On different aspects of network analysis in systems biology

Chaiboonchoe, Amphun; Jurkowski, Wiktor; Pellet, Johann; Glaab, Enrico; Kolodkin, Alexey; Raussel, Antonio; Le Béchec, Antony; Ballereau, Stéphane; Meyniel, Laurene; Crespo, Isaac; Ahmed, Hassan; Volpert, Vitaly; Lotteau, Vincent; Baliga, Nitin; Hood, Leroy; Sol, Antonio del; Balling, Rudi; Auffray, Charles

doi:10.1007/978-94-007-6803-1_6

Reference : On different aspects of network analysis in systems biology


	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Biochemistry, biophysics & molecular biology
	To cite this reference:	http://hdl.handle.net/10993/27261

Title :	On different aspects of network analysis in systems biology
Language :	English
Author, co-author :	Chaiboonchoe, Amphun [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
	Jurkowski, Wiktor [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Pellet, Johann [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
	Glaab, Enrico [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Kolodkin, Alexey [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Raussel, Antonio [Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg]
	Le Béchec, Antony [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit]
	Ballereau, Stéphane [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
	Meyniel, Laurene [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
	Crespo, Isaac [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Ahmed, Hassan [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
	Volpert, Vitaly [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
	Lotteau, Vincent [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
	Baliga, Nitin [Institute for Systems Biology, 401 Terry Avenue North, Seattle, United States]
	Hood, Leroy [Institute for Systems Biology, 401 Terry Avenue North, Seattle, United States]
	Sol, Antonio del [Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg]
	Balling, Rudi [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
	Auffray, Charles [European Institute for Systems Biology and Medicine, CNRS-UCBL-ENS, Université de Lyon, 50, Avenue Tony Garnier, Lyon cedex 07, France]
Publication date :	2013
Journal title :	Systems Biology
Publisher :	Springer Netherlands
Volume :	1
Pages :	181-207
Peer reviewed :	Yes
Audience :	International
Keywords :	[en] Boolean models ; Cell-cell interaction ; Continuous models ; Database ; Discrete models ; Diseasome ; Gene regulatory networks ; Hybrid models ; Integrative disease map ; Metabolic networks ; Multi-scale modeling ; Network analysis tools ; Network modeling ; Network pharmacology ; Network topology ; Ordinary differential equations ; Protein-protein interaction ; Signalling networks
Abstract :	[en] Network analysis is an essential component of systems biology approaches toward understanding the molecular and cellular interactions underlying biological systems functionalities and their perturbations in disease. Regulatory and signalling pathways involve DNA, RNA, proteins and metabolites as key elements to coordinate most aspects of cellular functioning. Cellular processes depend on the structure and dynamics of gene regulatory networks and can be studied by employing a network representation of molecular interactions. This chapter describes several types of biological networks, how combination of different analytic approaches can be used to study diseases, and provides a list of selected tools for network visualization and analysis. It also introduces protein-protein interaction networks, gene regulatory networks, signalling networks and metabolic networks to illustrate concepts underlying network representation of cellular processes and molecular interactions. It finally discusses how the level of accuracy in inferring functional relationships influences the choice of methods applied for the analysis of a particular biological network type. © Springer Science+Business Media Dordrecht 2013. All rights are reserved.
Permalink :	http://hdl.handle.net/10993/27261
DOI :	10.1007/978-94-007-6803-1_6
Commentary :	9789400768031; 9400768028; 9789400768024

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