Journal
SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL
Volume 79, Issue 12, Pages 703-716Publisher
SAGE PUBLICATIONS LTD
DOI: 10.1177/0037549703040940
Keywords
systems biology; functional units; biochemical reaction networks; systems analysis; cluster analysis
Ask authors/readers for more resources
Biological reaction networks consist of many substances and reactions between them. Like many other biological systems, they have a modular structure. Therefore, a division of a biological reaction network into smaller units highly facilitates its investigation. The authors propose an algorithm to divide an ordinary differential equation (ODE) model of a biological reaction network hierarchically into functional units. For every compound, an activity function dependent on concentration or concentration change rate is defined. After performing suitable simulations, distances between the compounds are computed by comparing the activities along the trajectories of the simulation. The distance information is used to generate a dendrogram revealing the internal structure of the reaction network. The algorithm identifies functional units in two models of different networks: catabolite repression in Escherichia coli and epidermal growth factor (EGF) signal transduction in mammalian cells.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available