Figure 2

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.