muma, An R Package for Metabolomics Univariate and Multivariate Statistical Analysis

Gaude, Edoardo; Chignola, Francesca; Spiliotopoulos, Dimitrios; Spitaleri, Andrea; Ghitti, Michela; García-Manteiga, José Manuel; Mari, Silvia; Musco, Giovanna

doi:10.2174/2213235x11301020005

Cited by 108 publications

(81 citation statements)

References 20 publications

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“…Each variable is then transformed as a fraction of the total spectral sum. All data preprocessing, data scaling (e.g., pareto) and univariate analysis were performed in R utilizing the MUMA package (Gaude et al 2013). Multivariate data analysis was performed by SIMCA v13.0.3 (Unimetrics, Malmö, Sweden).…”

Section: Discussionmentioning

confidence: 99%

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

Abela

Simmons

Steindl

et al. 2015

J of Inher Metab Disea

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Clinical metabolomics has emerged as a powerful tool to study human metabolism in health and disease. Comparative statistical analysis of untargeted metabolic profiles can reveal perturbations of metabolite levels in diseases and thus has the potential to identify novel biomarkers. Here we have applied a simultaneous genetic-metabolomic approach in twin boys with epileptic encephalopathy of unclear etiology. Clinical exome sequencing identified a novel missense mutation in the spermine synthase gene (SMS) that causes Snyder-Robinson syndrome (SRS). Untargeted plasma metabolome analysis revealed significantly elevated levels of N(8)-acetylspermidine, a precursor derivative of spermine biosynthesis, as a potential novel plasma biomarker for SRS. This result was verified in a third patient with genetically confirmed SRS. This study illustrates the potential of metabolomics as a translational technique to support exome data on a functional and clinical level. Abstract Clinical metabolomics has emerged as a powerful tool to study human metabolism in health and disease. Comparative statistical analysis of untargeted metabolic profiles can reveal perturbations of metabolite levels in diseases and thus has the potential to identify novel biomarkers. Here we have applied a simultaneous genetic-metabolomic approach in twin boys with epileptic encephalopathy of unclear etiology. Clinical exome sequencing identified a novel missense mutation in the spermine synthase gene (SMS) that causes Snyder-Robinson syndrome (SRS). Untargeted plasma metabolome analysis revealed significantly elevated levels of N 8 -acetylspermidine, a precursor derivative of spermine biosynthesis, as a potential novel plasma biomarker for SRS. This result was verified in a third patient with genetically confirmed SRS. This study illustrates the potential of metabolomics as a translational technique to support exome data on a functional and clinical level.

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Section: Discussionmentioning

confidence: 99%

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

Abela

Simmons

Steindl

et al. 2015

J of Inher Metab Disea

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“…Subsequently, to further test the main influence of vacuum drying on individual polyphenols of loquat fruit, the data matrix of the polyphenol content was analyzed by PLS‐DA and OPLS‐DA (Gaude et al., ). The PLS‐DA and OPLS‐DA multivariate pattern recognition with Pareto scaling were performed using the muma package of R (Gaude et al., ). To further define effective markers, the result of multivariate analysis was cross‐selected by examining the volcano plot by considering a fold‐change threshold of 1.5 and t ‐test P ‐value less than 0.05 (Cheema et al., ; Li et al., ).…”

Section: Methodsmentioning

confidence: 99%

Multivariate Analysis Illuminates the Effects of Vacuum Drying on the Extractable and Nonextractable Polyphenols Profile of Loquat Fruit

Wang

Zhang

et al. 2019

Journal of Food Science

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The current study evaluated the effects of vacuum drying on the whole polyphenol profile of loquat fruit, including extractive and nonextractive polyphenols. Absorbance analysis determined that total polyphenol content and antioxidant levels were higher in loquat fruit vacuum dried at 140 °C than in loquat fruit vacuum dried at 70 °C. The results of ultra‐HPLC–triple quadruple mass spectrum analysis showed that 15 phenolic acids and 17 flavonoids were found in dried loquat fruit. Multivariate integrative (MINT) sparse partial least square‐discriminant analysis showed that vacuum drying affects the polyphenol profile of loquat fruit. Co‐analysis of principal component analysis, partial least square‐discriminant analysis, and orthometric partial least square‐discriminant analysis revealed that vacuum drying mainly changed the content of chlorogenic acid, cryptochlorogenic acid, protocatechuic acid, phloretin, and hesperidin in loquat fruit. Chlorogenic acid (12.020 to 39.153 µg/g d.b. [dried base weight]), the main polyphenol in dried loquat fruit, was degraded to caffeic acid (0.028 to 2.365 µg/g d.b.) and protocatechuic acid (0.014 to 18.285 µg/g d.b.) during vacuum drying. Moreover, vacuum drying also induced the isomerization of chlorogenic acid into cryptochlorogenic acid (1.628 to 12.737 µg/g d.b.). These results might be used to develop dried loquat fruit with high levels of polyphenols and antioxidant activity. Practical Application Interests in polyphenols of loquat fruit had increased greatly because of their possible role in health benefits. This work provided a holistic insight in the effects of vacuum drying on polyphenols profile of loquat fruit. Current results have contributed to the development of vacuum‐drying method, which produced loquat fruit rich in polyphenols. Furthermore, it also suggested that multivariate analysis was a feasible method to reveal the important changes of polyphenols profile during food processing.

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“…A principal component analysis (PCA) was run for each species using the library muma (Gaude et al. ), followed by a hierarchical cluster analysis using the library pvclust (Borcard et al. ; Suzuki and Shimodaira ).…”

Section: Methodsmentioning

confidence: 99%

Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development inInga, a genus of tropical trees

Wiggins

Forrister

Endara

et al. 2016

Ecology and Evolution

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Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few‐week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

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muma, An R Package for Metabolomics Univariate and Multivariate Statistical Analysis

Cited by 108 publications

References 20 publications

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

Multivariate Analysis Illuminates the Effects of Vacuum Drying on the Extractable and Nonextractable Polyphenols Profile of Loquat Fruit

Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development inInga, a genus of tropical trees

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muma, An R Package for Metabolomics Univariate and Multivariate Statistical Analysis

Cited by 108 publications

References 20 publications

N8‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

N8‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

Multivariate Analysis Illuminates the Effects of Vacuum Drying on the Extractable and Nonextractable Polyphenols Profile of Loquat Fruit

Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development inInga, a genus of tropical trees

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N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics