Skip to Main content Skip to Navigation
Reports

Reaction Motifs in Metabolic Networks

Vincent Lacroix 1 Cristina Gomes Fernandes Marie-France Sagot
1 HELIX - Computer science and genomics
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unlike in previous works on (other) biochemical networks, this definition is not based only on topological features. We propose instead to use an alternative definition based on the functional nature of the components that form the motif. After introducing a formal framework motivated by biological considerations, we present complexity results on the problem of searching for all occurrences of a reaction motif in a network, and introduce an algorithm that is fast in practice in most situations. We then show some initial applications to the study of pathway evolution and of the global structure of metabolic networks.
Document type :
Reports
Complete list of metadata

Cited literature [1 references]  Display  Hide  Download

https://hal.inria.fr/inria-00070443
Contributor : Rapport de Recherche Inria <>
Submitted on : Friday, May 19, 2006 - 8:29:46 PM
Last modification on : Tuesday, July 20, 2021 - 5:20:02 PM
Long-term archiving on: : Sunday, April 4, 2010 - 9:14:04 PM

Identifiers

  • HAL Id : inria-00070443, version 1

Collections

Citation

Vincent Lacroix, Cristina Gomes Fernandes, Marie-France Sagot. Reaction Motifs in Metabolic Networks. RR-5563, INRIA. 2005, pp.14. ⟨inria-00070443⟩

Share

Metrics

Record views

376

Files downloads

1066