Fig. 2: Stimulation-induced changes in gene expression: identification and characterisation of reGenes in multiple conditions.

a Fraction of expressed genes (protein coding and lincRNAs) that are eGenes (genes with at least one eQTL) in our study (red diamond) and in different GTEx tissues (circles) as a function of the sample size (mean sample size across all conditions in our study). GTEx studies of single cell types (cultured fibroblast and lymphocytes) and tissues with similar sample size to our study (Brain-cortex and Liver) are highlighted. b Number and fraction of reGenes (pink) and the total number of eGenes (green) per stimulation condition (left hand panel) and number and fraction of reGenes that were differentially expressed (dark purple, up-regulated, dark pink, down-regulated) and not differentially expressed (pink) (right hand panel). Examples of genes where reQTL was detected following stimulation and genes were significantly up- (c), downregulated (d) or where there was no significant change in expression (e) in the stimulated condition (sLPS at 6 h, n = 191 vs. Ctrl at 6 h, n = 179). Data are presented as individual points, jittered for visibility. Box plots represent the median (centre line), the first and third quartiles (bounds of the box), and the whiskers, which extend to the smallest and largest values within 1.5x the interquartile range from the bounds of the box. Data points outside this range are plotted as outliers. Shaded areas represent linear regression lines fitted to the data, with 95% confidence intervals.