  Background: Gene regulatory networks coordinate the expression of genes
across physiological states and ensure a synchronized expression of genes in
cellular subsystems, critical for the coherent functioning of cells. Here we
address the questions whether it is possible to predict gene synchronization
from network structure alone. We have recently shown that synchronized gene
expression may be predicted from symmetries in the gene regulatory networks
(GRN) and described by the concept of symmetry fibrations. We showed that
symmetry fibrations partition the genes into groups called fibers based on the
symmetries of their 'input trees', the set of paths in the network through
which signals can reach a gene. In idealized dynamic gene expression models,
all genes in a fiber are perfectly synchronized, while less idealized models -
with gene input functions differencing between genes - predict symmetry
breaking and desynchronization.
  Results: To study the functional role of gene fibers and to test whether some
of the fiber-induced coexpression remains in reality, we analyze gene
fibrations for the gene regulatory networks of E. coli and B. subtilis and
confront them with expression data. We find approximate gene coexpression
patterns consistent with symmetry fibrations with idealized gene expression
dynamics. This shows that network structure alone provides useful information
about gene synchronization, and suggest that gene input functions within fibers
may be further streamlined by evolutionary pressures to realize a coexpression
of genes.
  Conclusions: Thus, gene fibrations provides a sound conceptual tool to
describe tunable coexpression induced by network topology and shaped by
mechanistic details of gene expression.
