ArticleBMC bioinformatics2018
FELLA: an R package to enrich metabolomics data.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 2 of them syntheses that pooled it.
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Who cites it
77 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Microbial metabolites associated in stool and left ventricle of heart failure patients revealed by meta-analysis.Scientific reports · 2025Pooled it
- Exhaled volatile organic compounds analysis in clinical pediatrics: a systematic review.Pediatric research · 2021Pooled it
- Streamlining feature elaboration and statistics analysis in metabolomics: the GetFeatistics R-package.Journal of integrative bioinformatics · 2026Article
- Protocol for integrative transcriptomic/metabolomic analysis: A case study on factors influencing the oyster-POMS disease.STAR protocols · 2026Article
- Urinary volatilomics for biomarker discovery in kidney stone patients and healthy controls.Urolithiasis · 2026Article
- Squamocin as the Principal Toxic Constituent ofInternational journal of molecular sciences · 2026Article
- Untargeted metabolomics and proteomics reveals cocoa-mediated mitigation of valproic acid-induced dysregulation in a zebrafish model of autism: pilot study.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Adaptive metabolic reprogramming conserves energy status in Antarctic giants.Scientific reports · 2026Article
- Comparative Analysis of Microbial Community Structure and Functional Traits of Baijiu Daqu Across Diverse Geographical Regions in China.Foods (Basel, Switzerland) · 2026Article
- These Boots Are Made for Walking: Sex-Specific Physiological and Metabolomic Strategies Reflect Male-Skewed Vulnerability to Ocean Warming in a Keystone Amphipod.Global change biology · 2026Article
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- Systemic Metabolic Alterations After Aneurysmal Subarachnoid Hemorrhage: A Plasma Metabolomics Approach.Neurocritical care · 2026Article
- Investigating uncharacterised genes in Saccharomyces cerevisiae using robot scientists.Scientific reports · 2026Article
- Identifying the shared genes and their related microRNAs, metabolites, and pathways in ischemic stroke and epilepsy.Scientific reports · 2026Article
- Mechanistic Analysis of Physiological and Metabolic Responses in Non-Jointed Water Dropwort Under Phosphorus Stress.Metabolites · 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
- Food deprivation enhances disease resistance: Underlying mechanisms in oysters confronted with pacific oyster mortality syndrome.iScience · 2026Article
- Early-Life Climbing Stratifies the Metabolome and Mortality Risk in Genetically Identical Flies.Aging cell · 2026Article
- Untargeted metabolomics reveals distinct metabolic profiles and putative bioactive metabolites in cell-free supernatants of food-grade microorganisms.Frontiers in microbiology · 2026Article
- Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver.Gut microbes · 2025Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
backgroundPathway enrichment techniques are useful for understanding experimental metabolomics data. Their purpose is to give context to the affected metabolites in terms of the prior knowledge contained in metabolic pathways. However, the interpretation of a prioritized pathway list is still challenging, as pathways show overlap and cross talk effects.
resultsWe introduce FELLA, an R package to perform a network-based enrichment of a list of affected metabolites. FELLA builds a hierarchical representation of an organism biochemistry from the Kyoto Encyclopedia of Genes and Genomes (KEGG), containing pathways, modules, enzymes, reactions and metabolites. In addition to providing a list of pathways, FELLA reports intermediate entities (modules, enzymes, reactions) that link the input metabolites to them. This sheds light on pathway cross talk and potential enzymes or metabolites as targets for the condition under study. FELLA has been applied to six public datasets -three from Homo sapiens, two from Danio rerio and one from Mus musculus- and has reproduced findings from the original studies and from independent literature.
conclusionsThe R package FELLA offers an innovative enrichment concept starting from a list of metabolites, based on a knowledge graph representation of the KEGG database that focuses on interpretability. Besides reporting a list of pathways, FELLA suggests intermediate entities that are of interest per se. Its usefulness has been shown at several molecular levels on six public datasets, including human and animal models. The user can run the enrichment analysis through a simple interactive graphical interface or programmatically. FELLA is publicly available in Bioconductor under the GPL-3 license.
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