gene regulation and metabolism post-genomic computational approaches - julio collado-vides

[...]... specific questions of gene regulation and metabolism without explicit mention of the connection between networks and the phenotype One of the challenges, computationally, in understanding gene regulation is finding, capturing, and leveraging the information in better-studied networks It is standard practice to apply conclusions from well-studied proteins to similar, but less well-understood, proteins... Bolker and Raff, 1997) These include the failure to distinguish between orthology and paralogy,1 the confusion of analogy (convergence) and homology (noting that gene- swapping experiments do not resolve this question), the failure to notice that orthologous genes can be recruited and expressed in structures whose similarities may not be due to common ancestry So, for example, the distal-less gene (the... Systems: Development and Evolution London: Academic Press 14 Jeremy Ahouse Gehring, Walter J., and Ruddle, Frank (1998) Master Control Genes in Development and Evolution: The Homeobox Story New Haven, Conn.: Yale University Press (Terry Lectures) Gerhart, John, and Kirschner, Marc W (1997) Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary... pathways and processes in which the protein may be involved, similarities to other proteins, and so on The Annotation Concept of SWISS-PROT and TrEMBL The SWISS-PROT protein sequence database (Bairoch and Apweiler, 2000) strives to provide extensive annotation as defined above The increased data flow from genome projects to the protein sequence databases, however, challenges this time- and labor-intensive... conflicts between genetic and developmental viewpoints and their attempted resolution in molecular biology In M L Dalla Chiara (ed.), Structures and Norms in Science Dordrecht, The Netherlands: Kluwer Academic Publishers, pp 243–264 de Beer, S G (1971) Homology, an Unsolved Problem London: Oxford University Press Depew, D J., and Weber, B (1996) Darwinism Evolving: Systems Dynamics and the Genealogy of... origin of morphological character and the biological basis of homology Evolution 43: 1157–1171 Webster, G., and Goodwin, B (1996) Form and Transformation: Generative and Relational Principles in Biology Cambridge: Cambridge University Press SUGGESTED READING Carroll, Sean B., Grenier, Jennifer K., and Weatherbee, Scott D (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design... regions, and an individual locus may give rise to multiple gene products This has stimulated experimental approaches to identify the full spectrum of messenger RNAs (the transcriptome) and their corresponding protein products (the proteome) (RIKEN, 2001) If we now ask about the many modifications of proteins, and the numerous interactions and the detailed biophysics of protein-protein, proteinDNA, protein-RNA,... that are generated when we focus on differences attributed to selection rather than on similarities attributed to homology C J Lowe and G A Wray studied several homeobox genes and concluded that they were recruited into new roles: ‘‘Each of these cases [orthodenticle, distal-less, engrailed expression in brittle stars, sea urchins, and sea stars] represents recruitment (co-option) of a homeobox gene to... sequence database Many other annotation approaches try to predict functions by comparative analysis with SWISS-PROT and other protein databases like TrEMBL and Genpept There are three main reasons for using only SWISS-PROT annotation in automatic approaches First, SWISS-PROT is a comprehensive protein sequence database This may seem surprising, since as of October 2000 SWISS-PROT contains only 88,000 proteins... KW (Keyword) and DE (Description) lines As of August 2000, there are more than 410,000 CC lines, 460,000 FT lines, and 110,000 DE lines in SWISS-PROT This information in SWISS-PROT is abstracted from more than 70,000 literature citations reporting sequencing and/ or characterization Another important reason is the standardization of annotation in SWISS-PROT This unique feature of SWISS-PROT allows the . Congress Cataloging-in-Publication Data Gene regulation and metabolism : postgenomic computational approaches/ edited by Julio Collado-Vides & Ralf Hofes ta ¨ dt. p. cm. — (Computational molecular. Genomics Isaac S. Kohane, Alvin Kho, and Atul J. Butte, 2002 Gene Regulation and Metabolism Postgenomic Computational Approaches edited by Julio Collado-Vides and Ralf Hofesta ¨ dt A Bradford Book The. Jiang, Ying Xu, and Michael Q. Zhang, editors, 2002 Gene Regulation and Metabolism: Postgenomic Computational Approaches Julio Collado-Vides and Ralf Hofesta ¨ dt, editors, 2002 Microarrays for