OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines
| Autor: | Robin B. Gasser, Puzi Jiang, Neil D. Young, Túlio de Lima Campos, Xing-Ming Zhao, Xiaowen Hao, Sanathoi Gurumayum, Peer Bork, Pasi K. Korhonen, Wei-Hua Chen, Li-Jie He |
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| Rok vydání: | 2020 |
| Předmět: |
AcademicSubjects/SCI00010
Genomics Biology computer.software_genre Genome RNA interference Cell Line Tumor Neoplasms Databases Genetic Gene expression Genetics Database Issue Animals Data Mining Humans Genetic Predisposition to Disease Gene Internet Genes Essential Database Computational Biology Oncogenes Methylation Drug development Ogee RNA Interference CRISPR-Cas Systems computer |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkaa884 |
| Popis: | OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info. |
| Databáze: | OpenAIRE |
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