Networks

The expression level of a gene depends on many factors, among these the expression levels of other genes. We can build gene networks that attempt to
model such relations, and these networks can reveal global as well as local properties of various cellular systems. We are developing ways of building gene networks, analyzing these and integrating them with other types of networks, for instance built from scientific literature or protein-protein interactions.

Global mRNA decay in fission yeast

To shape gene expression patterns, cells need to coordinate transcriptional and post-transcriptional regulation. The impact of post-translational mechanisms such as mRNA turnover on gene expression is not well understood. We are investigating whether changes in mRNA stability can be detected by combining data from both transcription arrays and expression arrays.

Combinatorial logic of transcriptional regulation from gene expression timecourse data

Transcriptional regulation networks are used to represent regulatory relationships between sets of genes. Regulation models range from whole-genome topologies of potential regulation between sets of genes, to full dynamic models constructed for a handful of genes. We are looking at tractable network models which combine microarray-based gene expression timecourses with recent DNA-binding site maps and other genomic scale data in S. cerevisiae. Such models need to take account of the significant errors which are typical of genomewide datasets.

More Information:

• Reconstruction of gene networks by supervised learning - 2003 - Lev Soinov
• Gene disruption networks - 2002 - Thomas Schlitt and Johan Rung
• Presentation on "Gene Regulation Networks - a Finite State Linear Model" - 02/03/00 - Alvis Brazma