DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

By Ren Zhang, Yan Lin. Nucleic Acids Res., 2008

509 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2dd7b6cfcffd83ce52695b2b984e7223517486f5

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Citations in the corpus

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements (2013, background): “Compared to DEG 5 (19), the number of bacteria with saturated genome-wide gene essentiality screens has nearly tripled in DEG 10, which has data for 31 bacteria.”
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs (2012, methodology): “For bacteria, gene annotations are extended with phenotype data from EcoGene (51) for Escherichia coli genes and from the Database of Essential Genes (52) which covers 16 bacteria including E. coli, Haemophilus influenza and Mycobacterium tuberculosis (Table 1).”
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis (2010, result): “The orthologues of some of the genes — ArgR, lrp/AsnC, SigH — were also found to be essential for growth in well studied organisms like E. coli and Bacillus subtilis using the Database of Essential Genes (33), which further supports our results.”
Vital nodes identification in complex networks (2016, result): “spammers, and 2 times for the case without spammers. 10.2. Predicting essential proteins Identiﬁcation of essential proteins can help us in understanding the basic requirements to sustain a life form [335]. It also plays a signiﬁcant role in the emerging ﬁeld of synthetic biology that aims to create”