Topic outline

  • General

    Bioinformatics of transcriptional regulation

    Lausanne, 28 January - 1 February 2008

    The course attempts to present the state of the art of bioinformatics methods and resources for studying transcriptional regulation. The practical part is largely based on databases and web-servers developed by our group and can be viewed as an introduction to the usage of these tools:

    • The Eukaryotic Promoter Database EPD: Retrieval of useful and reliable information on promoters, and how to use this information for studying transcriptional regulatory mechanisms.
    • CleanEx: How to access, combine and effectively use public gene expression data.
    • HTP SELEX: A database of quantitative predictive models for transcription factor binding sites.
    • Signal Search Analysis (SSA): Motif discovery in functionally related DNA sequences and new tools to study the architecture of gene regulatory regions.

    The theoretical part is aimed at providing an overview of public data and computational methods relevant to the understanding of gene regulation. Particular emphasis will be on the analysis of so-called mass genome annotation (MGA) data such as CAGE for mapping transcription start sites, or ChIP-seq for mapping in vivo transcription factor binding sites.