title: Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli.
abstract: BACKGROUND
  The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli.
  
  
  RESULTS
  We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses.
  
  
  BACKGROUND
  gary.bader@utoronto.ca; mohan.babu@uregina.ca
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: James
authors.initials: J
authors.lastname: Vlasblom
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Khalid
authors.initials: K
authors.lastname: Zuberi
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Harold
authors.initials: H
authors.lastname: Rodriguez
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Roland
authors.initials: R
authors.lastname: Arnold
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Alla
authors.initials: A
authors.lastname: Gagarinova
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Viktor
authors.initials: V
authors.lastname: Deineko
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Ashwani
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Elisa
authors.initials: E
authors.lastname: Leung
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Kamran
authors.initials: K
authors.lastname: Rizzolo
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Bahram
authors.initials: B
authors.lastname: Samanfar
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Luke
authors.initials: L
authors.lastname: Chang
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Sadhna
authors.initials: S
authors.lastname: Phanse
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Ashkan
authors.initials: A
authors.lastname: Golshani
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Jack F
authors.initials: JF
authors.lastname: Greenblatt
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Walid A
authors.initials: WA
authors.lastname: Houry
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Quaid
authors.initials: Q
authors.lastname: Morris
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, Univ
authors.forename: Gary
authors.initials: G
authors.lastname: Bader
authors.affiliation: Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
authors.forename: Mohan
authors.initials: M
authors.lastname: Babu
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D053263:Gene Regulatory Networks; D010641:Phenotype; D012984:Software
chemical_list: D029968:Escherichia coli Proteins