Statistical significance analysis of nuclear magnetic resonance-based metabonomics data

Goodpaster, Aaron M.; Romick-Rosendale, Lindsey E.; Kennedy, Michael A.

doi:10.1016/j.ab.2010.02.005

Cited by 82 publications

(74 citation statements)

References 26 publications

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“…Statistical significance was considered at p < 0.05 (Goodpaster et al 2010). The small size of the non-exposed group does not allow its use as a control group or identify significant differences between concentrations determined in toenails of exposed and non-exposed groups.…”

Section: Discussionmentioning

confidence: 99%

Investigating relationships between biomarkers of exposure and environmental copper and manganese levels in house dusts from a Portuguese industrial city

Reis

Costa

Santos

et al. 2015

Environ Geochem Health

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This study reports on data obtained from a pilot survey focusing on house dust and toenail metal (loids) concentrations in residents living in the industrial city of Estarreja. The study design hereby described aims at investigating relationships between human toenails and both copper and manganese levels in house dusts. A total of 21 households and 30 individuals were recruited for the pilot study: 19 households corresponding to 27 residents living near the industrial complex, forming the exposed group, plus 2 households and 3 residents from residential areas with no anticipated environmental contaminants that were used for comparison. Factorial analysis was used for source apportionment purposes. Investigation on the potential influence of environmental factors over copper and manganese levels in the toenails was carried out via questionnaire data and multiple correspondence analysis. The results show that copper concentrations are more elevated in the indoor dusts while manganese concentrations are more elevated in the outdoor dust samples. The geometrical relationships in the datasets suggest that the backyard soil is a probable source of manganese to the indoor dust. Copper and manganese contents in the toenail clippings are more elevated in children than in adults but the difference between the two age groups is not statistically significant (p> 0.05). Investigation of environmental factors influencing the exposurebiomarker association indicates a probable relationship between manganese contents in indoor dust and manganese levels in toenail clippings, a result that is partially supported by the bioaccessibility estimates.However, for copper no relationship was found between indoor dusts and the biomarkers of exposure.

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Section: Discussionmentioning

confidence: 99%

Investigating relationships between biomarkers of exposure and environmental copper and manganese levels in house dusts from a Portuguese industrial city

Reis

Costa

Santos

et al. 2015

Environ Geochem Health

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“…The results were analyzed in the context of the statistical significance of the PCA loadings that drive cluster separation in the PCA scores plot according to an approach developed previously in our lab [5]. PCA and PLS-DA scores plot separations were assessed by comparing “no scaling” and Pareto scaling data pretreatment prior to PCA and PLS-DA.…”

Section: Resultsmentioning

confidence: 99%

“…Application of the statistical test to the total separation dataset analyzed using PLS-DA resulted in a 14% increase in the T 2 statistic for the cluster separation (661.56) (Table 1) compared to simple PCA with a corresponding F-score of 322.30 (Table 1), which when subjected to the F-test using a critical F-value of 3.96, indicated statistically significant separation between the clusters. Note that the statistical significance of the variances in the bucket intensities [5] do not change as a result of analyzing the data using PLS-DA compared to PCA, although the magnitude of the cluster separation and the statistical significance of the cluster separation increases; this point will be discussed further below.…”

Section: Resultsmentioning

confidence: 99%

“…While statistical validation of metabolite changes between groups identified by either PCA or PLS-DA is essential [5], examples exist in the metabonomics literature where metabolites are identified as changing between groups based on PCA or PLS-DA group separation in scores plots even though the visual separation between groups is questionable. Unfortunately no standard metric has been introduced or widely adopted to quantify cluster separation and to assess the statistical significance of cluster separation in PCA and PLS-DA scores plots.…”

Section: Introductionmentioning

confidence: 99%

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Quantification and statistical significance analysis of group separation in NMR-based metabonomics studies

