title: Finding New Order in Biological Functions from the Network Structure of Gene Annotations.
abstract: The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to one another. These term-term relationships encode how scientists conceive the organization of biological functions, and they take the form of a directed acyclic graph (DAG). Here, we propose that the network structure of gene-term annotations made using GO can be employed to establish an alternative approach for grouping functional terms that captures intrinsic functional relationships that are not evident in the hierarchical structure established in the GO DAG. Instead of relying on an externally defined organization for biological functions, our approach connects biological functions together if they are performed by the same genes, as indicated in a compendium of gene annotation data from numerous different sources. We show that grouping terms by this alternate scheme provides a new framework with which to describe and predict the functions of experimentally identified sets of genes.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America.|Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.|Physics Department, University of Maryland, College Park, Maryland, United States of America.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Glass
authors.affiliation: Physics Department, University of Maryland, College Park, Maryland, United States of America.|Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.|Santa Fe Institute, Santa Fe, New Mexico, United States of America.
authors.forename: Michelle
authors.initials: M
authors.lastname: Girvan
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D005796:Genes / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D058977:Molecular Sequence Annotation / Q000379:methods*; D009369:Neoplasms / Q000235:genetics