FAIRsharing.hsy066; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.497146

ogee
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.497146

Other names: OGEE, ogee

Online GEne Essentiality database

Webpage:

https://v3.ogee.info

Publications:

Publications
More detailed information about this field from each metasource.

OGEE: an online gene essentiality database
PMID: 22075992
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.497146

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines
PMID: 27799467
metasource: Fairsharing.org
version: FAIRsharing.org: OGEE; Online GEne Essentiality database; DOI: https://doi.org/10.25504/FAIRsharing.hsy066; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

https://doi.org/10.1093/nar/gkaa884
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

OGEE: an online gene essentiality database PubMed citations: 84.

84 articles citing: OGEE: an online gene essentiality database

merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. PMID:35694833
Research on the Computational Prediction of Essential Genes. PMID:34938741
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
A Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9. PMID:34709608
Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. PMID:34529933
Identification of Therapeutic Targets for the Selective Killing of HBV-Positive Hepatocytes. PMID:34357116
In vivo and in vitro human gene essentiality estimations capture contrasting functional constraints. PMID:34268495
On the relation of gene essentiality to intron structure: a computational and deep learning approach. PMID:33906938
Internetwork connectivity of molecular networks across species of life. PMID:33441907
Essential gene prediction using limited gene essentiality information-An integrative semi-supervised machine learning strategy. PMID:33253254
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. PMID:33084874
DeeplyEssential: a deep neural network for predicting essential genes in microbes. PMID:32998698
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. PMID:32900868
Pig-specific RNA editing during early embryo development revealed by genome-wide comparisons. PMID:32433824
Ancient genes can be served as pan-cancer diagnostic and prognostic biomarkers. PMID:32368859
Single-cell expression and Mendelian randomization analyses identify blood genes associated with lifespan and chronic diseases. PMID:32358504
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. PMID:32194617
Controllability analysis of molecular pathways points to proteins that control the entire interaction network. PMID:32076007
ePath: an online database towards comprehensive essential gene annotation for prokaryotes. PMID:31506471
New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. PMID:31504171
An Evaluation of Machine Learning Approaches for the Prediction of Essential Genes in Eukaryotes Using Protein Sequence-Derived Features. PMID:31312416
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. PMID:31293525
Prioritizing target-disease associations with novel safety and efficacy scoring methods. PMID:31285471
Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. PMID:31239393
Collective influencers in protein interaction networks. PMID:30850642
Identifying mouse developmental essential genes using machine learning. PMID:30563825
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PMID:30444863
Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes. PMID:30233390
ARIADNA: machine learning method for ancient DNA variant discovery. PMID:30215675
An analysis of aging-related genes derived from the Genotype-Tissue Expression project (GTEx). PMID:30155276
Developmental Constraints on Genome Evolution in Four Bilaterian Model Species. PMID:30137380
Global view of a drug-sensitivity gene network. PMID:29423044
A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes. PMID:29230204
Properties of human genes guided by their enrichment in rare and common variants. PMID:29197136
Sequence-based information-theoretic features for gene essentiality prediction. PMID:29121868
Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities. PMID:28985264
Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network. PMID:28854629
Comparative analysis of genes frequently regulated by drugs based on connectivity map transcriptome data. PMID:28575118
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. PMID:28444480
Why are essential genes essential? - The essentiality of Saccharomyces genes. PMID:28357303
Accurate prediction of human essential genes using only nucleotide composition and association information. PMID:28158612
Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. PMID:28013235
Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights. PMID:27957775
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. PMID:27799467
Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PMID:27632082
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets. PMID:27091990
Critical controllability in proteome-wide protein interaction network integrating transcriptome. PMID:27040162
Predicting Essential Genes and Proteins Based on Machine Learning and Network Topological Features: A Comprehensive Review. PMID:27014079
Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics. PMID:26904540
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution. PMID:26801093
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. PMID:26655498
Towards a compendium of essential genes - From model organisms to synthetic lethality in cancer cells. PMID:26627871
CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis. PMID:26571275
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
New genes drive the evolution of gene interaction networks in the human and mouse genomes. PMID:26424194
Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents. PMID:26394156
A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types. PMID:26352260
Identifying and characterising key alternative splicing events in Drosophila development. PMID:26275604
Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse. PMID:26121354
Essentiality and centrality in protein interaction networks revisited. PMID:25880655
Investigating different duplication pattern of essential genes in mouse and human. PMID:25751152
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PMID:25268881
Systems biology perspectives on minimal and simpler cells. PMID:25184563
Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". PMID:25077479
Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy. PMID:25003367
IFIM: a database of integrated fitness information for microbial genes. PMID:24923821
Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. PMID:24881052
Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. PMID:24865553
Training set selection for the prediction of essential genes. PMID:24466248
A new computational strategy for predicting essential genes. PMID:24359534
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. PMID:24308365
DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. PMID:24243843
CEG: a database of essential gene clusters. PMID:24209780
Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes. PMID:23814130
Evolution of the correlation between expression divergence and protein divergence in mammals. PMID:23781097
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
A statistical framework for improving genomic annotations of prokaryotic essential genes. PMID:23520492
Linking genome-scale metabolic modeling and genome annotation. PMID:23417799
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. PMID:23260136
Network rewiring is an important mechanism of gene essentiality change. PMID:23198090
ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. PMID:22900082
Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age. PMID:22319151
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines PubMed citations: 70.