Goodpaster

Kennedy

2011

Chemometrics and Intelligent Laboratory Systems

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Currently, no standard metrics are used to quantify cluster separation in PCA or PLS-DA scores plots for metabonomics studies or to determine if cluster separation is statistically significant. Lack of such measures makes it virtually impossible to compare independent or inter-laboratory studies and can lead to confusion in the metabonomics literature when authors putatively identify metabolites distinguishing classes of samples based on visual and qualitative inspection of scores plots that exhibit marginal separation. While previous papers have addressed quantification of cluster separation in PCA scores plots, none have advocated routine use of a quantitative measure of separation that is supported by a standard and rigorous assessment of whether or not the cluster separation is statistically significant. Here quantification and statistical significance of separation of group centroids in PCA and PLS-DA scores plots are considered. The Mahalanobis distance is used to quantify the distance between group centroids, and the two-sample Hotelling's T2 test is computed for the data, related to an F-statistic, and then an F-test is applied to determine if the cluster separation is statistically significant. We demonstrate the value of this approach using four datasets containing various degrees of separation, ranging from groups that had no apparent visual cluster separation to groups that had no visual cluster overlap. Widespread adoption of such concrete metrics to quantify and evaluate the statistical significance of PCA and PLS-DA cluster separation would help standardize reporting of metabonomics data.

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“…Statistically significant changing buckets for pair-wise analysis (FM vs EC/NEC/NECM/ECM) were determined using both AMIX and MetaboAnalyst 2.0. The significant bucket intensity values identified by AMIX ( p <0.011875, 0.021591, 0.0084821, and 0.0095, respectively; Bonferroni-corrected confidence intervals for significant metabolite analysis) were exported to Microsoft Excel and fold changes were manually calculated by subtracting two corresponding buckets [27]. Calculations of fold changes and T tests were also performed with MetaboAnalyst 2.0 in order to determine whether or not the changes in bucket intensities were statistically significant.…”

Section: Methodsmentioning

confidence: 99%

NMR-based metabolomics study of the biochemical relationship between sugarcane callus tissues and their respective nutrient culture media

et al. 2014

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The culture of sugarcane leaf explant onto culture induction medium triggers the stimulation of cell metabolism into both embryogenic and non-embryogenic callus tissues. Previous analyses demonstrated that embryogenic and nonembryogenic callus tissues have distinct metabolic profiles. This study is the follow-up to understand the biochemical relationship between the nutrient media and callus tissues using one-dimensional (1D 1H) and two-dimensional (2D 1H–13C) NMR spectroscopy followed by principal component analysis (PCA). 1D 1H spectral comparisons of fresh unspent media (FM), embryogenic callus media (ECM), non-embryogenic callus media (NECM), embryogenic callus (EC), and non-embryogenic callus (NEC), showed different metabolic relationships between callus tissues and media. Based on metabolite fold change analysis, significantly changing sugar compounds such as glucose, fructose, sucrose, and maltose were maintained in large quantities by EC only. Significantly different amino acid compounds such as valine, leucine, alanine, threonine, asparagine, and glutamine and different organic acid derivatives such as lactate, 2-hydroxyisobutyrate, 4-aminobutyrate, malonate, and choline were present in EC, NEC, and NECM, which indicates that EC maintained these nutrients, while NEC either maintained or secreted the metabolites. These media and callus-specific results suggest that EC and NEC utilize and/or secrete media nutrients differently.

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Statistical significance analysis of nuclear magnetic resonance-based metabonomics data

Cited by 82 publications

References 26 publications

Investigating relationships between biomarkers of exposure and environmental copper and manganese levels in house dusts from a Portuguese industrial city

Investigating relationships between biomarkers of exposure and environmental copper and manganese levels in house dusts from a Portuguese industrial city

Quantification and statistical significance analysis of group separation in NMR-based metabonomics studies

NMR-based metabolomics study of the biochemical relationship between sugarcane callus tissues and their respective nutrient culture media

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