Inferring Gene Transcription Networks: The Davidson Model

book where he reports on 30 years of work, together with his colleagues,
on purple sea urchin. Their work provided a general experimental
framework for the study of a gene?s cis-regulatory region (an upstream
DNA sequence containing a series of consecutive binding sites). Their
approach consisted of systematic, almost exhaustive, series of mutations
of individual binding sites, together with the associated measurements
of the transcription rates. By quantitative analysis, they were able
to infer a complete set of minimal functional units of regulation and
their interrelations. They proceeded hierarchically to uncover ?modularity?
and ?hardwired information processing logic? of a gene?s cis-region.
Most of their work was focused on the endo16 gene.
Their extraordinary technology and the inference of the underlying
?network? for this gene resulted in the most completely understood
transcriptional system to date.

It is quite remarkable how combinatorial and robust their approach is.
We will present an analysis and a mathematical formalism for the Davidson
transcriptional network inference technology. We will also present a
glance into our recent work with Eric Davidson towards the identification of
the regulatory ?programming language.?