Finding Compensatory Pathways in Yeast Genome

Pathways of genes found in protein interaction networks are used to establish a functional linkage between genes. A challenging problem in analysis of gene networks is to find pairs of compensatory pathways which can substitute for each other in case of a defective gene. All previous approaches on finding between-pathway models (BPMs) use the genetic network, while some of them also require each pathway to be a connected component in the physical network. In this thesis, we show that physical interactions can be used to induce missing genetic information and assist in finding BPMs. We extend the definition of a pair of compensatory pathways and propose a new method for finding BPMs which takes into account both networks. Experimental results on yeast interactome data set show that our method reveals more functionally enriched BPMs according to Gene Ontology database than previous work.