70 articles citing: OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines

Multiplex base editing to convert TAG into TAA codons in the human genome. PMID:35918324
Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals. PMID:35035788
Identifying essential genes across eukaryotes by machine learning. PMID:34859210
A Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9. PMID:34709608
Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. PMID:34572495
Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. PMID:34529933
Predicting host dependency factors of pathogens in Drosophila melanogaster using machine learning. PMID:34471501
Identification of Therapeutic Targets for the Selective Killing of HBV-Positive Hepatocytes. PMID:34357116
Genome-scale metabolic network reconstruction of model animals as a platform for translational research. PMID:34282017
In vivo and in vitro human gene essentiality estimations capture contrasting functional constraints. PMID:34268495
The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality. PMID:33973013
On the relation of gene essentiality to intron structure: a computational and deep learning approach. PMID:33906938
The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis. PMID:33671149
Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster. PMID:33575603
Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential. PMID:33541265
Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. PMID:33500331
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. PMID:33483502
Internetwork connectivity of molecular networks across species of life. PMID:33441907
CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms. PMID:33306800
OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers. PMID:33179738
DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features. PMID:33177077
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. PMID:33084874
PRIM1 deficiency causes a distinctive primordial dwarfism syndrome. PMID:33060134
Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. PMID:32967266
Predicting gene regulatory networks from cell atlases. PMID:32958603
Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo. PMID:32950053
Comprehensive host-pathogen protein-protein interaction network analysis. PMID:32912135
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. PMID:32900868
A-to-I RNA editing in bacteria increases pathogenicity and tolerance to oxidative stress. PMID:32822429
Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. PMID:32718697
Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis. PMID:32674507
A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks. PMID:32542021
Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. PMID:32487729
Ancient genes can be served as pan-cancer diagnostic and prognostic biomarkers. PMID:32368859
Essential gene prediction in Drosophila melanogaster using machine learning approaches based on sequence and functional features. PMID:32257045
MaveQuest: a web resource for planning experimental tests of human variant effects. PMID:32251504
A catalogue of new incidence estimates of monogenic neurodevelopmental disorders caused by de novo variants. PMID:32168371
Human and mouse essentiality screens as a resource for disease gene discovery. PMID:32005800
Intragenic MicroRNAs Autoregulate Their Host Genes in Both Direct and Indirect Ways-A Cross-Species Analysis. PMID:31963421
Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning. PMID:31926940
A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations. PMID:31515285
GMrepo: a database of curated and consistently annotated human gut metagenomes. PMID:31504765
Three miRNAs cooperate with host genes involved in human cardiovascular disease. PMID:31464655
Link clustering explains non-central and contextually essential genes in protein interaction networks. PMID:31406201
Cancer Cell Lines Are Useful Model Systems for Medical Research. PMID:31374935
An Evaluation of Machine Learning Approaches for the Prediction of Essential Genes in Eukaryotes Using Protein Sequence-Derived Features. PMID:31312416
Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae. PMID:31231774
Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes. PMID:31214154
Ligands and Receptors with Broad Binding Capabilities Have Common Structural Characteristics: An Antibiotic Design Perspective. PMID:31188598
Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes. PMID:31160636
Immunoinformatics Approach to Design a Novel Epitope-Based Oral Vaccine Against Helicobacter pylori. PMID:31120321
Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE. PMID:30912442
Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery. PMID:30866765
Analysis of the Functional Relevance of Epigenetic Chromatin Marks in the First Intron Associated with Specific Gene Expression Patterns. PMID:30753418
NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans. PMID:30744685
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
Network-based features enable prediction of essential genes across diverse organisms. PMID:30543651
Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism. PMID:30397099
Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes. PMID:30233390
Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes. PMID:30190679
Genetic Network Complexity Shapes Background-Dependent Phenotypic Expression. PMID:29903533
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
MicroRNA-focused CRISPR-Cas9 library screen reveals fitness-associated miRNAs. PMID:29720387
Review: Genomics of bull fertility. PMID:29618393
Human C-to-U Coding RNA Editing Is Largely Nonadaptive. PMID:29385526
Phenotype inference in an Escherichia coli strain panel. PMID:29280730
A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes. PMID:29230204
Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis. PMID:28938601
Selection for energy efficiency drives strand-biased gene distribution in prokaryotes. PMID:28874819
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. PMID:28854368
https://doi.org/10.1093/nar/gkaa884

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curated information
metasource: Fairsharing.org
version: FAIRsharing.org: OGEE; Online GEne Essentiality database; DOI: https://doi.org/10.25504/FAIRsharing.hsy066; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

publication
metasource: Fairsharing.org
version: FAIRsharing.org: OGEE; Online GEne Essentiality database; DOI: https://doi.org/10.25504/FAIRsharing.hsy066; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

text mining
metasource: Fairsharing.org
version: FAIRsharing.org: OGEE; Online GEne Essentiality database; DOI: https://doi.org/10.25504/FAIRsharing.hsy066; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.497146

gene structure
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.497146

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.497146

gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.497146

publication text mining human and other vertebrate genomes model organisms gene expression gene structure model organisms gene and protein families

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