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Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.

Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G - Anal. Chem. (2014)

Bottom Line: On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity.The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots.The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria.

View Article: PubMed Central - PubMed

Affiliation: Scripps Center for Metabolomics and Mass Spectrometry and ‡Department of Cell Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

ABSTRACT
XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, "control" versus "disease" experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.

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Related in: MedlinePlus

Scheme representing the experimental designof two-group comparison,meta-analysis, and multigroup analysis. Meta-analysis is a higher-orderanalysis that aims to identify shared metabolic patterns among multipleindependent two-group comparisons. Shared dysregulated features arerepresented by the region at the center of the Venn diagram. In contrast,multigroup analysis aims to identify differences between groups andreveal the diversity of metabolic patterns across different groups:wt, bacterial wild type; mut, bacterial mutant.
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fig1: Scheme representing the experimental designof two-group comparison,meta-analysis, and multigroup analysis. Meta-analysis is a higher-orderanalysis that aims to identify shared metabolic patterns among multipleindependent two-group comparisons. Shared dysregulated features arerepresented by the region at the center of the Venn diagram. In contrast,multigroup analysis aims to identify differences between groups andreveal the diversity of metabolic patterns across different groups:wt, bacterial wild type; mut, bacterial mutant.

Mentions: Our new interactive XCMS Online platform integratesunivariateand multivariate data processing, metabolite feature annotation, andmetabolite identification. This easy-to-use graphical interface hasbeen significantly improved to support the statistical analysis ofmore complex experimental designs. It now performs two-group, multiplegroup, and meta-analysis (Figure 1), providingXCMS Online users with a comprehensive univariate and multivariatestatistical report through an interactive display. Novel interactivevisualization tools, including two-group and multigroup cloud plots,principal component analysis, and Venn and relational diagrams, havebeen developed to deconvolve metabolomic data, simplify data analysis,customize data output, and through integration with METLIN, facilitatemetabolite identification. The utility of these approaches is demonstratedon several different data sets that fit the experimental design oftwo-group comparison, of meta-analysis, and of multigroup comparison(Figure 1).


Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.

Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G - Anal. Chem. (2014)

Scheme representing the experimental designof two-group comparison,meta-analysis, and multigroup analysis. Meta-analysis is a higher-orderanalysis that aims to identify shared metabolic patterns among multipleindependent two-group comparisons. Shared dysregulated features arerepresented by the region at the center of the Venn diagram. In contrast,multigroup analysis aims to identify differences between groups andreveal the diversity of metabolic patterns across different groups:wt, bacterial wild type; mut, bacterial mutant.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215863&req=5

fig1: Scheme representing the experimental designof two-group comparison,meta-analysis, and multigroup analysis. Meta-analysis is a higher-orderanalysis that aims to identify shared metabolic patterns among multipleindependent two-group comparisons. Shared dysregulated features arerepresented by the region at the center of the Venn diagram. In contrast,multigroup analysis aims to identify differences between groups andreveal the diversity of metabolic patterns across different groups:wt, bacterial wild type; mut, bacterial mutant.
Mentions: Our new interactive XCMS Online platform integratesunivariateand multivariate data processing, metabolite feature annotation, andmetabolite identification. This easy-to-use graphical interface hasbeen significantly improved to support the statistical analysis ofmore complex experimental designs. It now performs two-group, multiplegroup, and meta-analysis (Figure 1), providingXCMS Online users with a comprehensive univariate and multivariatestatistical report through an interactive display. Novel interactivevisualization tools, including two-group and multigroup cloud plots,principal component analysis, and Venn and relational diagrams, havebeen developed to deconvolve metabolomic data, simplify data analysis,customize data output, and through integration with METLIN, facilitatemetabolite identification. The utility of these approaches is demonstratedon several different data sets that fit the experimental design oftwo-group comparison, of meta-analysis, and of multigroup comparison(Figure 1).

Bottom Line: On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity.The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots.The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria.

View Article: PubMed Central - PubMed

Affiliation: Scripps Center for Metabolomics and Mass Spectrometry and ‡Department of Cell Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

ABSTRACT
XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, "control" versus "disease" experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.

Show MeSH
Related in: MedlinePlus