Fig. 2

Common trends across CD4⁺ T-cell populations from the Discovery Set. A Inverse cumulative distributions of DE genes (FDR < 0.05) in the Discovery Set for each time point during activation compared to unactivated CD4⁺ T-cells. The colored curves represent the number of DE genes in at least n T-cell populations. Analysis time points 12 to 72 h were available for all 5 CD4⁺ T-cell populations. B Depicting the number of T-cell populations in which genes were identified as DE (y-axis) and the number of genes with consistent fold changes across T-cell populations (x-axis). For example, a gene that is significantly differentially expressed in 3 T-cell populations after 12 h of activation, of which it is down-regulated in 2 populations, will get a fold change sign consistency of 1 + (− 2) =  − 1 (x-axis). An example of how to read the numbers: 7920 genes (top right) were identified as DE in all 5 T-cell populations. These DE genes were also upregulated in all 5 T-cell populations at the same time point of activation. Colors represent the number of T-cell populations in which genes were significantly differentially expressed. C Shown are DE genes with a combined effect size identified in the meta-analysis using a random effect model in at least 2 T-cell populations. The x-axis represents the combined effect size, the y-axis the “confect” value, a confident inner bound of the calculated combined effect size (see the “Methods” sction). Genes that do not show a significant combined effect size (FDR > 0.05) have a “confect” value of 0