SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

13 years 10 months ago

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Abstract. We consider the problem of aligning two metabolic pathways. Unlike traditional approaches, we do not restrict the alignment to one-to-one mappings between the molecules of the input pathways. We follow the observation that in nature diﬀerent organisms can perform the same or similar functions through diﬀerent sets of reactions and molecules. The number and the topology of the molecules in these alternative sets often vary from one organism to another. In other words, given two metabolic pathways of arbitrary topology, we would like to ﬁnd a mapping that maximizes the similarity between the molecule subsets of query pathways of size at most a given integer k. We transform this problem into an eigenvalue problem. The solution to this eigenvalue problem produces alternative mappings in the form of a weighted bipartite graph. We then convert this graph to a vertex weighted graph. The maximum weight independent subset of this new graph is the alignment that maximizes the ali...

Ferhat Ay, Tamer Kahveci

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