Gene-wise linear and quadratic effects of transcription levels. Example plot for two genes showing a linearly increasing (A) and decreasing (B) mean log2 intensity level as a function of the 6 days in the time-course. These genes map to two of the top detected regions with a linear time effect for the forward strand of chromosome 1. The mean of the linear time effect parameter estimates corresponding with the probes in these regions are 1.08 and -1.16 respectively. Plots C and D give two examples of genes with a strong quadratic effect on the forward strand of chromosome 1. The dotted black lines represent the mean observed log2 expression for the probes over the three biological replicates at the different time points. The dotted grey line is the mean observed log2 expression over all the probes in the region. The orange lines are the probe-wise fitted log2 expression values when only considering the intercept and the linear time effect in the model for the two upper-part genes, and considering the intercept, the linear and the quadratic time effect in the model for the two lower-part genes. The purple line gives the corresponding mean fitted log2 expression values at the different time points over all the probes in the region.