Algebraic method for the analysis of signaling crosstalk

Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Kotaro Oka, Masaru Tomita

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

A unified mathematical description that expresses the characteristics of whole systems is necessary for an understanding of signal transduction cascades. In this study we explore an algebraic method, named extreme signaling flow, enhanced from the concept of extreme pathway, to analyze signal transduction systems. This method enables us to represent the long-term potentiation (LTP) and the long-term depression (LTD) of hippocampal neuronal plasticity in an integrated simulation model. The model is validated by comparing the results of redundancy, reaction participation, and in silico knockout analysis with biological knowledge available from the literature. The following properties are assumed in these computational analyses: (1) LTP is fault-tolerant under network modification, (2) protein kinase C and MAPK have numerous routes to LTP induction, (3) calcium-calmodulin kinase II has a few routes to LTP induction, and (4) calcineurin has many routes to LTD induction. These results demonstrate that our approach produces an integrated framework for analyzing properties of large-scale systems with complicated signal transduction.

Original languageEnglish
Pages (from-to)81-94
Number of pages14
JournalArtificial Life
Volume14
Issue number1
DOIs
Publication statusPublished - 2008 Dec

Fingerprint

Signal transduction
Signal Transduction
Long-Term Potentiation
Algebraic Methods
Crosstalk
Proof by induction
Extremes
Calmodulin
Protein Kinase C
Calcium-Calmodulin-Dependent Protein Kinases
MAP Kinase Kinase 2
Calcineurin
Integrated Model
Large-scale Systems
Fault-tolerant
Calcium
Plasticity
Neuronal Plasticity
Cascade
Redundancy

Keywords

  • Extreme pathway
  • Hippocampus
  • Neuronal plasticity
  • Signal transduction

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Artificial Intelligence
  • Theoretical Computer Science
  • Computational Theory and Mathematics
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Algebraic method for the analysis of signaling crosstalk. / Matsubara, Yoshiya; Kikuchi, Shinichi; Sugimoto, Masahiro; Oka, Kotaro; Tomita, Masaru.

In: Artificial Life, Vol. 14, No. 1, 12.2008, p. 81-94.

Research output: Contribution to journalArticle

Matsubara, Yoshiya ; Kikuchi, Shinichi ; Sugimoto, Masahiro ; Oka, Kotaro ; Tomita, Masaru. / Algebraic method for the analysis of signaling crosstalk. In: Artificial Life. 2008 ; Vol. 14, No. 1. pp. 81-94.
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