ArticleNucleic acids research2017
Using predictive specificity to determine when gene set analysis is biologically meaningful.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- BenchmarkingInternational journal of molecular sciences · 2026Article
- Pool PaRTI: a PageRank-based pooling method for identifying critical residues and enhancing protein sequence representations.Bioinformatics (Oxford, England) · 2025Article
- Article
- Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics.PLoS computational biology · 2025Article
- Pool PaRTI: A PageRank-Based Pooling Method for Identifying Critical Residues and Enhancing Protein Sequence Representations.bioRxiv : the preprint server for biology · 2025Article
- To Tweak or Not to Tweak. How Exploiting Flexibilities in Gene Set Analysis Leads to Overoptimism.Biometrical journal. Biometrische Zeitschrift · 2025Article
- Article
- On the influence of several factors on pathway enrichment analysis.Briefings in bioinformatics · 2022Review
- Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids.Cellular and molecular gastroenterology and hepatology · 2022Article
- Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data.Nature communications · 2021Article
- The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort.PloS one · 2021Article
- Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting.Molecular metabolism · 2020Article
- Thermal cues drive plasticity of desiccation resistance in montane salamanders with implications for climate change.Nature communications · 2019Article
- Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.Nature protocols · 2019Article
- CEA: Combination-based gene set functional enrichment analysis.Scientific reports · 2018Article
- Monitoring changes in the Gene Ontology and their impact on genomic data analysis.GigaScience · 2018Article
- Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations.Scientific reports · 2018Article
- Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues.Frontiers in genetics · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Gene set analysis, which translates gene lists into enriched functions, is among the most common bioinformatic methods. Yet few would advocate taking the results at face value. Not only is there no agreement on the algorithms themselves, there is no agreement on how to benchmark them. In this paper, we evaluate the robustness and uniqueness of enrichment results as a means of assessing methods even where correctness is unknown. We show that heavily annotated (‘multifunctional’) genes are likely to appear in genomics study results and drive the generation of biologically non-specific enrichment results as well as highly fragile significances. By providing a means of determining where enrichment analyses report non-specific and non-robust findings, we are able to assess where we can be confident in their use. We find significant progress in recent bias correction methods for enrichment and provide our own software implementation. Our approach can be readily adapted to any pre-existing package.
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Registered trials
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.