ReviewComputational biology and chemistry2021
Beyond standard pipeline and p < 0.05 in pathway enrichment analyses.
Review in Computational biology and chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A composite ranking of risk factors for COVID-19 time-to-event data from a Turkish cohort.Computational biology and chemistry · 2022Pooled it
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- paraORA: GPU-Accelerated Exact Over-Representation Analysis for Repeated Queries of Large Gene-Set Libraries.Biology · 2026Article
- Analytical Methods and Application of Single-Cell and Single-Nucleus Transcriptomics in the Study of Ischemic Stroke.Biomolecules · 2026Review
- The impact of nationwide folic acid fortification on genetic variants associated with conotruncal heart defects.Research square · 2026Article
- Review
- Robustness Analyses Substantially Narrow in silico Network-Toxicology Signals Linking Selected Pharmaceuticals and Caffeine to Vitiligo.Clinical, cosmetic and investigational dermatology · 2026Article
- Precision Target Discovery for Migraine: An Integrated GWAS-eQTL-PheWAS Pipeline.Molecules (Basel, Switzerland) · 2025Article
- Metabolomics biomarkers of frailty: a longitudinal study of aging female and male mice.npj aging · 2025Article
- Osmolality as a strong predictor of COVID-19 mortality and its possible links to other biomarkers.PloS one · 2025Article
- Deciphering the Role of CD14 inJournal of Cancer · 2025Article
- A Cyclic Permutation Approach to Removing Spatial Dependency between Clustered Gene Ontology Terms.Biology · 2024Article
- Blood-Type-A is a COVID-19 infection and hospitalization risk in a Turkish cohort.Transfusion clinique et biologique : journal de la Societe francaise de transfusion sanguine · 2023Article
- Diabetes and bacterial co-infection are two independent risk factors for respiratory syncytial virus disease severity.Frontiers in medicine · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
A standard pathway/gene-set enrichment analysis, the over-representation analysis, is based on four values: the size of two gene-sets, size of their overlap, and size of the gene universe from which the gene-sets are chosen. The standard result of such an analysis is based on the p-value of a statistical test. We supplement this standard pipeline by six cautions: (1) any p-value threshold to distinguish enriched gene-sets from not-enriched ones is to certain degree arbitrary; (2) genes in a gene-set may be correlated, which potentially overcount the gene-set size; (3) any attempt to impose multiple testing correction will increase the false negative rate; (4) gene-sets in a gene-set database may be correlated, potentially overcount the factor for multiple testing correction; (5) the discrete nature of the data make it possible that a minimum change in counts may lead to a quantum change in the p-value threshold-based conclusion; (6) the two gene-sets may not be chosen from the universe of all human genes, but in fact from a subset of that universe, or even two different subsets of all genes. Careful reconsideration of these issues can have an impact on an enrichment analysis conclusion. Part of our cautions mirror the call from statistician that reaching conclusion from data is not a simple matter of p-value smaller than 0.05, but a thoughtful process with due diligences.
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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 Socratic graph.