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Functional characterization and topological modularity of molecular interaction networks

BACKGROUND: Analyzing interaction networks for functional characterization poses significant challenges arising from the noisy, incomplete, and generic nature of both the interaction data as well as functional annotation of molecules. Network-based methods focus on interacting molecules (pairs or se...

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Detalles Bibliográficos
Autores principales: Pandey, Jayesh, Koyutürk, Mehmet, Grama, Ananth
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009507/
https://www.ncbi.nlm.nih.gov/pubmed/20122208
http://dx.doi.org/10.1186/1471-2105-11-S1-S35
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author Pandey, Jayesh
Koyutürk, Mehmet
Grama, Ananth
author_facet Pandey, Jayesh
Koyutürk, Mehmet
Grama, Ananth
author_sort Pandey, Jayesh
collection PubMed
description BACKGROUND: Analyzing interaction networks for functional characterization poses significant challenges arising from the noisy, incomplete, and generic nature of both the interaction data as well as functional annotation of molecules. Network-based methods focus on interacting molecules (pairs or sets) occurring in close proximity to infer functional associations. RESULTS: In this paper we perform a formal comparative investigation of the relationship between functional coherence and topological proximity in networks. We investigate the problem of assessing the coherence of sets of biomolecules (or segments thereof) taking into account functional specificity as well as the distribution of functional attributes across entity groups. We also propose novel measures of topological proximity that are more robust to noisy and incomplete interaction data. CONCLUSION: We derive the following results in this paper: (i) there exists strong correlation between functional similarity and topological proximity in various network abstractions, with domain interaction networks (DDIs) demonstrating higher correlation than protein interaction networks (PPIs); (ii) measures that quantify coherence among entire sets of proteins are superior to aggregates of known pair-wise measures; and (iii) random-walk based measures of topological proximity are better suited to existing interaction data. We validate our methods on diverse data, including experimentally and computationally derived PPIs and DDIs, as well as on sets of known biologically related groups of molecules.
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spelling pubmed-30095072010-12-23 Functional characterization and topological modularity of molecular interaction networks Pandey, Jayesh Koyutürk, Mehmet Grama, Ananth BMC Bioinformatics Research BACKGROUND: Analyzing interaction networks for functional characterization poses significant challenges arising from the noisy, incomplete, and generic nature of both the interaction data as well as functional annotation of molecules. Network-based methods focus on interacting molecules (pairs or sets) occurring in close proximity to infer functional associations. RESULTS: In this paper we perform a formal comparative investigation of the relationship between functional coherence and topological proximity in networks. We investigate the problem of assessing the coherence of sets of biomolecules (or segments thereof) taking into account functional specificity as well as the distribution of functional attributes across entity groups. We also propose novel measures of topological proximity that are more robust to noisy and incomplete interaction data. CONCLUSION: We derive the following results in this paper: (i) there exists strong correlation between functional similarity and topological proximity in various network abstractions, with domain interaction networks (DDIs) demonstrating higher correlation than protein interaction networks (PPIs); (ii) measures that quantify coherence among entire sets of proteins are superior to aggregates of known pair-wise measures; and (iii) random-walk based measures of topological proximity are better suited to existing interaction data. We validate our methods on diverse data, including experimentally and computationally derived PPIs and DDIs, as well as on sets of known biologically related groups of molecules. BioMed Central 2010-01-18 /pmc/articles/PMC3009507/ /pubmed/20122208 http://dx.doi.org/10.1186/1471-2105-11-S1-S35 Text en Copyright ©2010 Pandey 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
Pandey, Jayesh
Koyutürk, Mehmet
Grama, Ananth
Functional characterization and topological modularity of molecular interaction networks
title Functional characterization and topological modularity of molecular interaction networks
title_full Functional characterization and topological modularity of molecular interaction networks
title_fullStr Functional characterization and topological modularity of molecular interaction networks
title_full_unstemmed Functional characterization and topological modularity of molecular interaction networks
title_short Functional characterization and topological modularity of molecular interaction networks
title_sort functional characterization and topological modularity of molecular interaction networks
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009507/
https://www.ncbi.nlm.nih.gov/pubmed/20122208
http://dx.doi.org/10.1186/1471-2105-11-S1-S35
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