title: Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.
abstract: Integrative genomics predictors, which score highly in predicting bacterial essential genes, would be unfeasible in most species because the data sources are limited. We developed a universal approach and tool designated Geptop, based on orthology and phylogeny, to offer gene essentiality annotations. In a series of tests, our Geptop method yielded higher area under curve (AUC) scores in the receiver operating curves than the integrative approaches. In the ten-fold cross-validations among randomly upset samples, Geptop yielded an AUC of 0.918, and in the cross-organism predictions for 19 organisms Geptop yielded AUC scores between 0.569 and 0.959. A test applied to the very recently determined essential gene dataset from the Porphyromonas gingivalis, which belongs to a phylum different with all of the above 19 bacterial genomes, gave an AUC of 0.77. Therefore, Geptop can be applied to any bacterial species whose genome has been sequenced. Compared with the essential genes uniquely identified by the lethal screening, the essential genes predicted only by Gepop are associated with more protein-protein interactions, especially in the three bacteria with lower AUC scores (<0.7). This may further illustrate the reliability and feasibility of our method in some sense. The web server and standalone version of Geptop are available at http://cefg.uestc.edu.cn/geptop/ free of charge. The tool has been run on 968 bacterial genomes and the results are accessible at the website.
authors: Center of Bioinformatics and Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
authors: Wen
authors: W
authors: Wei
authors: Lu-Wen
authors: LW
authors: Ning
authors: Yuan-Nong
authors: YN
authors: Ye
authors: Feng-Biao
authors: FB
authors: Guo
mesh_terms: D019540:Area Under Curve; D001426:Bacterial Proteins / Q000235:genetics; D020043:Genes, Essential; D016680:Genome, Bacterial; D006090:Gram-Negative Bacteria / Q000145:classification / Q000235:genetics*; D006094:Gram-Positive Bacteria / Q000145:classification / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D025941:Protein Interaction Mapping; D012372:ROC Curve; D015203:Reproducibility of Results; D012984:Software
chemical_list: D001426:Bacterial Proteins
references: Mol Genet Genomics. 2008 Jan;279(1):87-94
references: 17943314
references: Bioinformatics. 2008 Sep 15;24(18):2086-93
references: 18718948
references: J Bacteriol. 2003 Oct;185(19):5673-84
references: 13129938
references: In Silico Biol. 2006;6(1-2):43-7
references: 16789912
references: Genet Mol Res. 2006 Mar 31;5(1):224-32
references: 16755513
references: Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):1009-14
references: 17215359
references: Cell. 2008 Jul 25;134(2):341-52
references: 18662548
references: J Drug Target. 2011 Jan;19(1):1-13
references: 20233082
references: In Silico Biol. 2006;6(6):485-93
references: 17518759
references: Science. 2001 Sep 21;293(5538):2266-9
references: 11567142
references: Mol Biol Evol. 2012 Jul;29(7):1703-6
references: 22319151
references: Trends Genet. 2004 Jun;20(6):227-31
references: 15145574
references: In Silico Biol. 2004;4(3):355-60
references: 15724285
references: Genome Res. 2006 Sep;16(9):1126-35
references: 16899653
references: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W174-8
references: 19398429
references: Nucleic Acids Res. 2011 Feb;39(3):795-807
references: 20870748
references: Bioinformatics. 2007 Jul 15;23(14):1866-7
references: 17496319
references: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7273-80
references: 19351897
references: Mol Microbiol. 2002 Mar;43(6):1387-400
references: 11952893
references: Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2833-8
references: 16477005
references: Microbiol Mol Biol Rev. 2004 Sep;68(3):518-37, table of contents
references: 15353568
references: BMC Bioinformatics. 2000;1:1
references: 11001586
references: Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
references: 3547335
references: Mol Syst Biol. 2006;2:2006.0008
references: 16738554
references: Trends Genet. 2013 May;29(5):273-9
references: 23219343
references: BMC Syst Biol. 2010 May 03;4:56
references: 20438628
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D455-8
references: 18974178
references: BMC Genomics. 2012 Oct 31;13:578
references: 23114059
references: Trends Cell Biol. 2011 Oct;21(10):562-8
references: 21889892
references: Methods. 2002 Feb;26(2):199-213
references: 12054897
references: Science. 1997 Oct 24;278(5338):631-7
references: 9381173
references: Methods Mol Biol. 2012;881:573-610
references: 22639227
references: Mol Syst Biol. 2008;4:174
references: 18319726
references: Mol Biol Evol. 2013 Jul;30(7):1559-62
references: 23533222
references: PLoS Comput Biol. 2007 Apr 20;3(4):e59
references: 17447836
references: Sci Rep. 2011;1:53
references: 22355572
references: Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10268-73
references: 8816789
references: Nucleic Acids Res. 2003 Nov 15;31(22):6570-7
references: 14602916
references: Trends Biotechnol. 2012 Nov;30(11):601-7
references: 22951051
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8
references: 21045058
references: PLoS Genet. 2012 Jun;8(6):e1002803
references: 22761596
references: Mol Biosyst. 2009 Dec;5(12):1672-8
references: 19452048
references: PLoS One. 2012;7(6):e40064
references: 22768221
references: Nat Rev Microbiol. 2003 Nov;1(2):127-36
references: 15035042
references: BMC Microbiol. 2009 Nov 28;9:243
references: 19943957
references: Mol Biosyst. 2010 Dec;6(12):2482-9
references: 20949199
references: Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):966-71
references: 11805338
references: Mol Biol Evol. 2004 Jan;21(1):108-16
references: 14595100
references: Mol Syst Biol. 2007;3:132
references: 17700540
references: In Silico Biol. 2009;9(4):225-31
references: 20109152
references: BMC Syst Biol. 2009 Oct 13;3:102
references: 19822021
references: In Silico Biol. 2008;8(3-4):331-8
references: 19032165
references: Bioinformatics. 2005 Mar 1;21(5):575-81
references: 15479713
references: Nat Genet. 2003 Aug;34(4):377-8
references: 12847524
references: Nat Methods. 2013 Mar;10(3):221-7
references: 23353650
references: Genome Res. 2005 Oct;15(10):1421-30
references: 16204195