Transcriptional Networks and Their Relatives

Abstract

Living cells are the product of gene expression programs involving regulated transcription of thousands of genes. Lee et al. used immunoprecipitation and microarray studies to build a global analysis of transcriptional regulatory networks in Saccharomyces cerevisiae . Patterns observed were characterized as motifs that were then combined by an automatic process into a network structure. Such transcriptional regulation represents a network of interactions, and similar networks underlie apparently unrelated systems, such as food webs and electronic circuits. To examine their fundamental design features, Milo et al. (see the Perspective by Oltvai and Barabási) looked at local organizing principles of networks, expressed as motifs of how different interactors are joined, that occurred at more than random frequencies. Motifs shared by food webs had features that were not shared by transcription networks from yeast and from Escherichia coli or by electronic circuits, although similarities were seen in information-processing circuits. T. I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, N. M. Hannett, C. T. Harbison, C. M. Thompson, I. Simon, J. Zeitlinger, E. G. Jennings, H, L. Murray, D. B. Gordon, B. Ren, J. J. Wyrick, J.-B. Tagne, T. L. Volkert, E. Fraenkel, D. K. Gifford, R. A. Young, Transcriptional regulatory networks in Saccharomyces cerevisiae . Science 298 , 799-804 (2002). [Abstract] [Full Text] R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon, Network motifs: Simple building blocks of complex networks. Science 298 , 824-827 (2002). [Abstract] [Full Text] Z. N. Oltvai, A.-L. Barabási, Life's complexity pyramid. Science 298 , 763-764 (2002). [Summary] [Full Text]