title: Global Network Alignment in the Context of Aging.
abstract: Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between nodes in different networks? 2) Which alignment strategy to use to rapidly identify "high-scoring" alignments from all possible alignments? We "break down" existing state-of-the-art methods that use both different cost functions and different alignment strategies to evaluate each combination of their cost functions and alignment strategies. We find that a combination of the cost function of one method and the alignment strategy of another method beats the existing methods. Hence, we propose this combination as a novel superior NA method. Then, since human aging is hard to study experimentally due to long lifespan, we use NA to transfer aging-related knowledge from well annotated model species to poorly annotated human. By doing so, we produce novel human aging-related knowledge, which complements currently available knowledge about aging that has been obtained mainly by sequence alignment. We demonstrate significant similarity between topological and functional properties of our novel predictions and those of known aging-related genes. We are the first to use NA to learn more about aging.
authors.forename: Fazle Elahi
authors.initials: FE
authors.lastname: Faisal
authors.forename: Han
authors.initials: H
authors.lastname: Zhao
authors.forename: Tijana
authors.initials: T
authors.lastname: Milenkovic
mesh_terms: D000375:Aging / Q000235:genetics*; D000465:Algorithms; D000818:Animals; D029742:Caenorhabditis elegans Proteins; D019295:Computational Biology / Q000379:methods*; D029721:Drosophila Proteins; D006801:Humans; D060066:Protein Interaction Maps / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D029701:Saccharomyces cerevisiae Proteins