Cosentino Lagomarsino M.
2012-10-31

Abstract

Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so the dynamics of the two objects are intrinsically linked. Here we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach. We then employ this unified framework to address the specific issue of the age dependence of protein interactions through the definition of three different node wiring or divergence schemes. A comparison with empirical data indicates that an age-dependent divergence move is necessary in order to reproduce the basic topological observables together with the age correlation between interacting nodes visible in empirical data. We also discuss the possibility of nontrivial joint partition and topology observables.
gene duplication; evolution; divergence; topology; model; complexes; genomes; family; yeast; laws
Settore FIS/02 - Fisica Teorica, Modelli e Metodi Matematici
Settore BIO/18 - Genetica
PHYSICAL REVIEW E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/257235
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