ArticleJournal of the Royal Society, Interface2014
Separate enrichment analysis of pathways for up- and downregulated genes.
Article in Journal of the Royal Society, Interface, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
128 citing papers in PubMed, 1 synthesis or guideline pooled it, 211 citations in OpenAlex.
- Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation.Scientific reports · 2020Pooled it
- Integrated multi-omic and symptom clustering reveals lower-gastrointestinal disorders of gut-brain interaction heterogeneity.Gut microbes · 2026Article
- CXCR4 Coordinates Long-Term Olfactory Epithelial Regeneration and Cellular Stress Response After Injury.Molecular neurobiology · 2026Article
- Growth Plate Morphogens as Potential Modulators of Cellular Tissue Remodeling by Annulus Fibrosus Cells.JOR spine · 2026Article
- Conserved and context-dependent changes in pathogen and host cell gene expression during Staphylococcus aureus intracellular infection.BMC microbiology · 2026Article
- Gut-Microbial Responses to Acute Polyester Microplastic Exposure in Zebrafish: Dysbiosis, Opportunistic Bacteria, and Functional Impact.International journal of molecular sciences · 2026Article
- Nuclear Transfer Perturbs Genomic Balance.Epigenomes · 2026Article
- Daily torpor in the Djungarian hamster (Phodopus sungorus) is orchestrated by the suprachiasmatic nucleus: evidence from immediate early gene mapping and nucleus-specific sequencing.Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · 2026Article
- Ten common mistakes that could ruin your enrichment analysis.PLoS computational biology · 2026Article
- Protein biomarkers associated with left bundle branch block in patients with heart failure and reduced ejection fraction.ESC heart failure · 2026Article
- Article
- The skeletal muscle of aged male mice exhibits sustained growth regulatory transcriptional profile following glucocorticoid exposure compared with young males.Physiological genomics · 2025Article
- Sustained Accumulation of Molecular Clock Suppressors Period 1 and Period 2 Promotes C2C12 Myotube Atrophy Through an Autocrine-Mediated Mechanism With Relevance to Androgen Deprivation-Induced Limb Muscle Mass Loss.Function (Oxford, England) · 2025Article
- Infections ofViruses · 2025Article
- Transcriptome Analysis Reveals Mechanisms of Stripe Rust Response in Wheat Cultivar Anmai1350.International journal of molecular sciences · 2025Article
- Differential expression of proliferation and immune response genes between children and adults influences survival of diffuse large B cell lymphoma.Scientific reports · 2025Article
- Can the Supplementation of Oocytes with Extra Copies of mtDNA Impact Development Without Being Transmitted? A Molecular Account.International journal of molecular sciences · 2025Article
- Metabolomic and transcriptomic insights into the mechanism of sugar and acid accumulation in the pulp of sour- and sweet-tastingFrontiers in plant science · 2025Article
- Article
- Life History-Dependent Brain Transcriptomic Signatures in Nothobranchids: Insights into Aging, Neurogenesis, and Life History Evolution.Integrative organismal biology (Oxford, England) · 2025Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.
Indexed as
Identifiers
What OpenQuestion holds
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.