ArticlePloS one2017
Null diffusion-based enrichment for metabolomics data.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Adaptive metabolic reprogramming conserves energy status in Antarctic giants.Scientific reports · 2026Article
- Chemical Attributes of UK-Grown Tea and Identifying Catechin and Metabolite Dynamics in Green and Black Tea Using Metabolomics and Machine Learning.Metabolites · 2026Article
- TraceMetrix: a traceable metabolomics interactive analysis platform.Journal of cheminformatics · 2025Article
- Quorum sensing in Saccharomyces cerevisiae brewing strains: effects of 2-phenylethanol on proteomic, lipidomic, and metabolomic profile.FEMS yeast research · 2025Article
- Chemical Diversity of UK-Grown Tea Explored Using Metabolomics and Machine Learning.Metabolites · 2025Article
- Effects of in situ experimental warming on metabolic expression in a soft sediment bivalve.Scientific reports · 2025Article
- Induced responses to the wheat pathogen: Tan Spot-(Pyrenophora tritici-repentis) in wheat (Triticum aestivum) focus on changes in defence associated and sugar metabolism.Metabolomics : Official journal of the Metabolomic Society · 2024Article
- Regulation of p53 by the mitotic surveillance/stopwatch pathway: implications in neurodevelopment and cancer.Frontiers in cell and developmental biology · 2024Review
- Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data.Briefings in bioinformatics · 2023Article
- Data Processing and Analysis in Mass Spectrometry-Based Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Analysis of the oral microbiome during hormonal cycle and its alterations in menopausal women: the "AMICA" project.Scientific reports · 2022Article
- Responses of the MacroalgaMarine drugs · 2022Article
- Article
- Insight into Lotusine and Puerarin in Repairing Alcohol-Induced Metabolic Disorder Based on UPLC-MS/MS.International journal of molecular sciences · 2022Article
- Metabolomics Mechanism and Lignin Response to Laxogenin C, a Natural Regulator of Plants Growth.International journal of molecular sciences · 2022Article
- Bioinformatics integrated analysis to investigate candidate biomarkers and associated metabolites in osteosarcoma.Journal of orthopaedic surgery and research · 2021Article
- The effect of statistical normalization on network propagation scores.Bioinformatics (Oxford, England) · 2021Article
- The metaRbolomics Toolbox in Bioconductor and beyond.Metabolites · 2019Review
- Benchmarking network propagation methods for disease gene identification.PLoS computational biology · 2019Article
- FELLA: an R package to enrich metabolomics data.BMC bioinformatics · 2018Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolomics experiments identify metabolites whose abundance varies as the conditions under study change. Pathway enrichment tools help in the identification of key metabolic processes and in building a plausible biological explanation for these variations. Although several methods are available for pathway enrichment using experimental evidence, metabolomics does not yet have a comprehensive overview in a network layout at multiple molecular levels. We propose a novel pathway enrichment procedure for analysing summary metabolomics data based on sub-network analysis in a graph representation of a reference database. Relevant entries are extracted from the database according to statistical measures over a null diffusive process that accounts for network topology and pathway crosstalk. Entries are reported as a sub-pathway network, including not only pathways, but also modules, enzymes, reactions and possibly other compound candidates for further analyses. This provides a richer biological context, suitable for generating new study hypotheses and potential enzymatic targets. Using this method, we report results from cells depleted for an uncharacterised mitochondrial gene using GC and LC-MS data and employing KEGG as a knowledge base. Partial validation is provided with NMR-based tracking of 13C glucose labelling of these cells.
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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.