Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

DEG (Database of Essential Genes)

General information

Description: DEG hosts records of currently available essential genomic elements,such as protein-coding genes and non-coding RNAs,among bacteria,archaea and eukaryotes.
Year founded: 2004
Last update: 2017-12-18
Version: v15.2
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
Data object:
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Keywords:

Contact information

University/Institution: Tianjin University
Address: Department of Physics,Tianjin University,Tianjin 300072,PeopleÕs Republic of China
City: Tianjin
Province/State:
Country/Region: China
Contact name (PI/Team): Ren Zhang
Contact email (PI/Helpdesk): rzhang@med.wayne.edu

Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2018-05-10]
Jian SA [2016-04-04]
Zhang Zhang [2015-12-30]
Jian SA [2015-12-06]
Jian SA [2015-07-01]
Jian SA [2015-06-26]

Ranking

All databases:
229/4516 (94.951%)
Gene genome and annotation:
88/1203 (92.768%)
229
Total Rank
496
Citations
31
z-index

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Publications

25636622
Gene essentiality analysis based on DEG 10, an updated database of essential genes. [PMID: 25636622]
Gao F, Luo H, Zhang CT, Zhang R.

The database of essential genes (DEG, available at http://www.essentialgene.org), constructed in 2003, has been timely updated to harbor essential-gene records of bacteria, archaea, and eukaryotes. DEG 10, the current release, includes not only essential protein-coding genes determined by genome-wide gene essentiality screens but also essential noncoding RNAs, promoters, regulatory sequences, and replication origins. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools. Based on the analysis of DEG 10, we show that the percentage of essential genes in bacterial genomes exhibits an exponential decay with increasing genome sizes. The functions, ATP binding (GO:0005524), GTP binding (GO:0005525), and DNA-directed RNA polymerase activity (GO:0003899), are likely required for organisms across life domains.

Methods Mol Biol. 2015:1279() | 12 Citations (from Europe PMC, 2020-01-25)
24243843
DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. [PMID: 24243843]
Luo H, Lin Y, Gao F, Zhang CT, Zhang R.

The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. DEG 10, a new release of the Database of Essential Genes (available at http://www.essentialgene.org), has been developed to accommodate these quantitative and qualitative advancements. In addition to increasing the number of bacterial and archaeal essential genes determined by genome-wide gene essentiality screens, DEG 10 also harbors essential noncoding RNAs, promoters, regulatory sequences and replication origins. These essential genomic elements are determined not only in vitro, but also in vivo, under diverse conditions including those for survival, pathogenesis and antibiotic resistance. We have developed customizable BLAST tools that allow users to perform species- and experiment-specific BLAST searches for a single gene, a list of genes, annotated or unannotated genomes. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools.

Nucleic Acids Res. 2014:42(Database issue) | 152 Citations (from Europe PMC, 2020-01-25)
18974178
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. [PMID: 18974178]
Zhang R, Lin Y.

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology. Five years after we constructed DEG, a database of essential genes, DEG 5.0 has significant advances over the 2004 version in both the number of essential genes and the number of organisms in which these genes are determined. The number of prokaryotic essential genes in DEG has increased about 10-fold, mainly owing to genome-wide gene essentiality screens performed in a wide range of bacteria. The number of eukaryotic essential genes has increased more than 5-fold, because DEG 1.0 only had yeast ones, but DEG 5.0 also has those in humans, mice, worms, fruit flies, zebrafish and the plant Arabidopsis thaliana. These updates not only represent significant advances of DEG, but also represent the rapid progress of the essential-gene field. DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Nucleic Acids Res. 2009:37(Database issue) | 192 Citations (from Europe PMC, 2020-01-25)
14681410
DEG: a database of essential genes. [PMID: 14681410]
Zhang R, Ou HY, Zhang CT.

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/.

Nucleic Acids Res. 2004:32(Database issue) | 140 Citations (from Europe PMC, 2020-01-25)