ArticleNucleic acids research2021
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it, 93 citations in OpenAlex.
- Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models.Database : the journal of biological databases and curation · 2025Pooled it
- ELE: Estimating tissue-specific long noncoding RNA gene essentiality using graph neural networks.Quantitative biology (Beijing, China) · 2026Article
- Universal and Lineage-Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms.Proteins · 2026Article
- Essentiality-driven prediction of anticancer drug responses in preclinical and clinical contexts.iScience · 2026Article
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- Unveiling Putative Functions of Burkholderia pseudomallei K96243 Hypothetical Proteins Via High-Throughput Characterization of Structural Similarities.Interdisciplinary sciences, computational life sciences · 2026Article
- ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Rational Targeting and gRNA Design for Enhancing Quorum Quenching inComputational and structural biotechnology journal · 2026Article
- The dysregulation score method identifies epigenetic regulator genes that predict cancer prognosis and efficiency of cancer immunotherapy.Molecular therapy. Nucleic acids · 2025Article
- tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations.bioRxiv : the preprint server for biology · 2025Article
- Drug toxicity prediction based on genotype-phenotype differences between preclinical models and humans.EBioMedicine · 2025Article
- Repurposing rupatadine as topical treatment against methicillin-resistant Staphylococcus aureus.AMB Express · 2025Article
- Computational guided identification of novel anti-mycobacterial agent proved by in-vitro and in-vivo validation.BMC microbiology · 2025Article
- A structural machine learning approach for rapid prediction of thermodynamically destabilizing tyrosine phosphorylations.Cell reports methods · 2025Article
- VarPPUD: Pinpointing diagnostic variants from sets of prioritized, strong candidate variants.PLoS computational biology · 2025Article
- Enzyme-constrained metabolic model ofmSystems · 2025Article
- Systematic identification of cancer-type-specific drugs based on essential genes and validations in lung adenocarcinoma.Briefings in bioinformatics · 2025Article
- Advances in Anthelmintic Target Identification.International journal of molecular sciences · 2025Review
- Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs.Patterns (New York, N.Y.) · 2025Article
- RNA-Binding Motif Protein 22 Induces Apoptosis via c-Myc Pathway in Colon Cancer Cells.Molecules (Basel, Switzerland) · 2025Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.