ArticleScientific reports2018
Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
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Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The characteristics of early-stage research into human genes are substantially different from subsequent research.PLoS biology · 2022Pooled it
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- thematicGO: A Keyword-Based Framework for Interpreting Gene Ontology Enrichment via Biological Themes.bioRxiv : the preprint server for biology · 2026Article
- The Gene Ontology knowledgebase in 2026.Nucleic acids research · 2026Article
- A practical guide to functional enrichment analysis.Frontiers in bioinformatics · 2026Article
- Benchmarking multiple gene ontology enrichment tools reveals high biological significance, ranking, and stringency heterogeneity among datasets.Frontiers in bioinformatics · 2026Article
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- Unravelling the developmental toxicity of heavy metals using zebrafish as a model: a narrative review.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2025Review
18 more citing papers are in PubMed but not listed here.
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12 authors.
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Abstract
Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks of this analysis - the ontology and the annotations - evolve rapidly. We used gene signatures derived from 104 disease analyses to systematically evaluate how enrichment analysis results were affected by evolution of the GO over a decade. We found low consistency between enrichment analyses results obtained with early and more recent GO versions. Furthermore, there continues to be a strong annotation bias in the GO annotations where 58% of the annotations are for 16% of the human genes. Our analysis suggests that GO evolution may have affected the interpretation and possibly reproducibility of experiments over time. Hence, researchers must exercise caution when interpreting GO enrichment analyses and should reexamine previous analyses with the most recent GO version.
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