Local and global responses in complex gene regulation networks

Masa Tsuchiya, Kumar Selvarajoo, Vincent Piras, Masaru Tomita, Alessandro Giuliani

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

An exacerbated sensitivity to apparently minor stimuli and a general resilience of the entire system stay together side-by-side in biological systems. This apparent paradox can be explained by the consideration of biological systems as very strongly interconnected network systems. Some nodes of these networks, thanks to their peculiar location in the network architecture, are responsible for the sensitivity aspects, while the large degree of interconnection is at the basis of the resilience properties of the system. One relevant feature of the high degree of connectivity of gene regulation networks is the emergence of collective ordered phenomena influencing the entire genome and not only a specific portion of transcripts. The great majority of existing gene regulation models give the impression of purely local 'hard-wired' mechanisms disregarding the emergence of global ordered behavior encompassing thousands of genes while the general, genome wide, aspects are less known. Here we address, on a data analysis perspective, the discrimination between local and global scale regulations, this goal was achieved by means of the examination of two biological systems: innate immune response in macrophages and oscillating growth dynamics in yeast. Our aim was to reconcile the 'hard-wired' local view of gene regulation with a global continuous and scalable one borrowed from statistical physics. This reconciliation is based on the network paradigm in which the local 'hard-wired' activities correspond to the activation of specific crucial nodes in the regulation network, while the scalable continuous responses can be equated to the collective oscillations of the network after a perturbation.

Original languageEnglish
Pages (from-to)1738-1746
Number of pages9
JournalPhysica A: Statistical Mechanics and its Applications
Volume388
Issue number8
DOIs
Publication statusPublished - 2009 Apr 15

Fingerprint

Gene Regulation
gene expression
Biological Systems
Resilience
resilience
genome
Genome
Entire
Reconciliation
Macrophage
Immune Response
immune systems
Statistical Physics
Network Architecture
Paradox
Vertex of a graph
macrophages
Interconnection
sensitivity
yeast

Keywords

  • Biological statistical mechanics
  • Cell cultures
  • Networks
  • Systems biology

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Statistics and Probability

Cite this

Local and global responses in complex gene regulation networks. / Tsuchiya, Masa; Selvarajoo, Kumar; Piras, Vincent; Tomita, Masaru; Giuliani, Alessandro.

In: Physica A: Statistical Mechanics and its Applications, Vol. 388, No. 8, 15.04.2009, p. 1738-1746.

Research output: Contribution to journalArticle

Tsuchiya, Masa ; Selvarajoo, Kumar ; Piras, Vincent ; Tomita, Masaru ; Giuliani, Alessandro. / Local and global responses in complex gene regulation networks. In: Physica A: Statistical Mechanics and its Applications. 2009 ; Vol. 388, No. 8. pp. 1738-1746.
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