Cargando…

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis

Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced im...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wieder, Cecilia, Frainay, Clément, Poupin, Nathalie, Rodríguez-Mier, Pablo, Vinson, Florence, Cooke, Juliette, Lai, Rachel PJ, Bundy, Jacob G., Jourdan, Fabien, Ebbels, Timothy
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2021
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448349/ https://www.ncbi.nlm.nih.gov/pubmed/34492007 http://dx.doi.org/10.1371/journal.pcbi.1009105

Ejemplares similares

Avoiding the Misuse of Pathway Analysis Tools in Environmental Metabolomics
por: Wieder, Cecilia, et al.
Publicado: (2022)

MetExploreViz: web component for interactive metabolic network visualization
por: Chazalviel, Maxime, et al.
Publicado: (2018)

A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks
por: Merlet, Benjamin, et al.
Publicado: (2016)

MetaboRank: network-based recommendation system to interpret and enrich metabolomics results
por: Frainay, Clément, et al.
Publicado: (2019)

MetExplore: collaborative edition and exploration of metabolic networks
por: Cottret, Ludovic, et al.
Publicado: (2018)

Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors
por: Delmas, Maxime, et al.
Publicado: (2023)

Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126
por: Mesnage, Robin, et al.
Publicado: (2018)

Single sample pathway analysis in metabolomics: performance evaluation and application
por: Wieder, Cecilia, et al.
Publicado: (2022)

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation
por: Amara, Adam, et al.
Publicado: (2022)

DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
por: Rodríguez-Mier, Pablo, et al.
Publicado: (2021)

FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases
por: Delmas, Maxime, et al.
Publicado: (2021)

Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men
por: Comte, Blandine, et al.
Publicado: (2021)

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
por: Cottret, Ludovic, et al.
Publicado: (2010)

An Untargeted Metabolomics Approach to Investigate the Metabolic Modulations of HepG2 Cells Exposed to Low Doses of Bisphenol A and 17β-Estradiol
por: Cabaton, Nicolas J., et al.
Publicado: (2018)

Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas
por: Frainay, Clément, et al.
Publicado: (2018)

Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig
por: Poupin, Nathalie, et al.
Publicado: (2019)

Improving lipid mapping in Genome Scale Metabolic Networks using ontologies
por: Poupin, Nathalie, et al.
Publicado: (2020)

Representational change is integral to reasoning
por: Bundy, Alan, et al.
Publicado: (2023)

Problems, principles and progress in computational annotation of NMR metabolomics data
por: Judge, Michael T., et al.
Publicado: (2022)

Multiple-testing correction in metabolome-wide association studies
por: Peluso, Alina, et al.
Publicado: (2021)

Machine learning to identify pairwise interactions between specific IgE antibodies and their association with asthma: A cross-sectional analysis within a population-based birth cohort
por: Fontanella, Sara, et al.
Publicado: (2018)

Postprandial NMR-Based Metabolic Exchanges Reflect Impaired Phenotypic Flexibility across Splanchnic Organs in the Obese Yucatan Mini-Pig
por: Tremblay-Franco, Marie, et al.
Publicado: (2020)

Comparison of Bi- and Tri-Linear PLS Models for Variable Selection in Metabolomic Time-Series Experiments
por: Gao, Qian, et al.
Publicado: (2019)

Representation of Women in Contemporary Kidney Transplant Trials
por: Vinson, A. J., et al.
Publicado: (2023)

Neural representations underlying mental imagery as unveiled by representation similarity analysis
por: Boccia, Maddalena, et al.
Publicado: (2021)

Reactor safety recommendations
por: Vinson, Kenton I, et al.
Publicado: (2012)

Transgenerational metabolomic fingerprints in mice ancestrally exposed to the obesogen TBT
por: Chamorro-García, Raquel, et al.
Publicado: (2021)

Modelling the acid/base (1)H NMR chemical shift limits of metabolites in human urine
por: Tredwell, Gregory D., et al.
Publicado: (2016)

Fashion Recommendation with Multi-relational Representation Learning
por: Li, Yang, et al.
Publicado: (2020)

Hierarchical Graph Representation of Pharmacophore Models
por: Arthur, Garon, et al.
Publicado: (2020)

Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity
por: Valcárcel, Beatriz, et al.
Publicado: (2014)

Structural Representation of Organometallics and Coordination Compounds and a Recommended Representation by Use of Dashed Lines
por: Lin, Shu-Kun
Publicado: (2002)

The Development of Metabolomic Sampling Procedures for Pichia pastoris, and Baseline Metabolome Data
por: Tredwell, Gregory D., et al.
Publicado: (2011)

Influence of action video gaming on spatial representation in the haptic modality
por: Van Mier, Hanneke I., et al.
Publicado: (2020)

Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis
por: Poupin, Nathalie, et al.
Publicado: (2014)

Classification of Pediatric Asthma: From Phenotype Discovery to Clinical Practice
por: Oksel, Ceyda, et al.
Publicado: (2018)

Variational autoencoders learn transferrable representations of metabolomics data
por: Gomari, Daniel P., et al.
Publicado: (2022)

Personalized movie recommendations based on deep representation learning
por: Li, Luyao, et al.
Publicado: (2023)

PhenoMeNal: processing and analysis of metabolomics data in the cloud
por: Peters, Kristian, et al.
Publicado: (2018)

ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
por: Silva, Ricardo R., et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_80dqtui0aqutge70l127hrpfq6