Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data
Which mechanism is responsible for the coordinated transcriptional response of the genes? This question is approached by extracting motifs that are shared between the upstream sequences of these genes. The motifs extracted are putative cis-acting regulatory elements.
What is the physiological meaning for the cell to express together these genes? One way to answer the question is to search for potential metabolic pathways that could be catalyzed by the products of the genes. This can be done by selecting the genes from the cluster that code for enzymes, and trying to assemble the catalyzed reactions to form metabolic pathways.
We present tools to answer these two questions, and we illustrate their use with selected examples in the yeast Saccharomyces cerevisiae. The tools are available on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/; http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/).
KeywordsGene Expression Data Significance Index Methionine Biosynthesis Sulfur Assimilation Putative Regulatory Element
Unable to display preview. Download preview PDF.
- Vilo, J., Brazma, A., Jonassen, I. & Ukkonen, E. Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. ISMB (2000).Google Scholar
- van Helden, J. et al. From molecular activities and processes to biological function. Briefings in Bioinformatics in press(2001).Google Scholar
- Spellman, P.T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273–97 (1998).Google Scholar
- Brazma, A., Jonassen, I., Vilo, J. & Ukkonen, E. Predicting gene regulatory elements in silico on a genomic scale. Genome Res 8, 1202–15 (1998).Google Scholar
- Thomas, D. & Surdin-Kerjan, Y. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 61, 503–32 (1997).Google Scholar