ArticleBriefings in bioinformatics2024
Generalized reporter score-based enrichment analysis for omics data.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- The functional structure of foxtail millet rhizoplane microbiome and its association with yield.Microbiology spectrum · 2026Article
- MetaNet: a scalable and integrated tool for reproducible omics network analysis.Bioinformatics (Oxford, England) · 2026Article
- Oil-Coated Nanoplastics Induce Rapid Membrane Disruption and Severe Intestinal Injury.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Distinct gut microbiota signatures in white leghorn and silky fowl are associated with divergent laying performance.Poultry science · 2026Article
- Gastrointestinal microbial nitrogen metabolic landscape underlies nitrogen utilization efficiency of goats fed distinct dietary protein sources.Microbiome · 2026Article
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- Extracellular vesicles as structured vectors of quorum sensing signals influence aquatic microbial communities.NPJ biofilms and microbiomes · 2026Article
- Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses.Frontiers in microbiology · 2026Article
- Fecal microbiome and metabolome dynamics during immunotherapy-based total neoadjuvant therapy in rectal cancer: associations with treatment response and toxicity.Frontiers in immunology · 2026Article
- Gut microbiota of sprint athletes: signature microbes and dietary links.Frontiers in nutrition · 2026Article
- OLFML2B promotes hepatocellular carcinoma malignancy via the PI3K/AKT-EMT axis and correlates with an immunosuppressive tumor microenvironment.Frontiers in immunology · 2026Article
- Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.Frontiers in microbiology · 2026Article
- Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.NPJ biofilms and microbiomes · 2025Article
- Multi-Habitat Landscape Promotes Microbial Diversity: Insights from the Traditional Agricultural Heritage and the Global Trend.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Lon peptidase 1 promotes proliferation and metastasis in breast cancer via interleukin 6 signaling.Discover oncology · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enrichment analysis contextualizes biological features in pathways to facilitate a systematic understanding of high-dimensional data and is widely used in biomedical research. The emerging reporter score-based analysis (RSA) method shows more promising sensitivity, as it relies on P-values instead of raw values of features. However, RSA cannot be directly applied to multi-group and longitudinal experimental designs and is often misused due to the lack of a proper tool. Here, we propose the Generalized Reporter Score-based Analysis (GRSA) method for multi-group and longitudinal omics data. A comparison with other popular enrichment analysis methods demonstrated that GRSA had increased sensitivity across multiple benchmark datasets. We applied GRSA to microbiome, transcriptome and metabolome data and discovered new biological insights in omics studies. Finally, we demonstrated the application of GRSA beyond functional enrichment using a taxonomy database. We implemented GRSA in an R package, ReporterScore, integrating with a powerful visualization module and updatable pathway databases, which is available on the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/ReporterScore). We believe that the ReporterScore package will be a valuable asset for broad biomedical research fields.
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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.