What is a gene regulatory network?
Tomas Gedeon (Department of Mathematical Sciences, Montana State University)
(June 7, 2007 10:30 AM - 11:30 AM)
Gene regulation is currently at the center of attention of bio-medical community. The genomes of many species are known and the next big challenge of systems biology is to understand complex interactions between genes and their products in the context of a wide variety of pre- and post- transcriptional control and modification.
In this endeavour the concept of a "network" plays a central role. The biological data is often recorded and transmitted in literature and a list of proteins, genes or ligands which either up- or down- regulate the production, expression or concentration of other agents. This leads to a common picture of the network as a graph with nodes that correspond to the agents and signed arrows, that describe the interactions between them.
There are recent attempts to model the interaction at each node of the graph as a logical gate, where inputs are transformed to an output by a set of logic rules.
We discuss the situations in which both network and logical gate models of gene regulation are incomplete. While these widely used models may lead to important insights, one should be aware of pitfalls and limitation of such simplified view of gene regulation.