ArticleBioinformatics (Oxford, England)2013
Assessing identity, redundancy and confounds in Gene Ontology annotations over time.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it, 65 citations in OpenAlex.
- The characteristics of early-stage research into human genes are substantially different from subsequent research.PLoS biology · 2022Pooled it
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- Ten common mistakes that could ruin your enrichment analysis.PLoS computational biology · 2026Article
- The Gene Ontology knowledgebase in 2026.Nucleic acids research · 2026Article
- Natural language processing of gene descriptions for overrepresentation analysis with GeneTEA.Genome biology · 2025Article
- gymnotoa-db: a database and application to optimize functional annotation in gymnosperms.Database : the journal of biological databases and curation · 2025Article
- A review on Gene Ontology evaluations.Database : the journal of biological databases and curation · 2025Review
- Functional genomics of human skeletal development and the patterning of height heritability.Cell · 2025Article
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- Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results.bioRxiv : the preprint server for biology · 2024Article
- bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses.Frontiers in bioinformatics · 2024Article
- Delving into gene-set multiplex networks facilitated by a k-nearest neighbor-based measure of similarity.Computational and structural biotechnology journal · 2023Article
- The developmental impacts of natural selection on human pelvic morphology.Science advances · 2022Article
- Ensemble of Multiple Classifiers for Multilabel Classification of Plant Protein Subcellular Localization.Life (Basel, Switzerland) · 2021Article
- COVID-19 research risks ignoring important host genes due to pre-established research patterns.eLife · 2020Article
- Article
- Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.Nature communications · 2019Article
- Analysis of Protein-Protein Functional Associations by Using Gene Ontology and KEGG Pathway.BioMed research international · 2019Article
- Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationThe Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored.
resultsWe report that GO annotations are stable over short periods, with 3% of genes not being most semantically similar to themselves between monthly GO editions. However, we find that genes can alter their 'functional identity' over time, with 20% of genes not matching to themselves (by semantic similarity) after 2 years. We further find that annotation bias in GO, in which some genes are more characterized than others, has declined in yeast, but generally increased in humans. Finally, we discovered that many entries in protein interaction databases are owing to the same published reports that are used for GO annotations, with 66% of assessed GO groups exhibiting this confound. We provide a case study to illustrate how this information can be used in analyses of gene sets and networks. AVAILABILITY: Data available at http://chibi.ubc.ca/assessGO.
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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.