  In systems biology new ways are required to analyze the large amount of
existing data on regulation of cellular processes. Recent work can be roughly
classified into either dynamical models of well-described subsystems, or
coarse-grained descriptions of the topology of the molecular networks at the
scale of the whole organism. In order to bridge these two disparate approaches
one needs to develop simplified descriptions of dynamics and topological
measures which address the propagation of signals in molecular networks. Here,
we consider the directed network of protein regulation in E. coli,
characterizing its modularity in terms of its potential to transmit signals. We
demonstrate that the simplest measure based on identifying sub-networks of
strong components, within which each node could send a signal to every other
node, indeed partitions the network into functional modules. We then suggest
measures to quantify the cost and spread associated with sending a signal
between any particular pair of proteins. Thereby, we address the signalling
specificity within and between modules, and show that in the regulation of
E.coli there is a systematic reduction of the cost and spread for signals
traveling over more than two intermediate reactions.
