Contributions des entrées sur les sorties pour les réseaux métaboliques sur génomes entiers: performances et utilisation pour des études en nutrition humaine
Résumé
Metabolic networks are composed by all the biochemical reactions that can take place within an organism, as well as the exchanges of metabolites between the organism and its environment. The metabolic network of many organisms has been reconstructed, either manually or automatically, including at the scale of the entire genome. These models are stored in biological reference databases. Diets can be applied to these networks to model the behavior of organisms, when subjected to a specific diet. In this work, we automate an approach that allows, for each input nutrient in the network, to determine the percentages that are distributed in the different outputs when the organism is forced to evolve in a given diet. We name this approach nAIO (normalized Allocation of inputs on outputs. The nAIO is computed thanks to the inversion of a large-scale matrix and is combined with linear optimization problems. We apply this calculation to all known bacterial networks from studies of the gut microbiota and stored in the Virtual Metabolic Human database. The calculation of nAIOs shows that computation times do not depend on the size of the network but rather on the selected diet. The nAIO calculation also shows that for some bacteria the nAIOs
are independent of diet. For these bacteria the nAIOs can be used to make predictions that result
in a linear relationship between the inputs of the system and its outputs.
Domaines
Informatique [cs]
Origine : Fichiers produits par l'(les) auteur(s)