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 proceedingChapterpeer-review

4 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 languageEnglish
Title of host publicationSystems Biology
Subtitle of host publicationIntegrative Biology and Simulation Tools
PublisherSpringer Netherlands
Pages181-207
Number of pages27
Volume1
ISBN (Electronic)9789400768031
ISBN (Print)9789400768024
DOIs
Publication statusPublished - 1 Jan 2013
Externally publishedYes

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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