Novel function discovery with GeneMANIA: A new integrated resource for gene function prediction in Escherichia coli

Bioinformatics

Volumn 31, Issue 3, 2015, Pages 306-310

  Vlasblom, James ^a   Zuberi, Khalid ^b   Rodriguez, Harold ^b   Arnold, Roland ^b   Gagarinova, Alla ^b   Deineko, Viktor ^a   Kumar, Ashwani ^a   Leung, Elisa ^b   Rizzolo, Kamran ^b   Samanfar, Bahram ^c   Chang, Luke ^b   Phanse, Sadhna ^a   Golshani, Ashkan ^c   Greenblatt, Jack F ^b   Houry, Walid A ^b   Emili, Andrew ^b   Morris, Quaid ^b   Bader, Gary ^b,d   Babu, Mohan ^a  

^a UNIVERSITY OF REGINA   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c CARLETON UNIVERSITY   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

ESCHERICHIA COLI PROTEIN;

ALGORITHM; COMPUTER PROGRAM; ESCHERICHIA COLI; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PHENOTYPE;

ALGORITHMS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE REGULATORY NETWORKS; PHENOTYPE; SOFTWARE;

EID: 84929143148     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu671     Document Type: Article

References (28)

1. Alexeyenko, A. and Sonnhammer, E.L. (2009) Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res., 19, 1107-1116.
2. Andres Leon, E. et al. (2009) EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res., 37, D629-D635.
3. Arifuzzaman, M. et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res., 16, 686-691.
4. Baba, T. et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol., 2, 2006.0008.
5. Babu, M. et al. (2011a) Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation. PLoS One, 6, e18510.
6. Babu, M. et al. (2011b) Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet., 7, e1002377.
7. Babu, M. et al. (2014) Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet., 10, e1004120.
8. Campbell, T.L. and Brown, E.D. (2008) Genetic interaction screens with ordered overexpression and deletion clone sets implicate the Escherichia coli GTPase YjeQ in late ribosome biogenesis. J. Bacteriol., 190, 2537-2545.
9. Flynn, J.M. et al. (2003) Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell, 11, 671-683.
10. Franceschini, A. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res., 41, D808-815.
11. Hu, P. et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol., 7, e1000096.
12. Jiang, M. et al. (2007) Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J. Bacteriol., 189, 3434-3444.
13. Kohanski, M.A. et al. (2007) A common mechanism of cellular death induced by bactericidal antibiotics. Cell, 130, 797-810.
14. Lotia, S. et al. (2013) Cytoscape app store. Bioinformatics, 29, 1350-1351.
15. Ma, Q. and Wood, T.K. (2009) OmpA influences Escherichia coli biofilm formation by repressing cellulose production through the CpxRA two-component system. Environ. Microbiol., 11, 2735-2746.
16. Montojo, J. (2014) Network assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. Frontiers Genet., 5, 123.
17. Montojo, J. et al. (2010) GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics, 26, 2927-2928.
18. Mostafavi, S. et al. (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol., 9(Suppl 1), S4.
19. Nichols, R.J. et al. (2011) Phenotypic landscape of a bacterial cell. Cell, 144, 143-156.
20. O'Connor, M. et al. (1992) A ribosomal ambiguity mutation in the 530 loop of E. coli 16S rRNA. Nucleic Acids Res., 20, 4221-4227.
21. O'Toole, G.A. et al. (1999) Genetic approaches to study of biofilms. Methods Enzymol., 310, 91-109.
22. Oliver, S. (2000) Guilt-by-association goes global. Nature, 403, 601-603.
23. Rajagopala, S.V. et al. (2014) The binary protein-protein interaction landscape of Escherichia coli. Nat. Biotechnol., 32, 285-290.
24. Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
25. Thompson, J. et al. (2002) The protein synthesis inhibitors, oxazolidinones and chloramphenicol, cause extensive translational inaccuracy in vivo. J. Mol. Biol., 322, 273-279.
26. Typas, A. et al. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat. Methods, 5, 781-787.
27. Wong, K.S. et al. (2014) The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli. PLoS One, 9, e85529.
28. Zuberi, K. et al. (2013) GeneMANIA prediction server 2013 update. Nucleic Acids Res., 41, W115-W122.