The application of abstract topology to RAS-related signal transduction pathways

Ras is a protein related to cancer development. It is a convergence point for different signal transduction pathways that allow the cell to respond to external stimuli with different cell functions like growth, division, death, etc. In this paper, we analyze the signal pathways generated by different Ras effectors (Raf, RalGDS and PI3K), and the pathway relating Ras to the cell cycle control. We show that the interaction among different elements of these pathways induces a topologic structure in the set of elements. We discuss properties of this topology and give an algorithm to build it. The application of topological concepts makes easier the interaction analysis. Using a computational algorithm, we can create isolated, independently manageable sub-groups. Then we construct their hierarchical structure. The procedure allows us to visualize groups of elements related to the Ras effectors involved in cell growth, the elements involved in the cytoskeleton regulation, and the elements related to the cell cycle control. Thus the division in sub-groups does not only make easier the analysis, but it also provides a biologically meaningful subdivision.