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, http://www.qiagen.com/ingenuity) 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