Nucleic Acids Research Advance Access originally published online on October 16, 2007
Nucleic Acids Research 2008 36(Database issue):D632-D636; doi:10.1093/nar/gkm807
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Nucleic Acids Research, 2008, Vol. 36, Database issue D632-D636
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
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Bacteriome.org—an integrated protein interaction database for E. coli
1Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada, 2Department of Molecular Biology and Biochemistry, University of Malaga, 29071 Malaga, Spain, 3Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada, 4Life Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS84R0171, Berkeley, CA 94720, USA, 5Department of Molecular and Medical Genetics and 6Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A1, Canada
* To whom correspondence should be addressed. Tel: +1 416 813 5746; Fax: +1 416 813 4931; Email: jparkin{at}sickkids.ca
Received August 15, 2007. Revised September 14, 2007. Accepted September 17, 2007.
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.
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