Candidate gene prioritization with Endeavour

Genomic studies and high-throughput experiments often produce large lists of candidate genes among which only a small fraction are truly relevant to the disease, phenotype or biological process of interest. Gene prioritization tackles this problem by ranking candidate genes by profiling candidates across multiple genomic data sources and integrating this heterogeneous information into a global ranking. We describe an extended version of our gene prioritization method, Endeavour, now available for six species and integrating 75 data sources. The performance (Area Under the Curve) of Endeavour on cross-validation benchmarks using ‘gold standard’ gene sets varies from 88% (for human phenotypes) to 95% (for worm gene function). In addition, we have also validated our approach using a time-stamped benchmark derived from the Human Phenotype Ontology, which provides a setting close to prospective validation. With this benchmark, using 3854 novel gene–phenotype associations, we observe a performance of 82%. Altogether, our results indicate that this extended version of Endeavour efficiently prioritizes candidate genes. The Endeavour web server is freely available at https://endeavour.esat.kuleuven.be/.

• Publication year

  2016

• Venue

  Nucleic Acids Res.

• Publication date

  2016-04-30

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/gkw365PMID 27131783PMCID 4987917
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Reactome pathway Knowledgebase

  2015cited by this paper
• The human disease network in terms of dysfunctional regulatory mechanisms

  2015cited by this paper
• Predicting effective microRNA target sites in mammalian mRNAs

  2015cited by this paper
• Gene Ontology Consortium: going forward

  2014cited by this paper
• The InterPro protein families database: the classification resource after 15 years

  2014cited by this paper
• The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

  2014cited by this paper
• The BioGRID interaction database: 2015 update

  2014cited by this paper
• OTX2 Duplication Is Implicated in Hemifacial Microsomia

  2014cited by this paper
• A large-scale evaluation of computational protein function prediction

  2013cited by this paper
• MetaRanker 2.0: a web server for prioritization of genetic variation data

  2013cited by this paper
• The Reactome pathway knowledgebase

  2013cited by this paper
• Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia

  2013cited by this paper
• PaGenBase: A Pattern Gene Database for the Global and Dynamic Understanding of Gene Function

  2013cited by this paper
• The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

  2013cited by this paper
• Computational tools for prioritizing candidate genes: boosting disease gene discovery

  2012cited by this paper
• Computational approaches to disease‐gene prediction: rationale, classification and successes

  2012cited by this paper
• Génie: literature-based gene prioritization at multi genomic scale

  2011cited by this paper
• DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs

  2010cited by this paper
• ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

  2009cited by this paper
• MirZ: an integrated microRNA expression atlas and target prediction resource

  2009cited by this paper
• GeneDistiller—Distilling Candidate Genes from Linkage Intervals

  2008cited by this paper
• Endeavour update: a web resource for gene prioritization in multiple species

  2008cited by this paper
• The human disease network

  2007cited by this paper
• Finding function: evaluation methods for functional genomic data

  2006cited by this paper
• Gene prioritization through genomic data fusion

  2006cited by this paper
• Human disease genes: patterns and predictions.

  2003cited by this paper
• Online Mendelian Inheritance In Man (OMIM)

  2000cited by this paper
• HUMAN DISEASE

  1957cited by this paper

• eVGeMdb: a manually curated database for experimentally validated genetic modifiers of neurodegenerative disorders

  2026cites this paper
• Using multi-scale genomics to associate poorly annotated genes with rare diseases

  2024cites this paper
• Genetic heterogeneity in familial forms of genetic generalized epilepsy: from mono- to oligogenism

  2024cites this paper
• Tissue-aware interpretation of genetic variants advances the etiology of rare diseases

  2024cites this paper
• Yves Moreau has received the 2023 Einstein Foundation Individual Award for Promoting Quality in Research

  2024cites this paper
• Associative gene networks reveal novel candidates important for ADHD and dyslexia comorbidity

  2023cites this paper
• Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers

  2023cites this paper
• Imperfect gold standard gene sets yield inaccurate evaluation of causal gene identification methods

  2023cites this paper
• Predicting disease genes based on multi-head attention fusion

  2023cites this paper
• Biological Network Mining.

