Evolutionary Computation in Gene Regulatory Network Research

CHAPTER 3GENE REGULATORY NETWORKS: REAL DATA SOURCES AND THEIR ANALYSIS

Yuji Zhang

Department of Epidemiology and Public Health, University of MarylandSchool of Medicine, Baltimore, MD, USAandDivision of Biostatistics and Bioinformatics, University of MarylandGreenebaum Cancer Center, Baltimore, MD, USA

3.1 INTRODUCTION

In all living organisms, deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein are three types of biological macromolecules that are indispensable for all biological processes. They are unbranched polymer chains, formed by the string together of monomeric building blocks drawn from a standard repertoire that is the same for all living cells. These molecules interact with each other frequently, and conditionally depend on each other to provide complex biological functions (e.g., functions of a protein are usually provided by its interactions with other proteins and genes). These molecules and their interactions compose complex networks, called gene regulatory networks (GRNs).

Gene regulatory networks are one of the most important biological networks in the bioinformatics and systems biology field. They play a vital role in almost every biological process, including cell differentiation, metabolism, cell cycle, and signal transduction. By understanding the properties and dynamics of these networks, we can shed light on the mechanisms of diseases that occur when these cellular processes are dysregulated. Analysis and inference of GRNs will also guide ...