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Evidence of probabilistic behaviour in protein interaction networks

BACKGROUND: Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling the...

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Detalles Bibliográficos
Autores principales: Ivanic, Joseph, Wallqvist, Anders, Reifman, Jaques
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267158/
https://www.ncbi.nlm.nih.gov/pubmed/18237403
http://dx.doi.org/10.1186/1752-0509-2-11
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author Ivanic, Joseph
Wallqvist, Anders
Reifman, Jaques
author_facet Ivanic, Joseph
Wallqvist, Anders
Reifman, Jaques
author_sort Ivanic, Joseph
collection PubMed
description BACKGROUND: Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling these networks may exhibit considerable probabilistic behaviour. RESULTS: We find that the probability of an interaction between two proteins is generally proportional to the numerical product of their individual interacting partners, or degrees. The degree-weighted behaviour is manifested throughout the protein-protein interaction networks studied here, except for the high-degree, or hub, interaction areas. However, we find that the probabilities of interaction between the hubs are still high. Further evidence is provided by path length analyses, which show that these hubs are separated by very few links. CONCLUSION: The results suggest that protein-protein interaction networks incorporate probabilistic elements that lead to scale-rich hierarchical architectures. These observations seem to be at odds with a biologically-guided organization. One interpretation of the findings is that we are witnessing the ability of proteins to indiscriminately bind rather than the protein-protein interactions that are actually utilized by the cell in biological processes. Therefore, the topological study of a degree-weighted network requires a more refined methodology to extract biological information about pathways, modules, or other inferred relationships among proteins.
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spelling pubmed-22671582008-03-13 Evidence of probabilistic behaviour in protein interaction networks Ivanic, Joseph Wallqvist, Anders Reifman, Jaques BMC Syst Biol Research Article BACKGROUND: Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling these networks may exhibit considerable probabilistic behaviour. RESULTS: We find that the probability of an interaction between two proteins is generally proportional to the numerical product of their individual interacting partners, or degrees. The degree-weighted behaviour is manifested throughout the protein-protein interaction networks studied here, except for the high-degree, or hub, interaction areas. However, we find that the probabilities of interaction between the hubs are still high. Further evidence is provided by path length analyses, which show that these hubs are separated by very few links. CONCLUSION: The results suggest that protein-protein interaction networks incorporate probabilistic elements that lead to scale-rich hierarchical architectures. These observations seem to be at odds with a biologically-guided organization. One interpretation of the findings is that we are witnessing the ability of proteins to indiscriminately bind rather than the protein-protein interactions that are actually utilized by the cell in biological processes. Therefore, the topological study of a degree-weighted network requires a more refined methodology to extract biological information about pathways, modules, or other inferred relationships among proteins. BioMed Central 2008-01-31 /pmc/articles/PMC2267158/ /pubmed/18237403 http://dx.doi.org/10.1186/1752-0509-2-11 Text en Copyright © 2008 Ivanic et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Ivanic, Joseph
Wallqvist, Anders
Reifman, Jaques
Evidence of probabilistic behaviour in protein interaction networks
title Evidence of probabilistic behaviour in protein interaction networks
title_full Evidence of probabilistic behaviour in protein interaction networks
title_fullStr Evidence of probabilistic behaviour in protein interaction networks
title_full_unstemmed Evidence of probabilistic behaviour in protein interaction networks
title_short Evidence of probabilistic behaviour in protein interaction networks
title_sort evidence of probabilistic behaviour in protein interaction networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267158/
https://www.ncbi.nlm.nih.gov/pubmed/18237403
http://dx.doi.org/10.1186/1752-0509-2-11
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