Computational protocol: Weight loss moderately affects the mixed meal challenge response of the plasma metabolome and transcriptome of peripheral blood mononuclear cells in abdominally obese subjects

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Protocol publication

[…] Microarray signals were normalized using the robust multichip average algorithm. Data was filtered using universal expression codes filtering with a 50% cut-off, corresponding to a 50% likelihood that a gene is expressed (Piccolo et al. ). Significant differences of individual genes were tested using the limma R library (Smyth ). At fasting, the expression of genes between groups was defined as different when P was < 0.05 in an unpaired t-test with empirical Bayes correction. Gene expression was defined as postprandial changed between T0 and T4 h when P < 0.05 in a paired t-test with empirical Bayesian correction. Data were further analysed with gene set enrichment analysis (GSEA) using pre-ranked lists based on the t-statistic (Subramanian et al. ). Gene sets with a false discovery rate (FDR Q < 0.2) were defined as significantly regulated. Pathway analyses were performed using ingenuity pathway analysis (Qiagen, Redwood City, on filtered dataset and filtered genes were used as background. Plots were made using the R libraries ggplot2 and gplots (Wickham ; Warnes et al. ). […]

Pipeline specifications

Software tools limma, GSEA, IPA, Ggplot2, gplots
Application Miscellaneous
Organisms Homo sapiens