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focus of this chapter is on network-wide coordination through a simple control
mechanism at every gene.
A basic assumption of the genetic model of expression is that each gene is closely
regulated by its products. If the rate of consumption of a gene's product exceeds the
rate of production, more is produced. If little is consumed, less is produced. How-
ever, production pathways are complex. Products can share pathways of consump-
tion or production. For example, different products may require similar enzymes.
Some molecules can be converted to common precursors. A product can contribute
to or be produced by separate pathways and consumed for different purposes. For
regulation to be effective the expression of the genes whose products intermix must
be coordinated. The hypothesis is that genes interact and regulate each other through
their common products. Yet each gene is regulated by a simple control mechanism.
Such networks show complex coordination, perform recognition, and have been pre-
viously described in the context of neuroscience [3, 4].
It is demonstrated that if a protocol of regulation is preserved, regulation can form
a genetic classifier. The classifier monitors product consumption and finds the most
efficient configuration of genes to replace the products. This configuration mini-
mizes the amount of unused products and responds to environmental demands. A
fundamental understanding of these regulatory mechanisms can guide experiment
design, reveal methods to control gene expression, and advance genetic therapy
approaches.
7.1.2 Background
Complex interactions occur between the genes and the cellular environment they
control. Genes not only autoregulate their expression but interact with each other via
numerous mechanisms within the process of converting DNA to final proteins. Gene
regulatory networks integrate multiple signals to determine protein production. Ex-
pression is ultimately regulated by concentrations of products and intermediaries of
metabolic pathways.
Understanding genetic-protein structure and dynamics relationships in networks
is a major goal of complex systems research [8]. Although numerous relationships
between specific structural and dynamical aspects of network components have been
investigated [5,6,10], general principles behind such relationships are still unknown
[9]. Thus a high degree of regulation occurs throughout genetic-protein production
pathways, but many aspects are unclear.
Instead of direct gene-to-gene interactions (i.e.,
gene1
promotes or inhibits
gene2
), our model focuses on a gene-product axis. Suppose
gene1
and
gene2
share
the same product or pathway. The genes also share regulation. A gene's regulation of
its product will affect the other gene that regulates that product. All genes that regu-
late the same product reach a communal equilibrium. Any change in the communal
equilibrium changes the expression of multiple genes. Gene-product regulation es-
tablishes indirect and nonlinear gene-to-gene interactions. With these interactions a
