title: Bacteriome.org--an integrated protein interaction database for E. coli.
abstract: High throughput methods are increasingly being used to examine the functions and interactions of gene products on a genome-scale. These include systematic large-scale proteomic studies of protein complexes and protein-protein interaction networks, functional genomic studies examining patterns of gene expression and comparative genomics studies examining patterns of conservation. Since these datasets offer different yet highly complementary perspectives on cell behavior it is expected that integration of these datasets will lead to conceptual advances in our understanding of the fundamental design and evolutionary principles that underlie the organization and function of proteins within biochemical pathways. Here we present Bacteriome.org, a resource that combines locally generated interaction and evolutionary datasets with a previously generated knowledgebase, to provide an integrated view of the Escherichia coli interactome. Tools are provided which allow the user to select and visualize functional, evolutionary and structural relationships between groups of interacting proteins and to focus on genes of interest. Currently the database contains three interaction datasets: a functional dataset consisting of 3989 interactions between 1927 proteins; a 'core' high quality experimental dataset of 4863 interactions between 1100 proteins and an 'extended' experimental dataset of 9860 interactions between 2131 proteins. Bacteriome.org is available online at http://www.bacteriome.org.
authors.affiliation: Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada.
authors.forename: Chong
authors.initials: C
authors.lastname: Su
authors.forename: Jose M
authors.initials: JM
authors.lastname: Peregrin-Alvarez
authors.forename: Gareth
authors.initials: G
authors.lastname: Butland
authors.forename: Sadhna
authors.initials: S
authors.lastname: Phanse
authors.forename: Vincent
authors.initials: V
authors.lastname: Fong
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
mesh_terms: D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D020407:Internet; D025941:Protein Interaction Mapping; D040901:Proteomics; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D029968:Escherichia coli Proteins