  2023cites this paper
• A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration

  2023cites this paper
• OSR1 disruption contributes to uterine factor infertility via impaired Müllerian duct development and endometrial receptivity

  2023cites this paper
• Increase the Accuracy of Detection of Pathogenic Genes of Breast Cancer using a Graph-Based Approach to the Gene Prioritization Problem

  2023cites this paper
• Identification and evaluation of midbrain specific longevity-related genes in exceptionally long-lived but healthy mice

  2023cites this paper
• DeepGenePrior: A deep learning model for prioritizing genes affected by copy number variants

  2023cites this paper
• Integration of genome-scale data identifies candidate sleep regulators.

  2022cites this paper
• Identifying Key Lysosome-Related Genes Associated with Drug-Resistant Breast Cancer Using Computational and Systems Biology Approach

  2022cites this paper
• Systems-level investigation of mucopolysaccharidosis IIIA identifies deficient synaptic activity as a key driver of disease progression

  2022cites this paper
• Prioritization of New Candidate Genes for Rare Genetic Diseases by a Disease-Aware Evaluation of Heterogeneous Molecular Networks

  2022cites this paper
• Investigation of the performance of driver mutation identification methods using biological networks and enriched biological networks

  2022influential citation
• Angiogenesis goes computational – The future way forward to discover new angiogenic targets?

  2022cites this paper
• Computational Resources for the Interpretation of Variations in Cancer.

  2022cites this paper
• AutoCaSc: Prioritizing candidate genes for neurodevelopmental disorders

  2022cites this paper
• Simulation of undiagnosed patients with novel genetic conditions

  2022cites this paper
• Prioritizing Suggestive Candidate Genes in Migraine: An Opinion

  2022cites this paper
• DeepGenePrior: A deep learning model to prioritize genes affected by copy number variants

  2022cites this paper
• Whole‐genome analysis reveals the hybrid formation of Chinese indigenous DHB pig following human migration

  2022cites this paper
• Genome-wide discovery of genetic loci that uncouple excess adiposity from its comorbidities

  2021cites this paper
• Using Gene Ontology to Annotate and Prioritize Microarray Data.

  2021cites this paper
• Immune Dysregulation in Patients With Chromosome 18q Deletions—Searching for Putative Loci for Autoimmunity and Immunodeficiency

  2021cites this paper
• New locus underlying auriculocondylar syndrome (ARCND): 430 kb duplication involving TWIST1 regulatory elements

  2021cites this paper
• Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors

  2021cites this paper
• Target identification and validation

  2021cites this paper
• Machine learning applications for therapeutic tasks with genomics data

  2021cites this paper
• NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction

  2021cites this paper
• Machine learning approaches to identify sleep genes

  2021cites this paper
• PRYNT: a tool for prioritization of disease candidates from proteomics data using a combination of shortest-path and random walk algorithms

  2021cites this paper
• Network Modeling in Biology: Statistical Methods for Gene and Brain Networks.

  2021cites this paper
• Predicting disease‐associated genes: Computational methods, databases, and evaluations

  2020cites this paper
• Network hub-node prioritization of gene regulation with intra-network association

  2020cites this paper
• Candidate gene prioritization using graph embedding

  2020cites this paper
• Milk microbial composition of Brazilian dairy cows entering the dry period and genomic comparison between Staphylococcus aureus strains susceptible to the bacteriophage vB_SauM-UFV_DC4

  2020cites this paper
• Predicting candidate genes from phenotypes, functions, and anatomical site of expression

  2020cites this paper
• Characterization of intellectual disability and autism comorbidity through gene panel sequencing

  2020cites this paper
• Rare loss-of-function mutations of PTGIR are enriched in fibromuscular dysplasia

  2020cites this paper
• Towards Structured Prediction in Bioinformatics with Deep Learning

  2020influential citation
• Ocular coloboma: Genetic variants reveal a dynamic model of eye development

  2020cites this paper
• Predicting candidate genes from phenotypes, functions and anatomical site of expression

  2020cites this paper
• Gene Function Similarity Method Based on Data Fusion

  2020cites this paper
• The Genes Associated with Drought Tolerance by Multi-Layer Approach in Potato

  2019cites this paper
• Characterization of Intellectual disability and Autism comorbidity through gene panel sequencing

  2019cites this paper
• Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem

  2019influential citation
• Enhancing the prediction of disease-gene associations with multimodal deep learning

  2019cites this paper
• Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways

  2019cites this paper
• Gene Prioritization Using Semantic Similarity

  2019cites this paper
• A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases

  2019cites this paper
• GeneFishing to reconstruct context specific portraits of biological processes

  2019influential citation
• A deep learning model based on sparse auto-encoder for prioritizing cancer-related genes and drug target combinations.

