title: Functional Alignment of Metabolic Networks.
abstract: Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction, and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.
authors.affiliation: 1 Blavatnik School of Computer Science, Tel Aviv University , Tel Aviv, Israel .
authors.forename: Arnon
authors.initials: A
authors.lastname: Mazza
authors.affiliation: 1 Blavatnik School of Computer Science, Tel Aviv University , Tel Aviv, Israel .|2 Department of Electrical Engineering and Computer Science, University of California , Berkeley, Berkeley, California.
authors.forename: Allon
authors.initials: A
authors.lastname: Wagner
authors.affiliation: 1 Blavatnik School of Computer Science, Tel Aviv University , Tel Aviv, Israel .|3 The Sackler School of Medicine, Tel Aviv University , Tel Aviv, Israel .|4 Center for Bioinformatics and Computational Biology and Department of Computer Science, University of Maryland , College Park, Maryland.
authors.forename: Eytan
authors.initials: E
authors.lastname: Ruppin
authors.affiliation: 1 Blavatnik School of Computer Science, Tel Aviv University , Tel Aviv, Israel .
authors.forename: Roded
authors.initials: R
authors.lastname: Sharan
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D016415:Sequence Alignment
keywords: genome-scale metabolic models; metabolic networks; network alignment