Dominating biological networks.

Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI netwo...

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Autores principales:	Tijana Milenković, Vesna Memišević, Anthony Bonato, Nataša Pržulj
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0399ecd6fad6422fa493ce71fee7eee5
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spelling	oai:doaj.org-article:0399ecd6fad6422fa493ce71fee7eee52021-11-18T06:47:12ZDominating biological networks.1932-620310.1371/journal.pone.0023016https://doaj.org/article/0399ecd6fad6422fa493ce71fee7eee52011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21887225/?tool=EBIhttps://doaj.org/toc/1932-6203Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC)" genes (i.e., their protein products), such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC) role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs) in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.Tijana MilenkovićVesna MemiševićAnthony BonatoNataša PržuljPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e23016 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tijana Milenković Vesna Memišević Anthony Bonato Nataša Pržulj Dominating biological networks.
description	Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC)" genes (i.e., their protein products), such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC) role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs) in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.
format	article
author	Tijana Milenković Vesna Memišević Anthony Bonato Nataša Pržulj
author_facet	Tijana Milenković Vesna Memišević Anthony Bonato Nataša Pržulj
author_sort	Tijana Milenković
title	Dominating biological networks.
title_short	Dominating biological networks.
title_full	Dominating biological networks.
title_fullStr	Dominating biological networks.
title_full_unstemmed	Dominating biological networks.
title_sort	dominating biological networks.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/0399ecd6fad6422fa493ce71fee7eee5
work_keys_str_mv	AT tijanamilenkovic dominatingbiologicalnetworks AT vesnamemisevic dominatingbiologicalnetworks AT anthonybonato dominatingbiologicalnetworks AT natasaprzulj dominatingbiologicalnetworks
_version_	1718424394293837824

Dominating biological networks.

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