Comparison of network-based pathway analysis methods.
Network-based definitions of biochemical pathways have emerged in recent years. These pathway definitions insist on the balanced use of a whole network of biochemical reactions. Two such related definitions, elementary modes and extreme pathways, have generated novel hypotheses regarding biochemical network function. The relationship between these two approaches can be illustrated by comparing and contrasting the elementary modes and extreme pathways of previously published metabolic reconstructions of the human red blood cell (RBC) and the human pathogen Helicobacter pylori. Descriptions of network properties generated by using these two approaches in the analysis of realistic metabolic networks need careful interpretation.
Papin
Jason A
JA
Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive #0412, La Jolla, CA 92093-0412, USA.
Stelling
Joerg
J
Price
Nathan D
ND
Klamt
Steffen
S
Schuster
Stefan
S
Palsson
Bernhard O
BO
D000465:Algorithms; D019295:Computational Biology; D004912:Erythrocytes / Q000378:metabolism*; D016480:Helicobacter pylori / Q000378:metabolism*; D006801:Humans; D015398:Signal Transduction / Q000502:physiology*