title: Deriving phylogenetic trees from the similarity analysis of metabolic pathways.
abstract: BACKGROUND
  Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type of analysis allows one to measure the evolution of complete processes (with different functional roles) rather than the individual elements of a conventional analysis. We present a new technique for the phylogenetic analysis of metabolic pathways based on the topology of the underlying graphs. A distance measure between graphs is defined using the similarity between nodes of the graphs and the structural relationship between them. This distance measure is applied to the enzyme-enzyme relational graphs derived from metabolic pathways. Using this approach, pathways and group of pathways of different organisms are compared to each other and the resulting distance matrix is used to obtain a phylogenetic tree.
  
  
  RESULTS
  We apply the method to the Citric Acid Cycle and the Glycolysis pathways of different groups of organisms, as well as to the Carbohydrate metabolic networks. Phylogenetic trees obtained from the experiments were close to existing phylogenies and revealed interesting relationships among organisms.
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, CA 93106, USA.
authors.forename: Maureen
authors.initials: M
authors.lastname: Heymans
authors.forename: Ambuj K
authors.initials: AK
authors.lastname: Singh
mesh_terms: D000465:Algorithms; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000235:genetics; D002952:Citric Acid Cycle / Q000502:physiology; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D006019:Glycolysis / Q000502:physiology; D008660:Metabolism / Q000502:physiology*; D008954:Models, Biological; D009097:Multienzyme Complexes / Q000235:genetics / Q000378:metabolism; D010363:Pattern Recognition, Automated; D010802:Phylogeny; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
chemical_list: D002241:Carbohydrates; D009097:Multienzyme Complexes