ArticleBioinformatics (Oxford, England)2016
Combining dependent P-values with an empirical adaptation of Brown's method.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 3 of them syntheses 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
78 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Interrogating DNA methylation associated with Lewy body pathology in a cross brain-region and multi-cohort study.Nature communications · 2026Pooled it
- Pooled it
- Uncovering Oncogenic Mechanisms of Tumor Suppressor Genes in Breast Cancer Multi-Omics Data.International journal of molecular sciences · 2022Pooled it
- Phenotypic screening for small molecules that lower PrP in cultured cells.Molecular and cellular neurosciences · 2026Article
- Label-Free Targeted Proteomics Data Analysis Workflow Selection - Benchmarking AI-based and Data-Driven Approaches.Molecular & cellular proteomics : MCP · 2026Article
- Abnormal B-Cell Exosome Proapoptotic and Antiapoptotic Cargo in Multiple Sclerosis: Potential Implication in Progressive Disease Biology.Neurology(R) neuroimmunology & neuroinflammation · 2026Article
- Preschool wheeze endotypes and their association with asthma attacks and inhaled corticosteroid response.ERJ open research · 2026Article
- Phenotypic screening for small molecules that lower PrP in cultured cells.bioRxiv : the preprint server for biology · 2026Article
- Setd1a Loss-of-function Disrupts Epigenetic Regulation of Ribosomal Genes via Altered DNA Methylation.Schizophrenia bulletin · 2026Article
- Decadal extreme drought reduces alpine subsoil carbon stocks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Phenotype-first patient matching with SimPheny identifies diagnostic candidates beyond curated gene associations.medRxiv : the preprint server for health sciences · 2026Article
- Methylomic signatures of tau and amyloid-beta in transgenic mouse models of Alzheimer's disease neuropathology.NPJ dementia · 2026Article
- metacp: a versatile software package for combining dependent or independent p-values.BMC bioinformatics · 2025Article
- A unified combination framework for dependent tests with applications to microbiome association studies.Biometrics · 2025Article
- Evaluating the Cauchy combination test for count data.PloS one · 2025Article
- Evidence that minocycline treatment confounds the interpretation of neurofilament as a biomarker.Brain communications · 2025Article
- Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides.Bioinformatics (Oxford, England) · 2024Article
- Article
- Directional integration and pathway enrichment analysis for multi-omics data.Nature communications · 2024Article
- Managing Microbiota Activity ofMicroorganisms · 2024Article
18 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.
Funding
Abstract
motivationCombining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure is non-trivial for dependent P-values. Here, we discuss an empirical adaptation of Brown's method (an extension of Fisher's method) for combining dependent P-values which is appropriate for the large and correlated datasets found in high-throughput biology.
resultsWe show that the Empirical Brown's method (EBM) outperforms Fisher's method as well as alternative approaches for combining dependent P-values using both noisy simulated data and gene expression data from The Cancer Genome Atlas. AVAILABILITY AND IMPLEMENTATION: The Empirical Brown's method is available in Python, R, and MATLAB and can be obtained from https://github.com/IlyaLab/CombiningDependentPvalues UsingEBM The R code is also available as a Bioconductor package from https://www.bioconductor.org/packages/devel/bioc/html/EmpiricalBrownsMethod.html CONTACT: Theo.Knijnenburg@systemsbiology.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.