DEG

The essential genes in DEG are extracted from the following papers:

Akerley, B. J., Rubin, E. J., Novick, V. L., Amaya K., Judson N. et al., 2002 A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc Natl Acad Sci U S A 99: 966-971. [PubMed]

Hutchison, C. A., Peterson, S. N., Gill, S. R. , Cline, R. T., White, O. et al., 1999 Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286: 2165-2169. [PubMed]

Ji, Y., Zhang, B., Van, S. F., Horn, Warren, P. et al., 2001 Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 293: 2266-2269. [PubMed]

Judson, N., Mekalanos, J. J., 2000 TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes. Nat Biotechnol 18: 740-745. [PubMed]

Kobayashi, K., Ehrlich, S. D., Albertini, A., Amati G., Andersen, K. K. et al., 2003 Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100: 4678-4683. [PubMed]

Forsyth, R. A., Haselbeck, R. J. et al., 2002 A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol. 43:1387-400. [PubMed]

Thanassi, J.A., Hartman-Neumann, S.L. et al., 2002 Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res. 30:3152-62. [PubMed]

Salama, N.R., Shepherd, B., Falkow, S., 2004 Global Transposon Mutagenesis and Essential Gene Analysis of Helicobacter pylori. J Bacteriol. 186:7926-7935. [PubMed]

The essential genes in E. coli genome were extracted from the web site, http://www.shigen.nig.ac.jp/ecoli/pec/index.jsp, in which the essential genes are collected from a large number of related references.

The essential genes in yeast genome were extracted from the yeast genome database (http://mips.gsf.de/genre/proj/yeast/), which is maintained by the Munich Information Center for Protein Sequences.

Glass, J.I., Assad-Garcia, N., Alperovich, N. et al., 2006 Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103: 425-30. [PubMed]

Gerdes, S.Y., Scholle, M.D., Campbell, J.W. et al., 2003 Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 185(19):5673-84. [PubMed]

Sassetti, C.M., Boyd, D.H., Rubin, E.J., 2003 Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol. 48(1):77-84. [PubMed]

Knuth, K., Niesalla, H., Hueck, C.J., Fuchs, T.M., 2004 Large-scale identification of essential Salmonella genes by trapping lethal insertions. Mol Microbiol. 51(6):1729-44. [PubMed]

Ko, K.S., Lee, J.Y., Song, J.H. et al., 2006 Screening of Essential Genes in Staphylococcus aureus N315 Using Comparative Genomics and Allelic Replacement Mutagenesis. J. Microbiol. Biotechnol. 16(4):623-632.

Song, J.H., Ko, K.S., Lee, J.Y. et al., 2005 Identification of Essential Genes in Streptococcus pneumoniae by Allelic Replacement Mutagenesis. Mol Cells. 19(3):365-74. [PubMed]

Gallagher LA, Ramage E, Jacobs MA, et al (2007). A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate. Proc Natl Acad Sci U S A, 104:1009-14. [PubMed]

de Berardinis V, Vallenet D, Castelli V, et al (2008). A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol. [PubMed]

French CT, Lao P, Loraine AE, et al (2008). Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol. [PubMed]

Baba T, Ara T, Hasegawa M, et al (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. [PubMed]

Liberati NT, Urbach JM, Miyata S, et al (2006). An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc Natl Acad Sci U S A, 103:2833-8. [PubMed]

Kamath RS, Fraser AG, Dong Y, et al (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421:231-7. [PubMed]

Meinke D, Muralla R, Sweeney C, et al(2008). Identifying essential genes in Arabidopsis thaliana. Trends Plant Sci, 13:483-91.[PubMed]

Amsterdam A, Nissen RM, Sun Z, et al (2004). Identification of 315 genes essential for early zebrafish development. Proc Natl Acad Sci U S A, 101:12792-7. [PubMed]

Liao BY, Zhang J (2007). Mouse duplicate genes are as essential as singletons. Trends Genet, 23:378-81. [PubMed]

Liao BY, Zhang J (2008). Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A, 105:6987-92. [PubMed]

Spradling AC, Stern D, Beaton A, et al (1999). The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics, 153:135-77. [PubMed]

Giaever G, Chu AM, Ni L, et al (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418:387-91. [PubMed]

Langridge GC, Phan MD, Turner DJ, et al (2009). Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res, 19:2308-16. [PubMed]

Chaudhuri RR, Allen AG, Owen PJ, et al (2009). Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH). BMC Genomics, 10:291. [PubMed]

Hu W, Sillaots S, Lemieux S, et al (2007). Essential gene identification and drug target prioritization in Aspergillus fumigatus. PLoS Pathog, 3:e24. [PubMed]

Cameron DE, Urbach MJ, Mekalanos JJ (2008). A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. PNAS, 105(25):8736-8741. [PubMed]

Christen B, Abeliuk E, Collier JM, et al (2011). The essential genome of a bacterium. Molecular Systems Biology, 7:528. [PubMed]

Xu P, Ge XC, Chen L, et al (2011). Genome-wide essential gene identification in Streptococcus sanguinis, Sci. Rep. 1, 125; DOI:10.1038/srep00125. [PubMed]

Goodman Al, et al (2009). Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat. Cell Host & Microbe, 6: 279-289. [PubMed]

Klein BA, et al (2012). Identification of essential genes of the periodontal pathogen Porphyromonas. BMC Genomics, 13: 578. [PubMed]

Baugh, Loren, et al. "Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome." PloS one 8.1 (2013): e53851. [PubMed]