Fig. 2

Variance in the global heat shock response. a Modelling of the genome-wide transcriptional response to heat-shock (component plot) based on PLS to identify latent structures in the data for cohort of 43 LCLs. The x-axis represents the first PLS component which segregates basal samples (left) and heat shocked samples (right). The y-axis represents the second PLS component which involves variation between cell lines in basal and heat shock response states. Each cell line’s basal and heat shock samples are similarly coloured and paired samples are connected with an arrow, which represents the vector used as quantitative trait in the genetic association test for genetic modulators of the global heat shock response. The average response is indicated by a black arrow. Overall, samples separate clearly by treatment, showing a consistent global effect on gene expression from heat shock. Heat shock stimulated samples show evidence of three distinct clusters (indicated by shaded ovals). b Unsupervised hierarchical cluster analysis with heat shock stimulated samples showing evidence of three distinct clusters (indicated on panel A by shaded ovals). Below the cluster dendrogram is a heatmap showing differential gene expression. Expression estimates for each gene were scaled and centred across samples. Blue cells correspond to lower than average expression and red cells correspond to higher than average expression. c Volcano plot of differential expression results between clusters 1 and 2. Probes with an adjusted p value below 0.01 and a log FC of at least 0.5 are shown as yellow and red dots