ArticleAnalytical biochemistry2010
Analysis of metabolomic PCA data using tree diagrams.
Article in Analytical biochemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Enhancing Spectrometer Performance with Unsupervised Machine Learning.The journal of physical chemistry. B · 2024Article
- Comparative chemical characters ofChinese herbal medicines · 2023Article
- Integrated multi-omics reveal important roles of gut contents in intestinal ischemia-reperfusion induced injuries in rats.Communications biology · 2022Article
- Progress Toward a Multiomic Understanding of Traumatic Brain Injury: A Review.Biomarker insights · 2022Review
- Current applications of capillary electrophoresis-mass spectrometry for the analysis of biologically important analytes in urine (2017 to mid-2021): A review.Journal of separation science · 2022Review
- Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories.Microorganisms · 2021Review
- GC-MS Based Metabolite Profiling to Monitor Ripening-Specific Metabolites in Pineapple (Metabolites · 2020Article
- Metabolic response of yellow mealworm larvae to two alternative rearing substrates.Metabolomics : Official journal of the Metabolomic Society · 2019Article
- Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility.Antimicrobial agents and chemotherapy · 2018Article
- Combining metabolomics and network analysis to improve tacrolimus production in Streptomyces tsukubaensis using different exogenous feedings.Journal of industrial microbiology & biotechnology · 2017Article
- Glucose Metabolism and AMPK Signaling Regulate Dopaminergic Cell Death Induced by Gene (α-Synuclein)-Environment (Paraquat) Interactions.Molecular neurobiology · 2017Article
- Assessment of Metabolic Changes in Mycobacterium smegmatis Wild-Type and alr Mutant Strains: Evidence of a New Pathway of d-Alanine Biosynthesis.Journal of proteome research · 2017Article
- Staphylococcus aureus metabolic adaptations during the transition from a daptomycin susceptibility phenotype to a daptomycin nonsusceptibility phenotype.Antimicrobial agents and chemotherapy · 2015Article
- Alterations in energy/redox metabolism induced by mitochondrial and environmental toxins: a specific role for glucose-6-phosphate-dehydrogenase and the pentose phosphate pathway in paraquat toxicity.ACS chemical biology · 2014Article
- The current state of drug discovery and a potential role for NMR metabolomics.Journal of medicinal chemistry · 2014Review
- Influence of iron and aeration on Staphylococcus aureus growth, metabolism, and transcription.Journal of bacteriology · 2014Article
- Principal components analysis of protein sequence clusters.Journal of structural and functional genomics · 2014Article
- Article
- Catabolite control protein E (CcpE) is a LysR-type transcriptional regulator of tricarboxylic acid cycle activity in Staphylococcus aureus.The Journal of biological chemistry · 2013Article
- Revisiting Protocols for the NMR Analysis of Bacterial Metabolomes.Journal of integrated OMICS · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Large amounts of data from high-throughput metabolomic experiments are commonly visualized using a principal component analysis (PCA) two-dimensional scores plot. The question of the similarity or difference between multiple metabolic states then becomes a question of the degree of overlap between their respective data point clusters in principal component (PC) scores space. A qualitative visual inspection of the clustering pattern in PCA scores plots is a common protocol. This article describes the application of tree diagrams and bootstrapping techniques for an improved quantitative analysis of metabolic PCA data clustering. Our PCAtoTree program creates a distance matrix with 100 bootstrap steps that describes the separation of all clusters in a metabolic data set. Using accepted phylogenetic software, the distance matrix resulting from the various metabolic states is organized into a phylogenetic-like tree format, where bootstrap values 50 indicate a statistically relevant branch separation. PCAtoTree analysis of two previously published data sets demonstrates the improved resolution of metabolic state differences using tree diagrams. In addition, for metabolomic studies of large numbers of different metabolic states, the tree format provides a better description of similarities and differences between each metabolic state. The approach is also tolerant of sample size variations between different metabolic states.
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