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Abstract: Gene regulation is a major source of phenotypic diversity between and within species. This aspect of evolution has long been addressed from the sole point of view of the genome sequence. The incredible development of transcriptomics approaches now allows one to actually study the topology and the properties of regulatory networks on an evolutionary perspective. This new discipline is called comparative functional genomics or comparative transcriptomics. This article reviews some of the main advances made in this field, using yeast species, and especially the species sequenced in the frame of the Genolevures program, as a model. [Copyright &y& Elsevier]

The molecular anatomy of the vertebrate embryo was systematically analysed through gene expression during early development of the Xenopus frog using whole-mount in situ hybridization. Expression patterns are documented and assembled into the database Axeldb (http://www.dkfz-heidelberg.de/abt0135/axeldb.htm). Synexpression groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation have been identified. These sets of co-regulated genes show a striking similarity with operons, and may be a key determinant facilitating evolutionary change leading to animal diversity. To cite this article: N. Pollet et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

The sequence of the human genome has been determined. The next task is to determine the function of the genes. Classifying cellular forms of proteins encoded by human cDNA clones is a primary step toward understanding the biological role of proteins and their coding genes. We report here our ongoing work on an automatic system to facilitate this classification. Our system handles the transfection, incubation, acquisition of microscopic images of the cells, and the classification of forms there appearing in the images. Our system correctly classified proteins by their forms at a rate of 90% in feasibility studies. To cite this article: R. Minamikawa-Tachino et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

To functionally characterize numerous novel proteins encoded by cDNAs sequenced by the German Consortium, 800 were tagged with green fluorescent protein. The subcellular localizations of the fusion proteins were examined in living cells, enabling their classification in subcellular groups. Their activity in cell growth, cell death, and protein transport was screened in high throughput using robotic liquid handling and reading stations. The resulting information is integrated with functional genomics and proteomics data for further understanding of protein functions in the cellular context. To cite this article: S. Wiemann et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

Systems biology is the iterative and integrative study of biological systems as systems in response to perturbations. It is founded on hypotheses formalized in models built from the results of global functional genomics analyses of the complexity of the genome, transcriptome, proteome, metabolome, etc. Its implementation by cross-disciplinary teams in a standardized mode under quality assurance should allow accessing the small variations of the large number of elements determining functioning of biological systems. Galactose utilization in yeast, and sea urchin development are two examples of emerging systems biology. To cite this article: C. Auffray et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

This thematic issue issue of the Comptes rendus Biologies contains review articles, original papers and conference reports presented at the first two Transcriptome conferences From Functional Genomics to Systems Biology and IMAGE Consortium Invitational workshops (Paris, November 2000 and Seattle, March 2002), and discussed during the inaugural meetings of the Systemoscope International Consortium (Paris, June 2003). We describe the founding principles, missions, working plan and policy for partnership and industrial development of Systemoscope to promote the study of the complexity of biological systems by integrating scientific, medical, ethical and economic issues in implementation of interdisciplinary projects for human health. To cite this article: C. Auffray et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]