Cargando…

CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms

Essential genes are key elements for organisms to maintain their living. Building databases that store essential genes in the form of homologous clusters, rather than storing them as a singleton, can provide more enlightening information such as the general essentiality of homologous genes in multip...

Descripción completa

Detalles Bibliográficos
Autores principales: Liu, Shuo, Wang, Shu-Xuan, Liu, Wei, Wang, Chen, Zhang, Fa-Zhan, Ye, Yuan-Nong, Wu, Candy-S, Zheng, Wen-Xin, Rao, Nini, Guo, Feng-Biao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7731928/
https://www.ncbi.nlm.nih.gov/pubmed/33306800
http://dx.doi.org/10.1093/database/baaa112
_version_ 1783621995710119936
author Liu, Shuo
Wang, Shu-Xuan
Liu, Wei
Wang, Chen
Zhang, Fa-Zhan
Ye, Yuan-Nong
Wu, Candy-S
Zheng, Wen-Xin
Rao, Nini
Guo, Feng-Biao
author_facet Liu, Shuo
Wang, Shu-Xuan
Liu, Wei
Wang, Chen
Zhang, Fa-Zhan
Ye, Yuan-Nong
Wu, Candy-S
Zheng, Wen-Xin
Rao, Nini
Guo, Feng-Biao
author_sort Liu, Shuo
collection PubMed
description Essential genes are key elements for organisms to maintain their living. Building databases that store essential genes in the form of homologous clusters, rather than storing them as a singleton, can provide more enlightening information such as the general essentiality of homologous genes in multiple organisms. In 2013, the first database to store prokaryotic essential genes in clusters, CEG (Clusters of Essential Genes), was constructed. Afterward, the amount of available data for essential genes increased by a factor >3 since the last revision. Herein, we updated CEG to version 2, including more prokaryotic essential genes (from 16 gene datasets to 29 gene datasets) and newly added eukaryotic essential genes (nine species), specifically the human essential genes of 12 cancer cell lines. For prokaryotes, information associated with drug targets, such as protein structure, ligand–protein interaction, virulence factor and matched drugs, is also provided. Finally, we provided the service of essential gene prediction for both prokaryotes and eukaryotes. We hope our updated database will benefit more researchers in drug targets and evolutionary genomics. Database URL: http://cefg.uestc.cn/ceg
format Online
Article
Text
id pubmed-7731928
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-77319282020-12-16 CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms Liu, Shuo Wang, Shu-Xuan Liu, Wei Wang, Chen Zhang, Fa-Zhan Ye, Yuan-Nong Wu, Candy-S Zheng, Wen-Xin Rao, Nini Guo, Feng-Biao Database (Oxford) Database Update Essential genes are key elements for organisms to maintain their living. Building databases that store essential genes in the form of homologous clusters, rather than storing them as a singleton, can provide more enlightening information such as the general essentiality of homologous genes in multiple organisms. In 2013, the first database to store prokaryotic essential genes in clusters, CEG (Clusters of Essential Genes), was constructed. Afterward, the amount of available data for essential genes increased by a factor >3 since the last revision. Herein, we updated CEG to version 2, including more prokaryotic essential genes (from 16 gene datasets to 29 gene datasets) and newly added eukaryotic essential genes (nine species), specifically the human essential genes of 12 cancer cell lines. For prokaryotes, information associated with drug targets, such as protein structure, ligand–protein interaction, virulence factor and matched drugs, is also provided. Finally, we provided the service of essential gene prediction for both prokaryotes and eukaryotes. We hope our updated database will benefit more researchers in drug targets and evolutionary genomics. Database URL: http://cefg.uestc.cn/ceg Oxford University Press 2020-12-11 /pmc/articles/PMC7731928/ /pubmed/33306800 http://dx.doi.org/10.1093/database/baaa112 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Update
Liu, Shuo
Wang, Shu-Xuan
Liu, Wei
Wang, Chen
Zhang, Fa-Zhan
Ye, Yuan-Nong
Wu, Candy-S
Zheng, Wen-Xin
Rao, Nini
Guo, Feng-Biao
CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
title CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
title_full CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
title_fullStr CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
title_full_unstemmed CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
title_short CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
title_sort ceg 2.0: an updated database of clusters of essential genes including eukaryotic organisms
topic Database Update
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7731928/
https://www.ncbi.nlm.nih.gov/pubmed/33306800
http://dx.doi.org/10.1093/database/baaa112
work_keys_str_mv AT liushuo ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT wangshuxuan ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT liuwei ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT wangchen ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT zhangfazhan ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT yeyuannong ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT wucandys ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT zhengwenxin ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT raonini ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms
AT guofengbiao ceg20anupdateddatabaseofclustersofessentialgenesincludingeukaryoticorganisms