  With the increasing amount of experimental data on gene expression and
regulation, there is a growing need for quantitative models to describe the
data and relate them to the different contexts. The thermodynamic models
reviewed in the preceding paper provide a useful framework for the quantitative
analysis of bacterial transcription regulation. We review a number of
well-characterized bacterial promoters that are regulated by one or two species
of transcription factors, and apply the thermodynamic framework to these
promoters. We show that the framework allows one to quantify vastly different
forms of gene expression using a few parameters. As such, it provides a compact
description useful for higher-level studies, e.g., of genetic networks, without
the need to invoke the biochemical details of every component. Moreover, it can
be used to generate hypotheses on the likely mechanisms of transcriptional
control.
