Inferring the Topology of Gene Regulatory Networks: An Algebraic Approach to Reverse Engineering - Mathematical Concepts and Methods in Modern Biology - page 74

CHAPTER

3

Inferring the Topology of
Gene Regulatory Networks:
An Algebraic Approach to
Reverse Engineering

Brandilyn Stigler and Elena Dimitrova
∗ Southern Methodist University, Dallas, TX 75275-0156, USA
† Clemson University, Clemson, SC 29634-0975, USA

3.1 INTRODUCTION
3.1.1 Gene Regulatory Networks in Molecular Biology
In everyday language the word “genes” has become synonymous with heredity.
Nowadays children learn early that who we, and the living world around us, are
is encoded in each and every cell of the organism. This, of course, is generally true. 1
Indeed genes hold the information to build and maintain an organism's cells and pass
genetic traits to offspring. However, thinking of a genome simply as a book full of
facts about an organism paints a rather incomplete static picture. It hides the fact
that the “book” also contains instructions for the mechanisms through which genetic
information is extracted and plays a role in cellular processes, such as controlling
the response of a cell to environmental signals and replication of the DNA preceding
the cell division. This process of genetic information extracting and utilizing is part
of what is know as gene regulation . Gene regulation is essential for prokaryotic and
eukaryotic cells, as well as for viruses, as it increases the cell's flexibility in respond-
ing to the environment, allowing it to synthesize gene products (which are most often
proteins) when needed.
Gene regulation is an intricate process whose complexity makes it an extreme chal-
lenge for mathematical modeling. For example, proteins synthesized from genes may
control the flow of genetic information from DNA to mRNA, function as enzymes
catalyzing metabolic reactions, or may be components of signal transduction path-
ways. Gene regulation also drives the processes of cellular differentiation and mor-
phogenesis, leading to the creation of different cell types in multicellular organisms
where the different types of cells may possess different gene expression profiles
though they all possess the same genome sequence. The degradation of proteins

1 If we overlook the distinction between genes and their alleles and the fact that some organelles are
self-replicating and are not coded for by the organism's DNA.