Literature DB >> 14681410

DEG: a database of essential genes.

Ren Zhang1, Hong-Yu Ou, Chun-Ting Zhang.   

Abstract

Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available. The functions encoded by essential genes are considered a foundation of life and therefore are likely to be common to all cells. Users can BLAST the query sequences against DEG. If homologous genes are found, it is possible that the queried genes are also essential. Users can search for essential genes by their function or name. Users can also browse and extract all the records in DEG. Essential gene products comprise excellent targets for antibacterial drugs. Analysis of essential genes could help to answer the question of what are the basic functions necessary to support cellular life. DEG is freely accessible from the website http://tubic.tju.edu.cn/deg/.

Mesh：

Year:  2004        PMID： 14681410      PMCID： PMC308758          DOI： 10.1093/nar/gkh024

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  10 in total

1.  Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA.

Authors:  Y Ji; B Zhang; S F Van; P Warren; G Woodnutt; M K Burnham; M Rosenberg
Journal:  Science       Date:  2001-09-21       Impact factor: 47.728

2.  Essential Bacillus subtilis genes.

Authors:  K Kobayashi; S D Ehrlich; A Albertini; G Amati; K K Andersen; M Arnaud; K Asai; S Ashikaga; S Aymerich; P Bessieres; F Boland; S C Brignell; S Bron; K Bunai; J Chapuis; L C Christiansen; A Danchin; M Débarbouille; E Dervyn; E Deuerling; K Devine; S K Devine; O Dreesen; J Errington; S Fillinger; S J Foster; Y Fujita; A Galizzi; R Gardan; C Eschevins; T Fukushima; K Haga; C R Harwood; M Hecker; D Hosoya; M F Hullo; H Kakeshita; D Karamata; Y Kasahara; F Kawamura; K Koga; P Koski; R Kuwana; D Imamura; M Ishimaru; S Ishikawa; I Ishio; D Le Coq; A Masson; C Mauël; R Meima; R P Mellado; A Moir; S Moriya; E Nagakawa; H Nanamiya; S Nakai; P Nygaard; M Ogura; T Ohanan; M O'Reilly; M O'Rourke; Z Pragai; H M Pooley; G Rapoport; J P Rawlins; L A Rivas; C Rivolta; A Sadaie; Y Sadaie; M Sarvas; T Sato; H H Saxild; E Scanlan; W Schumann; J F M L Seegers; J Sekiguchi; A Sekowska; S J Séror; M Simon; P Stragier; R Studer; H Takamatsu; T Tanaka; M Takeuchi; H B Thomaides; V Vagner; J M van Dijl; K Watabe; A Wipat; H Yamamoto; M Yamamoto; Y Yamamoto; K Yamane; K Yata; K Yoshida; H Yoshikawa; U Zuber; N Ogasawara
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-07       Impact factor: 11.205

3.  Global transposon mutagenesis and a minimal Mycoplasma genome.

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Journal:  Science       Date:  1999-12-10       Impact factor: 47.728

4.  A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae.

Authors:  Brian J Akerley; Eric J Rubin; Veronica L Novick; Kensey Amaya; Nicholas Judson; John J Mekalanos
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-22       Impact factor: 11.205

5.  MIPS: a database for genomes and protein sequences.

Authors:  H W Mewes; D Frishman; U Güldener; G Mannhaupt; K Mayer; M Mokrejs; B Morgenstern; M Münsterkötter; S Rudd; B Weil
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes.

Authors:  N Judson; J J Mekalanos
Journal:  Nat Biotechnol       Date:  2000-07       Impact factor: 54.908

7.  Functional analysis of the genes of yeast chromosome V by genetic footprinting.

Authors:  V Smith; K N Chou; D Lashkari; D Botstein; P O Brown
Journal:  Science       Date:  1996-12-20       Impact factor: 47.728

8.  A minimal gene set for cellular life derived by comparison of complete bacterial genomes.

Authors:  A R Mushegian; E V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  1996-09-17       Impact factor: 11.205

9.  An estimation of minimal genome size required for life.

Authors:  M Itaya
Journal:  FEBS Lett       Date:  1995-04-10       Impact factor: 4.124

10.  The complexity of simplicity.

Authors:  S N Peterson; C M Fraser
Journal:  Genome Biol       Date:  2001-02-08       Impact factor: 13.583
  10 in total
  142 in total

Review 1.  'Conserved hypothetical' proteins: prioritization of targets for experimental study.

Authors:  Michael Y Galperin; Eugene V Koonin
Journal:  Nucleic Acids Res       Date:  2004-10-12       Impact factor: 16.971

2.  High-throughput generation, optimization and analysis of genome-scale metabolic models.

Authors:  Christopher S Henry; Matthew DeJongh; Aaron A Best; Paul M Frybarger; Ben Linsay; Rick L Stevens
Journal:  Nat Biotechnol       Date:  2010-08-29       Impact factor: 54.908

3.  Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11.

Authors:  Shakhinur Islam Mondal; Zabed Mahmud; Montasir Elahi; Arzuba Akter; Nurnabi Azad Jewel; Md Muzahidul Islam; Sabiha Ferdous; Taisei Kikuchi
Journal:  In Silico Pharmacol       Date:  2017-04-11

Review 4.  Resistance to antibiotics targeted to the bacterial cell wall.

Authors:  I Nikolaidis; S Favini-Stabile; A Dessen
Journal:  Protein Sci       Date:  2014-01-17       Impact factor: 6.725

5.  Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli.

Authors:  Seung Min Yoo; Dokyun Na; Sang Yup Lee
Journal:  Nat Protoc       Date:  2013-08-08       Impact factor: 13.491

6.  Putative vaccine candidates and drug targets identified by reverse vaccinology and subtractive genomics approaches to control Haemophilus ducreyi, the causative agent of chancroid.

Authors:  Alissa de Sarom; Arun Kumar Jaiswal; Sandeep Tiwari; Letícia de Castro Oliveira; Debmalya Barh; Vasco Azevedo; Carlo Jose Oliveira; Siomar de Castro Soares
Journal:  J R Soc Interface       Date:  2018-05       Impact factor: 4.118

7.  Large-scale transposon mutagenesis of Mycoplasma pulmonis.

Authors:  Christopher T French; Ping Lao; Ann E Loraine; Brian T Matthews; Huilan Yu; Kevin Dybvig
Journal:  Mol Microbiol       Date:  2008-04-28       Impact factor: 3.501

8.  FLP-FRT-based method to obtain unmarked deletions of CHU_3237 (porU) and large genomic fragments of Cytophaga hutchinsonii.

Authors:  Ying Wang; Zhiquan Wang; Jing Cao; Zhiwei Guan; Xuemei Lu
Journal:  Appl Environ Microbiol       Date:  2014-07-25       Impact factor: 4.792

9.  The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon.

Authors:  Ruben E Valas; Philip E Bourne
Journal:  Biol Direct       Date:  2011-02-28       Impact factor: 4.540

10.  The protein interaction network of bacteriophage lambda with its host, Escherichia coli.

Authors:  Sonja Blasche; Stefan Wuchty; Seesandra V Rajagopala; Peter Uetz
Journal:  J Virol       Date:  2013-09-18       Impact factor: 5.103
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