We used reverse transcription-coupled PCR to produce a high-resolution temporal map of f luctuations in mRNA expression of 112 genes during rat central nervous system development, focusing on the cervical spinal cord. The data provide a temporal gene expression ''fingerprint'' of spinal cord development based on major families of inter-and intracellular signaling genes. By using distance matrices for the pair-wise comparison of these 112 temporal gene expression patterns as the basis for a cluster analysis, we found five basic ''waves'' of expression that characterize distinct phases of development. The results suggest functional relationships among the genes f luctuating in parallel. We found that genes belonging to distinct functional classes and gene families clearly map to particular expression profiles. The concepts and data analysis discussed herein may be useful in objectively identifying coherent patterns and sequences of events in the complex genetic signaling network of development. Functional genomics approaches such as this may have applications in the elucidation of complex developmental and degenerative disorders.The complexity of living organisms poses a challenge to biologists: considering the rapid accumulation of vast amounts of data in the fields of molecular and cell biology, how can we begin to organize these data into a coherent functional whole? To understand the nature of complex biological processes, such as development, we must determine the specific gene expression patterns and biochemical interactions within an organism but, equally important, seek out the organizing principles that allow them to function in a coherent way. Herein, we present a practical experimental-computational strategy that may allow us to advance our understanding of the nature of the complex self-organizing process underlying mammalian central nervous system (CNS) development.As a first step in this approach, we have addressed the question of whether the temporal expression patterns of large numbers of genes exhibit some degree of order across a tissue, in this case, the developing cervical spinal cord. Further, we are interested in forming hypotheses concerning possible functional relationships between gene families, by examining their patterns of expression over the course of development.The differentiation and maintenance of a cell phenotype may be viewed as the product of a system of well-coordinated interactions, with some cell types influencing the development of others. Therefore, we have taken a systems approach to CNS development in which the tissue is treated as a whole. In vivo gene expression patterns characteristic of stem cells, pluripotent progenitor cells, and mature neurons and glia should be reflected in the patterns of gene expression obtained at different developmental time points.Ongoing genome sequencing projects are based on the concept that proteins mediating the functions of organisms are strictly determined by the structure and activity of the genes that encode them. Data from g...

No abstract