ArticleBioinformatics (Oxford, England)2015
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli.
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Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29citing papers in PubMed
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Who cites it
29 citing papers in PubMed.
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- Diagnostic Value, Prognostic Value, and Immune Infiltration ofFrontiers in oncology · 2022Article
- An immunogenic cell death-associated classification predictions are important for breast invasive carcinoma prognosis and immunotherapy.Frontiers in genetics · 2022Article
- Identification and Verification of Potential Biomarkers in Gastric Cancer By Integrated Bioinformatic Analysis.Frontiers in genetics · 2022Article
- Comprehensive Analysis ofLife (Basel, Switzerland) · 2021Article
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- Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes.MicrobiologyOpen · 2019Article
- Integrated entropy-based approach for analyzing exons and introns in DNA sequences.BMC bioinformatics · 2019Article
- Gene co-expression analysis for functional classification and gene-disease predictions.Briefings in bioinformatics · 2018Article
- GeneMANIA update 2018.Nucleic acids research · 2018Article
- Uncovering the genetic lesions underlying the most severe form of Hirschsprung disease by whole-genome sequencing.European journal of human genetics : EJHG · 2018Article
- Effects of donor age on human adipose-derived adherent stromal cells under oxidative stress conditions.The Journal of international medical research · 2018Article
- Global landscape of cell envelope protein complexes in Escherichia coli.Nature biotechnology · 2018Article
- Can Peripheral Blood-Derived Gene Expressions Characterize Individuals at Ultra-high Risk for Psychosis?Computational psychiatry (Cambridge, Mass.) · 2017Article
- Identification of Linkages between EDCs in Personal Care Products and Breast Cancer through Data Integration Combined with Gene Network Analysis.International journal of environmental research and public health · 2017Article
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Authors and funding
19 authors.
James VlasblomDepartment 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.
Khalid ZuberiDepartment 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.
Harold RodriguezDepartment 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.
Roland ArnoldDepartment 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.
Alla GagarinovaDepartment 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.
Viktor DeinekoDepartment 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.
Ashwani KumarDepartment 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.
Elisa LeungDepartment 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.
Kamran RizzoloDepartment 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.
Bahram SamanfarDepartment 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.
Luke ChangDepartment 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.
Sadhna PhanseDepartment 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.
Ashkan GolshaniDepartment 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.
Jack F GreenblattDepartment 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.
Walid A HouryDepartment 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.
Andrew EmiliDepartment 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.
Quaid MorrisDepartment 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.
Gary BaderDepartment 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
Mohan BabuDepartment 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.
Funding
TR&D 3 - Network Guided Machine LearningP41GM103504 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2012 to 2024
$17.3MIntegrative functional mapping of the Escherichia coli membrane interactomeR01GM109895 · NIGMS · VIRGINIA COMMONWEALTH UNIVERSITY · PI SAIER, MILTON H., UETZ, PETER HANS · 2014 to 2017
$1.1MCIHR MOP-130374CIHR MOP-82852NIGMS NIH HHS P41 GM103504NIGMS NIH HHS R01 GM109895
Abstract
motivationThe 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.
resultsWe 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. CONTACT: gary.bader@utoronto.ca; mohan.babu@uregina.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
AlgorithmsGene Regulatory NetworksSoftwareEscherichia coliEscherichia coli ProteinsPhenotypeEscherichia coli Proteins
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