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Article Dans Une Revue PLoS ONE Année : 2012

Identifying neighborhoods of coordinated gene expression and metabolite profiles

Timothy Hancock
  • Fonction : Auteur
Ichigaku Takigawa
  • Fonction : Auteur
Hiroshi Mamitsuka
  • Fonction : Auteur

Résumé

In this paper we investigate how metabolic network structure affects any coordination between transcript and metabolite profiles. To achieve this goal we conduct two complementary analyses focused on the metabolic response to stress. First, we investigate the general size of any relationship between metabolic network gene expression and metabolite profiles. We find that strongly correlated transcript-metabolite profiles are sustained over surprisingly long network distances away from any target metabolite. Secondly, we employ a novel pathway mining method to investigate the structure of this transcript-metabolite relationship. The objective of this method is to identify a minimum set of metabolites which are the target of significantly correlated gene expression pathways. The results reveal that in general, a global regulation signature targeting a small number of metabolites is responsible for a large scale metabolic response. However, our method also reveals pathway specific effects that can degrade this global regulation signature and complicates the observed coordination between transcript-metabolite profiles.
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hal-04474127 , version 1 (22-02-2024)

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Timothy Hancock, Nicolas Wicker, Ichigaku Takigawa, Hiroshi Mamitsuka. Identifying neighborhoods of coordinated gene expression and metabolite profiles. PLoS ONE, 2012, 7 (2), ⟨10.1371/journal.pone.0031345⟩. ⟨hal-04474127⟩
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