Overview | Start at bench | Install TOUCAN | Get Sequences | Annotate | MotifScanner | Statistics | ModuleSearcher | MotifSampler | Return to bench | References 

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The TOUCAN program (Aerts et al., 2003) is a highly versatile package for the analysis of regulatory elements in clusters of genes, which may be derived from different species. TOUCAN provides access to a series of tools and databases which are essential for this purpose. The scope of this tutorial is not a comprehensive description of all features (like in a program manual) but to provide a detailed step-by-step procedure to address a very common biological question. As example, we will start "at the bench", where we performed microarray analyses to cluster genes which are significantly upregulated in human endothelial cells by the inflammatory mediator interleukin-1, over a time-course of 6 hours. We ask the question, if it is possible to delineate common regulatory elements in clusters of genes which show a common behavior upon stimulation.

For this purpose, several individual steps are needed, starting from the automated "in-batch" extraction of promoter sequences from genome databases ("Get Sequences"). We will also see how to generate an annotation table for these genes of interest ("Annotate"). Then, we will delineate the strategy to predict transcription factor binding sites (TFBS) in this set of promoters ("MotifScanner"), perform statistical analyses to identify over-represented TFBS ("Statistics"), and also screen for significant combinations or "modules" of TFBS ("ModuleSearcher"). Finally, we will address the question, if it is possible to predict potential novel regulatory elements via de novo screening for over-represented sequence motifs ("MotifSampler"). At the end, we will return to the bench to verify or support our hypotheses.
     

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