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    OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.

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    Author
    Gurumayum, S; Jiang, P; Hao, X; Campos, TL; Young, ND; Korhonen, PK; Gasser, RB; Bork, P; Zhao, X-M; He, L-J; ...
    Date
    2021-01-08
    Source Title
    Nucleic Acids Research
    Publisher
    Oxford University Press (OUP)
    University of Melbourne Author/s
    Gasser, Robin; Campos, Tulio; De Lima Campos, Túlio
    Affiliation
    Veterinary Biosciences
    Metadata
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    Document Type
    Journal Article
    Citations
    Gurumayum, S., Jiang, P., Hao, X., Campos, T. L., Young, N. D., Korhonen, P. K., Gasser, R. B., Bork, P., Zhao, X. -M., He, L. -J. & Chen, W. -H. (2021). OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.. Nucleic Acids Res, 49 (D1), pp.D998-D1003. https://doi.org/10.1093/nar/gkaa884.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/252620
    DOI
    10.1093/nar/gkaa884
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779042
    Abstract
    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.

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