Metabolic network visualization eliminating node redundance and preserving metabolic pathways.
BACKGROUND
The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult.


RESULTS
We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster.


CONCLUSIONS
The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism.
Bourqui
Romain
R
LaBRI, Université Bordeaux I, 351 Cours de la libération, 33405 Talence CEDEX, France. bourqui@labri.fr
Cottret
Ludovic
L
Lacroix
Vincent
V
Auber
David
D
Mary
Patrick
P
Sagot
Marie-France
MF
Jourdan
Fabien
F
D000465:Algorithms; D000818:Animals; D002952:Citric Acid Cycle; D003196:Computer Graphics; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D016678:Genome; D053858:Metabolic Networks and Pathways / Q000235:genetics; D051379:Mice; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014633:Valine / Q000096:biosynthesis
D014633:Valine