title: Use of logic relationships to decipher protein network organization.
abstract: A major focus of genome research is to decipher the networks of molecular interactions that underlie cellular function. We describe a computational approach for identifying detailed relationships between proteins on the basis of genomic data. Logic analysis of phylogenetic profiles identifies triplets of proteins whose presence or absence obey certain logic relationships. For example, protein C may be present in a genome only if proteins A and B are both present. The method reveals many previously unidentified higher order relationships. These relationships illustrate the complexities that arise in cellular networks because of branching and alternate pathways, and they also facilitate assignment of cellular functions to uncharacterized proteins.
authors.affiliation: Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Bowers
authors.forename: Shawn J
authors.initials: SJ
authors.lastname: Cokus
authors.forename: David
authors.initials: D
authors.lastname: Eisenberg
authors.forename: Todd O
authors.initials: TO
authors.lastname: Yeates
mesh_terms: D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000032:analysis* / Q000737:chemistry / Q000502:physiology*; D019295:Computational Biology; D016678:Genome; D016680:Genome, Bacterial; D008128:Logic; D009068:Movement; D010802:Phylogeny; D040081:Protein Array Analysis; D025941:Protein Interaction Mapping; D011506:Proteins / Q000032:analysis* / Q000235:genetics / Q000502:physiology*; D012765:Shikimic Acid / Q000378:metabolism; D014774:Virulence
chemical_list: D001426:Bacterial Proteins; D011506:Proteins; D012765:Shikimic Acid