Comparison of metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when studying diseases and in drugs engineering. In the literature many techniques have been proposed to compare metabolic pathways. Most of them focus on structural aspects, while behavioural or functional aspects are generally not considered. In this paper we propose a new method for comparing metabolic pathways of different organisms based on a similarity measure which considers both homology of reactions and functional aspects of the pathways. The latter are captured by relying on a Petri net representation of the pathways and comparing the corresponding T-invariant bases, which represent minimal subsets of reactions that can operate at a steady state. A prototype tool, CoMeta, implements this approach and allows us to test and validate our proposal. Some experiments with CoMeta are presented.

Comparing Metabolic Pathways through Reactions and Potential Fluxes

COCCO, Nicoletta;GIUMMOLE', Federica;SIMEONI, Marta
2013-01-01

Abstract

Comparison of metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when studying diseases and in drugs engineering. In the literature many techniques have been proposed to compare metabolic pathways. Most of them focus on structural aspects, while behavioural or functional aspects are generally not considered. In this paper we propose a new method for comparing metabolic pathways of different organisms based on a similarity measure which considers both homology of reactions and functional aspects of the pathways. The latter are captured by relying on a Petri net representation of the pathways and comparing the corresponding T-invariant bases, which represent minimal subsets of reactions that can operate at a steady state. A prototype tool, CoMeta, implements this approach and allows us to test and validate our proposal. Some experiments with CoMeta are presented.
2013
Transactions on Petri nets and other models of concurrency VIII
File in questo prodotto:
File Dimensione Formato  
cometaTopNocFinale.pdf

non disponibili

Tipologia: Documento in Pre-print
Licenza: Accesso chiuso-personale
Dimensione 682.24 kB
Formato Adobe PDF
682.24 kB Adobe PDF   Visualizza/Apri

I documenti in ARCA sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10278/37943
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 4
  • ???jsp.display-item.citation.isi??? 1
social impact