DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools.
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools.
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DEG 15，基本基因数据库的更新，包括内置分析工具
DOI：
10.1093/nar/gkaa917
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Zhang R
中科院分区：
文献类型：
--
作者：
Luo H;Lin Y;Liu T;Lai FL;Zhang CT;Gao F;Zhang R
摘要必需基因是指生物体在特定条件下生存所必需的基因。对细菌最小基因组的研究已经阐明了维持生命的基本细胞过程。在过去的五年中，在识别人类必需基因方面取得了重大进展，这主要归功于CRISPR/Cas9在各种类型的人类细胞中的成功使用。DEG 15是必需基因数据库（www.essentialgene.org）的新版本，与DEG 10相比，它提供了重大进步。具体来说，真核生物的必需基因数量增加了四倍多，原核生物的必需基因数量增加了一倍多。值得注意的是，人类必需基因的数量增加了十倍以上。此外，我们还开发了内置的分析模块，用户可以通过这些模块进行各种分析，例如细菌前导链和滞后链之间的必要基因分布，亚细胞定位分布，基因本体和KEGG途径的富集分析，以及生成维恩图来比较和对比实验之间的基因集。此外，该数据库提供了可定制的BLAST工具，用于执行物种和实验特定的BLAST搜索。因此，DEG全面地包含了原核生物和真核生物中更新的人类策划的必需基因记录，并内置了增强必需基因分析的工具。
Abstract Essential genes refer to genes that are required by an organism to survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes that sustain life. The past five years have seen a significant progress in identifying human essential genes, primarily due to the successful use of CRISPR/Cas9 in various types of human cells. DEG 15, a new release of the Database of Essential Genes (www.essentialgene.org), has provided major advancements, compared to DEG 10. Specifically, the number of eukaryotic essential genes has increased by more than fourfold, and that of prokaryotic ones has more than doubled. Of note, the human essential-gene number has increased by more than tenfold. Moreover, we have developed built-in analysis modules by which users can perform various analyses, such as essential-gene distributions between bacterial leading and lagging strands, sub-cellular localization distribution, enrichment analysis of gene ontology and KEGG pathways, and generation of Venn diagrams to compare and contrast gene sets between experiments. Additionally, the database offers customizable BLAST tools for performing species- and experiment-specific BLAST searches. Therefore, DEG comprehensively harbors updated human-curated essential-gene records among prokaryotes and eukaryotes with built-in tools to enhance essential-gene analysis.
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影响因子：
5.2
作者：
Carda-Diéguez M;Silva-Hernández FX;Hubbard TP;Chao MC;Waldor MK;Amaro C
通讯作者：
Amaro C
影响因子：
9.9
作者：
通讯作者：
--
影响因子：
9.9
作者：
de Berardinis, Veronique;Vallenet, David;Castelli, Vanina;Besnard, Marielle;Pinet, Agnes;Cruaud, Corinne;Samair, Sumitta;Lechaplais, Christophe;Gyapay, Gabor;Richez, Celine;Durot, Maxime;Kreimeyer, Annett;Le Fevre, Francois;Schaechter, Vincent;Pezo, Valerie;Doering, Volker;Scarpelli, Claude;Medigue, Claudine;Cohen, Georges N.;Marliere, Philippe;Salanoubat, Marcel;Weissenbach, Jean
通讯作者：
Weissenbach, Jean
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
影响因子：
4.4
作者：
Chaudhuri RR;Allen AG;Owen PJ;Shalom G;Stone K;Harrison M;Burgis TA;Lockyer M;Garcia-Lara J;Foster SJ;Pleasance SJ;Peters SE;Maskell DJ;Charles IG
通讯作者：
Charles IG