Inferring carbon sources from gene expression profiles using metabolic flux models.

ABSTRACT:

Background

Bacteria have evolved the ability to efficiently and resourcefully adapt to changing environments. A key means by which they optimize their use of available nutrients is through adjustments in gene expression with consequent changes in enzyme activity. We report a new method for drawing environmental inferences from gene expression data. Our method prioritizes a list of candidate carbon sources for their compatibility with a gene expression profile using the framework of flux balance analysis to model the organism's metabolic network.

Principal findings

For each of six gene expression profiles for Escherichia coli grown under differing nutrient conditions, we applied our method to prioritize a set of eighteen different candidate carbon sources. Our method ranked t

SUBMITTER: Brandes A 

PROVIDER: S-EPMC3351459 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature