On different aspects of network analysis in systems biology

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

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

On different aspects of network analysis in systems biology

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

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

5 Citations (Scopus)

Abstract

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.

Original language	English
Title of host publication	Systems Biology
Subtitle of host publication	Integrative Biology and Simulation Tools
Publisher	Springer Netherlands
Pages	181-207
Number of pages	27
ISBN (Electronic)	9789400768031
ISBN (Print)	9789400768024
DOIs	https://doi.org/10.1007/978-94-007-6803-1_6
Publication status	Published - 1 Jan 2013
Externally published	Yes

Keywords

Booleanmodels
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

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

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Chaiboonchoe, A., Jurkowski, W., Pellet, J., Glaab, E., Kolodkin, A., Raussel, A., Le Béchec, A., Ballereau, S., Meyniel, L., Crespo, I., Ahmed, H., Volpert, V., Lotteau, V., Baliga, N., Hood, L., Sol, A. D., Balling, R., & Auffray, C. (2013). On different aspects of network analysis in systems biology. In Systems Biology: Integrative Biology and Simulation Tools (pp. 181-207). Springer Netherlands. https://doi.org/10.1007/978-94-007-6803-1_6

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abstract = "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.",

keywords = "Booleanmodels, 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",

author = "Amphun Chaiboonchoe and Wiktor Jurkowski and Johann Pellet and Enrico Glaab and Alexey Kolodkin and Antonio Raussel and {Le B{\'e}chec}, Antony and St{\'e}phane Ballereau and Laurene Meyniel and Isaac Crespo and Hassan Ahmed and Vitaly Volpert and Vincent Lotteau and Nitin Baliga and Leroy Hood and Sol, {Antonio Del} and Rudi Balling and Charles Auffray",

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doi = "10.1007/978-94-007-6803-1_6",

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Chaiboonchoe, A, Jurkowski, W, Pellet, J, Glaab, E, Kolodkin, A, Raussel, A, Le Béchec, A, Ballereau, S, Meyniel, L, Crespo, I, Ahmed, H, Volpert, V, Lotteau, V, Baliga, N, Hood, L, Sol, AD, Balling, R & Auffray, C 2013, On different aspects of network analysis in systems biology. in Systems Biology: Integrative Biology and Simulation Tools. Springer Netherlands, pp. 181-207. https://doi.org/10.1007/978-94-007-6803-1_6

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T1 - On different aspects of network analysis in systems biology

AU - Chaiboonchoe, Amphun

AU - Jurkowski, Wiktor

AU - Pellet, Johann

AU - Glaab, Enrico

AU - Kolodkin, Alexey

AU - Raussel, Antonio

AU - Le Béchec, Antony

AU - Ballereau, Stéphane

AU - Meyniel, Laurene

AU - Crespo, Isaac

AU - Ahmed, Hassan

AU - Volpert, Vitaly

AU - Lotteau, Vincent

AU - Baliga, Nitin

AU - Hood, Leroy

AU - Sol, Antonio Del

AU - Balling, Rudi

AU - Auffray, Charles

N1 - Publisher Copyright: © Springer Science+Business Media Dordrecht 2013.

PY - 2013/1/1

Y1 - 2013/1/1

N2 - 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.

AB - 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.

KW - Booleanmodels

KW - Cell-cell interaction

KW - Continuous models

KW - Database

KW - Discrete models

KW - Diseasome

KW - Gene regulatory networks

KW - Hybrid models

KW - Integrative disease map

KW - Metabolic networks

KW - Multi-scale modeling

KW - Network analysis tools

KW - Network modeling

KW - Network pharmacology

KW - Network topology

KW - Ordinary differential equations

KW - Protein-protein interaction

KW - Signalling networks

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U2 - 10.1007/978-94-007-6803-1_6

DO - 10.1007/978-94-007-6803-1_6

M3 - Chapter

AN - SCOPUS:84899996863

SN - 9789400768024

SP - 181

EP - 207

BT - Systems Biology

PB - Springer Netherlands

ER -

On different aspects of network analysis in systems biology

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