Promoter Analysis

The transcription of genes depend on certain molecules, transcription factors, that bind to regulatory regions of the DNA, especially in the promoter of a
gene. We are developing methods for analyzing such regions, and for discovering DNA sequence patterns with regulatory functions.

Computational analysis of gene regulation in fission and budding yeasts

Regulatory sequences form a fraction of non-coding genome, yet they determine the order in which genes are activated, as well as the correct level of transcription. A popular approach to genome-wide discovery of regulatory sequences uses DNA microarrays under different environmental conditions to produce gene expression profiles, which can be used to cluster genes into co-expressed groups. It is reasonable to assume that co-expressed genes may also be coregulated, and thus may share regulatory sequences in non-coding regions surrounding them. Genes can also be grouped according to other properties, such as functional annotation, and search process repeated for "clusters" obtained this way.

We have compared gene expression and regulation in two single-celled eukaryotes; Schizosaccharomyces pombe and Saccharomyces cerevisiae, using clustering and pattern search tools inside Expression Profiler. We have used functional categories from Gene Ontology Consortium (GO) as clusters, and searched for upstream patterns common to most genes inside each cluster. We have also studied gene expression and regulation in both organisms using publicly available microarray data sets for sexual differentiation and stress response.