Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism.

ABSTRACT:

Background

Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distributions. Even though existing methods use transcript abundances as a proxy for enzyme activity, each method uses a different hypothesis and assumptions. Most methods implicitly assume a proportionality between transcript levels and flux through the corresponding function, although these proportionality constant(s) are often not explicitly mentioned nor discussed in any of the published methods. E-Flux is one such method and, in this algorithm, flux bounds are related to expression data, so that reactions associated with highly expressed genes are allowed to carry higher f

SUBMITTER: Sinha N 

PROVIDER: S-EPMC8628452 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature