title: Network analysis of systems elements.
abstract: A central goal of postgenomic research is to assign a function to every predicted gene. Because genes often cooperate in order to establish and regulate cellular events the examination of a gene has also included the search for at least a few interacting genes. This requires a strong hypothesis about possible interaction partners, which has often been derived from what was known about the gene or protein beforehand. Many times, though, this prior knowledge has either been completely lacking, biased towards favored concepts, or only partial due to the theoretically vast interaction space. With the advent of high-throughput technology and robotics in biological research, it has become possible to study gene function on a global scale, monitoring entire genomes and proteomes at once. These systematic approaches aim at considering all possible dependencies between genes or their products, thereby exploring the interaction space at a systems scale. This chapter provides an introduction to network analysis and illustrates the corresponding concepts on the basis of gene expression data. First, an overview of existing methods for the identification of co-regulated genes is given. Second, the issue of topology inference is discussed and as an example a specific inference method is presented. And lastly, the application of these techniques is demonstrated for the Arabidopsis thaliana isoprenoid pathway.
authors: Plant Biotechnology, Institute of Plant Sciences, Rämistr 2, Swiss Federal Institute of Technology, 8092 Zürich, Switzerland.
authors: Daniel
authors: D
authors: Schöner
authors: Simon
authors: S
authors: Barkow
authors: Stefan
authors: S
authors: Bleuler
authors: Anja
authors: A
authors: Wille
authors: Philip
authors: P
authors: Zimmermann
authors: Peter
authors: P
authors: Bühlmann
authors: Wilhelm
authors: W
authors: Gruissem
authors: Eckart
authors: E
authors: Zitzler
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D016000:Cluster Analysis; D053263:Gene Regulatory Networks; D013729:Terpenes / Q000378:metabolism; D015003:Yeasts / Q000378:metabolism
chemical_list: D013729:Terpenes