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Lecture 3 Case Studies
Lecture 3 Case Studies
Case Studies
Case Studies
1. Data Exploration and Analysis Planning Lung Cancer 2. Multifactorial Design Mouse Cerebellum 3. Time Course OGTT Metabolomics
Cluster structure in the adjusted data suggests that there is another unexplained covariate
Top changed unknown metabolites could be linked to named species 223566 tryptophan 225405 1/ beta-alanine 274174 methionine, glucuronic acid 228377 tryptophan 362112 tryptophan
Lung Cancer
Conclusions Metabolic data contained batch effects, which could be in part explained by data acquisition date Univariate analyses were limited by the effects of outliers Multivariate modeling was used to identify 64 features (21%) which best explain differences in plasma metabolites from patients with or without lung cancer hydroxylamine, aspartic acid, and tryptophan displayed patterns of change consistent with differences in patient cancer histology Correlation analysis was used to link many significant changes in unknowns to tryptophan
Analysis principal components analysis (PCA) two-way analysis of variance (ANOVA) orthogonal partial least squares discriminant analysis (OPLS-DA) network mapping
PLS-DA
PCA
genotype effect
treatment effect
interaction effect
OSC-PLS-DA/OPLS-DA
Validation
multiple Y
single Y
WT
CSB
Mouse Cerebellum
Conclusions
Major differences between CSB and WT : elevation of 2-hydroxyglutaric acid in CSB
2-hydroxyglutaric aciduria is either autosomal recessive or autosomal dominant
Independent of genotype, treatment effects can be classified on a continuum of metabolic change from CR >HFD > Resv > SD.
Treatment-related changes in citrulline were modified based on genotype (strong genotype/treatment interaction).
Similar changes due to treatment in both genotypes (e.g. 1,5anhydroglycitol) may be an outcome of diet composition and not biology.
Time Course
Oral Glucose Tolerance Test Metabolomics
Summary Analysis of changes in plasma primary metabolites during an oral glucose tolerance test (OGTT) before and after a 14 week diet and exercise intervention. Study Design Overweight women (12-15, obese sedentary, glucose 100 -128 mg/dL ) Pre and post intervention Clinical panel: insulin, glucose, lipids Primary metabolites at 0, 30, 60, 90, 120 minutes
Analysis principal components analysis (PCA) two-way analysis of variance (ANOVA) orthogonal partial least squares discriminant analysis (OPLS-DA) network mapping
PLS-DA modeling and feature selection of changes in Baseline (t =0) AUC Combined baseline and AUC
Analysis of correlations
PCA
Conclusion
Each data analysis is unique Which method should be used is defined by how the data looks and the goal of the analysis Different analysis techniques are used to get independent perspectives of the data Combination of similar evidence from different techniques is used to define the robust explanation of the experiment