  2019cites this paper
• GPS: Identification of disease genes by rank aggregation of multi-genomic scoring schemes.

  2019cites this paper
• Intégration de données multi-échelles et extraction de connaissances en agronomie : exemples et perspectives. (Multi-scale Data Integration and Knowledge Extraction in Agronomy: Examples and Prospects)

  2019cites this paper
• Improving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis

  2019influential citation
• TopControl: A Tool to Prioritize Candidate Disease-associated Genes based on Topological Network Features

  2019cites this paper
• Comorbidity of asthma and hypertension may be mediated by shared genetic dysregulation and drug side effects

  2019cites this paper
• Identifying disease-associated genes based on artificial intelligence

  2019cites this paper
• Genome-wide prediction and prioritization of human aging genes by data fusion: a machine learning approach

  2019cites this paper
• Tendon and Ligament Injuries in Elite Rugby: The Potential Genetic Influence

  2019cites this paper
• Human Mutation

  2019cites this paper
• A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions.

  2019cites this paper
• PGCN: Disease gene prioritization by disease and gene embedding through graph convolutional neural networks

  2019influential citation
• RARE LOSS-OF-FUNCTION MUTATIONS OF PTGIR IDENTIFIED IN FIBROMUSCULAR DYSPLASIA AND SPONTANEOUS CORONARY ARTERY DISSECTION

  2019cites this paper
• Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities

  2018cites this paper
• Constructing a Quantitative Fusion Layer over the Semantic Level for Scalable Inference

  2018cites this paper
• BCScreen: A gene panel to test for breast carcinogenesis in chemical safety screening.

  2018cites this paper
• pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion

  2018cites this paper
• Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

  2018cites this paper
• Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders.

  2018cites this paper
• In Silico Methods to Predict Disease-Resistance Candidate Genes in Plants

  2018cites this paper
• Benchmarker: an unbiased, association-data-driven strategy to evaluate gene prioritization algorithms

  2018cites this paper
• Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: use case in breast carcinogenesis.

  2018cites this paper
• Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature

  2018cites this paper
• Early‐onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms

  2018cites this paper
• Applying Two Different Bioinformatic Approaches to Discover Novel Genes Associated with Hereditary Hearing Loss via Whole-Exome Sequencing: ENDEAVOUR and HomozygosityMapper

  2018cites this paper
• Identification and Analysis of Rice Yield-Related Candidate Genes by Walking on the Functional Network

  2018cites this paper
• Evaluation of Prioritization Methods of Extrinsic Apoptotic Signaling Pathway Genes for Retrieval of the New Candidates Associated with Major Depressive Disorder

  2018influential citation
• Bottlenecks for genome-edited crops on the road from lab to farm

  2018cites this paper
• Understanding regulatory mechanisms underlying stem cells helps to identify cancer biomarkers

  2018influential citation
• Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine

  2018cites this paper
• Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations

  2018cites this paper
• Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information

  2018cites this paper
• Best practices for analysing microbiomes

  2018cites this paper
• Predicting Disease Genes from Clinical Single Sample-Based PPI Networks

  2018cites this paper
• Functional association networks for disease gene prediction

  2017cites this paper
• Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

  2017cites this paper
• Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network

  2017cites this paper
• An evaluation of the challenges to developing tumor BRCA1 and BRCA2 testing methodologies for clinical practice

  2017cites this paper
• Integration and visualisation of clinical-omics datasets for medical knowledge discovery

  2017cites this paper
• CRISPR/Cas9-Enabled Multiplex Genome Editing and Its Application.

  2017cites this paper
• Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism

  2017cites this paper
• Whole-genome sequencing suggests mechanisms for 22q11.2 deletion-associated Parkinson’s disease

  2017cites this paper
• Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

  2017cites this paper