ArticleBioinformatics (Oxford, England)2022
Metapone: a Bioconductor package for joint pathway testing for untargeted metabolomics data.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- High-resolution metabolomics of maternal polybrominated diphenyl ethers (PBDE) exposure and preterm birth in the Atlanta African American Maternal-Child Cohort.Communications medicine · 2026Article
- Prenatal Nitrogen Oxide (NOEnvironmental science & technology · 2025Article
- Metabolic dysregulation in Alzheimer's disease: A brain metabolomics approach.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Integrated chemical exposome-metabolome profiling of follicular fluid and associations with fertility outcomes during assisted reproduction.Environment international · 2025Article
- Novel and legacy per- and polyfluoroalkyl substances in humans: Long-term temporal variability and metabolic perturbations.Environment international · 2025Article
- Unraveling the Molecular Links between Fine Particulate Matter Exposure and Early Birth Risks in African American Mothers: A Metabolomics Study in the Atlanta African American Maternal-Child Cohort.Environmental science & technology · 2025Article
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- The need for a cancer exposome atlas: a scoping review.JNCI cancer spectrum · 2025Article
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- DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data.BMC bioinformatics · 2024Article
- Prenatal and Early Life Exposure to Ambient Air Pollutants Is Associated with the Fecal Metabolome in the First Two Years of Life.Environmental science & technology · 2024Article
- A new framework for exploratory network mediator analysis in omics data.Genome research · 2024Article
- Human Milk Composition Is Associated with Maternal Body Mass Index in a Cross-Sectional, Untargeted Metabolomics Analysis of Human Milk from Guatemalan Mothers.Current developments in nutrition · 2024Article
- Bayesian functional analysis for untargeted metabolomics data with matching uncertainty and small sample sizes.Briefings in bioinformatics · 2024Article
- Untargeted serum metabolomics reveals novel metabolite associations and disruptions in amino acid and lipid metabolism in Parkinson's disease.Molecular neurodegeneration · 2023Article
- Longitudinal profiles of the fecal metabolome during the first 2 years of life.Scientific reports · 2023Article
- Metabolome-wide association study of the relationship between chlorpyrifos exposure and first trimester serum metabolite levels in pregnant Thai farmworkers.Environmental research · 2022Article
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Authors and funding
9 authors.
Funding
Abstract
motivationTesting for pathway enrichment is an important aspect in the analysis of untargeted metabolomics data. Due to the unique characteristics of untargeted metabolomics data, some key issues have not been fully addressed in existing pathway testing algorithms: (i) matching uncertainty between data features and metabolites; (ii) lacking of method to analyze positive mode and negative mode liquid chromatography-mass spectrometry (LC/MS) data simultaneously on the same set of subjects; (iii) the incompleteness of pathways in individual software packages.
resultsWe developed an innovative R/Bioconductor package: metabolic pathway testing with positive and negative mode data (metapone), which can perform two novel statistical tests that take matching uncertainty into consideration-(i) a weighted gene set enrichment analysis-type test and (ii) a permutation-based weighted hypergeometric test. The package is capable of combining positive- and negative-ion mode results in a single testing scheme. For comprehensiveness, the built-in pathways were manually curated from three sources: Kyoto Encyclopedia of Genes and Genomes, Mummichog and The Small Molecule Pathway Database. AVAILABILITY AND IMPLEMENTATION: The package is available at https://bioconductor.org/packages/devel/bioc/html/metapone.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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