Hierarchy of metabolic compounds based on their synthesising capacity.
The concept of scopes is applied to analyse large metabolic networks. Scopes are defined as sets of metabolites that can be synthesised by a metabolic network when it is provided with given seeds (Sets of initial metabolic compounds). Thus, scopes represent synthesising capacities of the seeds in the network. A hierarchy is discussed in the sense that compounds, which are part of the scope of another compound, possess scopes themselves that are subsets of the former scope. This hierarchy is analysed by means of a directed acyclic graph. Using a simple chemical model, it is found that this hierarchy contains specific structures that can, to a large extent, be explained by the chemical composition of the participating compounds. In this way, it represents a new kind of map of metabolic networks, arranging the metabolic compounds according to their chemical capacity.
Handorf
T
T
Department of Theoretical Biophysics, Institute of Biology, Humboldt University, Ivalidenstr. 42, 10115 Berlin, Germany. Thomashandorf@gmx.de
Ebenhöh
O
O
Kahn
D
D
Heinrich
R
R
D000465:Algorithms; D002468:Cell Physiological Phenomena; D003196:Computer Graphics; D003198:Computer Simulation; D007287:Inorganic Chemicals / Q000145:classification / Q000378:metabolism*; D008660:Metabolism; D008954:Models, Biological; D008956:Models, Chemical; D009930:Organic Chemicals / Q000145:classification / Q000378:metabolism*; D011506:Proteins / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface
D007287:Inorganic Chemicals; D009930:Organic Chemicals; D011506:Proteins