E. coli gene regulatory networks are inconsistent with gene expression data.

ABSTRACT: Gene regulatory networks (GRNs) and gene expression data form a core element of systems biology-based phenotyping. Changes in the expression of transcription factors are commonly believed to have a causal effect on the expression of their targets. Here we evaluated in the best researched model organism, Escherichia coli, the consistency between a GRN and a large gene expression compendium. Surprisingly, a modest correlation was observed between the expression of transcription factors and their targets and, most noteworthy, both activating and repressing interactions were associated with positive correlation. When evaluated using a sign consistency model we found the regulatory network was not more consistent with measured expression than random network models. We conclude that, at least in

SUBMITTER: Larsen SJ 

PROVIDER: S-EPMC6326786 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature