ArticleBioinformatics (Oxford, England)2019
Colocalization analyses of genomic elements: approaches, recommendations and challenges.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 3 of them syntheses that pooled it.
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Who cites it
43 citing papers in PubMed, 3 syntheses or guidelines pooled it.
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- Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure.Nature communications · 2022Pooled it
- Systematic review of Mendelian randomization studies on risk of cancer.BMC medicine · 2022Pooled it
- Taming the reference genome jungle: the refget sequence collection standard.Bioinformatics (Oxford, England) · 2026Article
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- Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-2.Computational and structural biotechnology journal · 2026Article
- Taming the reference genome jungle: the refget sequence collection standard.bioRxiv : the preprint server for biology · 2025Article
- Systemic evaluation of the effects of monomeric GLP-1R-based agonists on MASLD and its complications.Diabetology & metabolic syndrome · 2025Article
- Multi-tissue expression and splicing data prioritise anatomical subsite- and sex-specific colorectal cancer susceptibility genes.Nature communications · 2025Article
- Exploring Therapeutic Targets for Age-Related Macular Degeneration From Circulating Proteins to Plasma Metabolites in the European Population.Translational vision science & technology · 2025Article
- Genetic associations of plasma proteins and breast cancer identify potential therapeutic drug candidates.Communications biology · 2025Article
- Repeat-based holocentromeres of the woodrush Luzula sylvatica reveal insights into the evolutionary transition to holocentricity.Nature communications · 2024Article
- Exploring potential therapeutic targets for asthma: a proteome-wide Mendelian randomization analysis.Journal of translational medicine · 2024Article
- Association of inflammatory cytokines with lung function, chronic lung diseases, and COVID-19.iScience · 2024Article
- Fast Context-Aware Analysis of Genome Annotation Colocalization.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Methods for constructing and evaluating consensus genomic interval sets.Nucleic acids research · 2024Article
- Association between rheumatoid arthritis and autoimmune thyroid disease: evidence from complementary genetic methods.Endocrine · 2024Article
- MoCoLo: a testing framework for motif co-localization.Briefings in bioinformatics · 2024Article
- The causal role of circulating inflammatory markers in osteoporosis: a bidirectional Mendelian randomized study.Frontiers in immunology · 2024Article
- bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMany high-throughput methods produce sets of genomic regions as one of their main outputs. Scientists often use genomic colocalization analysis to interpret such region sets, for example to identify interesting enrichments and to understand the interplay between the underlying biological processes. Although widely used, there is little standardization in how these analyses are performed. Different practices can substantially affect the conclusions of colocalization analyses.
resultsHere, we describe the different approaches and provide recommendations for performing genomic colocalization analysis, while also discussing common methodological challenges that may influence the conclusions. As illustrated by concrete example cases, careful attention to analysis details is needed in order to meet these challenges and to obtain a robust and biologically meaningful interpretation of genomic region set data. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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