SynthesisBioinformatics (Oxford, England)2020
P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications.
Synthesis in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 7 of them syntheses that pooled it.
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Who cites it
22 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Metabolome panels as potential noninvasive biomarkers for primary glomerulonephritis sub-types: meta-analysis of profiling metabolomics studies.Scientific reports · 2023Pooled it
- Transcriptomic meta-analysis reveals ERRα-mediated oxidative phosphorylation is downregulated in Fuchs' endothelial corneal dystrophy.PloS one · 2023Pooled it
- Pathogenomic Signature and Aberrant Neurogenic Events in Experimental Cerebral Ischemic Stroke: A Neurotranscriptomic-Based Implication for Dementia.Journal of Alzheimer's disease : JAD · 2023Pooled it
- Fused inverse-normal method for integrated differential expression analysis of RNA-seq data.BMC bioinformatics · 2022Pooled it
- Amanida: an R package for meta-analysis of metabolomics non-integral data.Bioinformatics (Oxford, England) · 2022Pooled it
- Reviewing and assessing existing meta-analysis models and tools.Briefings in bioinformatics · 2021Pooled it
- Pooled it
- AWmeta Empowers Adaptively Weighted Transcriptomic Meta-Analysis.Current issues in molecular biology · 2026Article
- Heterogeneous constraint and adaptation across the malaria parasite life cycle.Proceedings. Biological sciences · 2025Article
- Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides.Bioinformatics (Oxford, England) · 2024Article
- Sex differences in plasma proteomic markers in late-life depression.Psychiatry research · 2024Article
- Glucose dysregulation in antipsychotic-naive first-episode psychosis: in silico exploration of gene expression signatures.Translational psychiatry · 2024Article
- Central insulin dysregulation in antipsychotic-naïve first-episode psychosis: In silico exploration of gene expression signatures.Psychiatry research · 2024Article
- Accurate and Ultra-EfficientJournal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America · 2024Article
- Deciphering the causal relationship between blood pressure and regional white matter integrity: A two-sample Mendelian randomization study.Journal of neuroscience research · 2023Article
- Ranking Antibody Binding Epitopes and Proteins Across Samples from Whole Proteome Tiled Linear Peptides.bioRxiv : the preprint server for biology · 2023Article
- Article
- Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity.Journal of medical virology · 2023Article
- Article
- Circadian-Dependent and Sex-Dependent Increases in Intravenous Cocaine Self-Administration inThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationMeta-analysis methods have been widely used to combine results from multiple clinical or genomic studies to increase statistical powers and ensure robust and accurate conclusions. The adaptively weighted Fisher's method (AW-Fisher), initially developed for omics applications but applicable for general meta-analysis, is an effective approach to combine P-values from K independent studies and to provide better biological interpretability by characterizing which studies contribute to the meta-analysis. Currently, AW-Fisher suffers from the lack of fast P-value computation and variability estimate of AW weights. When the number of studies K is large, the 3K - 1 possible differential expression pattern categories generated by AW-Fisher can become intractable. In this paper, we develop an importance sampling scheme with spline interpolation to increase the accuracy and speed of the P-value calculation. We also apply bootstrapping to construct a variability index for the AW-Fisher weight estimator and a co-membership matrix to categorize (cluster) differentially expressed genes based on their meta-patterns for intuitive biological investigations.
resultsThe superior performance of the proposed methods is shown in simulations as well as two real omics meta-analysis applications to demonstrate its insightful biological findings. AVAILABILITY AND IMPLEMENTATION: An R package AWFisher (calling C++) is available at Bioconductor and GitHub (https://github.com/Caleb-Huo/AWFisher), and all datasets and programing codes for this paper are available in the Supplementary Material. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.