Protein interaction networks--more than mere modules.

PLoS Computational Biology
Stefan PinkertJörg Reichardt

Abstract

It is widely believed that the modular organization of cellular function is reflected in a modular structure of molecular networks. A common view is that a "module" in a network is a cohesively linked group of nodes, densely connected internally and sparsely interacting with the rest of the network. Many algorithms try to identify functional modules in protein-interaction networks (PIN) by searching for such cohesive groups of proteins. Here, we present an alternative approach independent of any prior definition of what actually constitutes a "module". In a self-consistent manner, proteins are grouped into "functional roles" if they interact in similar ways with other proteins according to their functional roles. Such grouping may well result in cohesive modules again, but only if the network structure actually supports this. We applied our method to the PIN from the Human Protein Reference Database (HPRD) and found that a representation of the network in terms of cohesive modules, at least on a global scale, does not optimally represent the network's structure because it focuses on finding independent groups of proteins. In contrast, a decomposition into functional roles is able to depict the structure much better as it also t...Continue Reading

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Citations

Dec 5, 2013·Omics : a Journal of Integrative Biology·Konstantina DimitrakopoulouAnastasios Bezerianos
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Jan 8, 2021·Molecular Neurobiology·Kartikay PrasadVijay Kumar
Apr 27, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Lovro Subelj, Marko Bajec

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Methods Mentioned

BETA
ubiquitination
Y2H
two hybrid

Software Mentioned

HPRD
InfoMod
âOntologizerâ
Ontologizer

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