Threshold insensitivity and robustness of RE-based analysis. (A) The RE frequency distributions for three liver data sets (blue: Sci, green: Sve and red: Sva) and corresponding null data set (gray dash line: Snull). The x-axis represents the gene RE frequency (up minus down) and the y-axis represents the gene numbers. (B) The comparison of threshold sensitivity for DEG (dashed line) and average RE (solid line) detections. Total regulations, including up and down direction, were counted by various detection thresholds (q-value, x-axis). The y-axis represents the number of filtered DEGs or REs. (C-E) The detection robustness of enrichment test for GS "lipid metabolic process" (GO:00006629) were compared between DEGs and average RE. The down-regulation and up-regulation are separately shown in red and green color, respectively. The y-axis represents the significance level of the GS across various detection thresholds of DEG or average RE.