Organization and evolution of prokaryotic transcriptional networks.

In this project we want to study to what extent transcriptional modularity exists in bacterial transcriptional networks and the level to which it is conserved through evolution. Modularity in a static network view is defined as sets of genes that are (co)regulated by the same (set of) regulator(s). When taking into account the condition dependency of transcriptional regulation, modularity can be defined as gene sets being coexpressed in a subset of conditions. This definition is more complex as modularity is variable over time and in different conditions. Modules can overlap in different conditions, genes can belong to different modules depending on the conditions, etc. In this WP, we will infer the module network of bacterial model organisms (e.g. Escherichia coli, Salmonella Typhimurium, Bacillus subtilis) by elaborating on our expertise in biclustering (T1). By using data integration we will try to unravel the underlying cause of modularity (i.e. combinatorial regulation by TFs or sRNAs (see below), operon organization, etc.) (T2), and finally, study the module properties through evolution (which pathways seem to be modular, to what extent is the modularity conserved over different species) [27] (T3).

Keywords:Transcriptional networks

Disciplines:Scientific computing, Bioinformatics and computational biology, Public health care, Public health services