Fig. 4

Consensus gene expression profiles for CD4⁺ T-cells from the Discovery Set. A Metagene landscape. We embedded all samples relative to temporally coherent metagenes using the pattern matrix. All genes that we used for NMF were embedded relative to the temporally coherent metagenes using the gene signature matrix and depicted as a density map. For IL2, IL2RA, CD4, and NF-κB (NFKBID) we calculated the average metagene weights across the CD4⁺ T-cell populations and depicted them as dots in the metagene landscape. B Each sample is colored by the rank normalized gene expression of the corresponding gene. C We grouped the consensus expression profiles over the course by genes associated with identity and shared metagenes. Each boxplot represents one CD4⁺ T-cell population from the Discovery Set. The y-axis depicts the standardized median expression of genes from samples with identical analysis time points. The number in parentheses represents the number of genes for the corresponding metagene. D Top 15 genes associated with identity metagenes. For each gene belonging to the consistent metagenes, we used the highest absolute “confect” value estimated in the meta-analysis. Genes were ranked according to their absolute highest “confect” value. Diamonds represent the combined effect size from the meta-analysis for the activation time point with the highest absolute “confect” value. The time point to the right of the gene represents the time point of the highest absolute “confect” value. The inner end of the horizontal line shows the “confect” value (inner confidence bound). E The top 10 (sorted by rich factor) significantly enriched GO terms of biological processes (FDR < 0.05) of metagene-associated genes identified by enrichment analysis. The dot size indicates the rich factor, which is the number of metagene-associated genes in the GO term divided by the number of background genes of the term. Colors indicate adjusted p-values of significantly enriched GO terms