Fig. 6

Arabidopsis clock repressilator circuit model and estimated transcriptional switch times. The top panel shows the core Arabidopsis clock repressilator circuit model from Pokhilko et al. [11], showing the 3 gene groups: LHY/CCA1 (black), PRRs (blue), EC (dark green). Direct regulatory interactions between the groups are shown by the solid lines, while the indirect interactions caused by the double-negative interactions are shown by dotted lines. The bottom panel shows the switch times and switch types heatmap estimated using the ReTrOS-Switch method for the selected 10 clock genes. The data used here is from microarray time-series for the clock genes in wild-type Arabidopsis plants (PRESTA project) [12]. Switches increasing the transcription rate are shown in red, decreasing transcription switches are shown in green. Darker colours represent more frequently sampled switch times. The direct interactions from the repressilator circuit model are shown by the black, blue and dark green solid lines and the indirect interactions are shown in dashed lines in the same colours. The oscillatory nature of the genes’ transcription is clearly identified in most of the genes and the putative interactions from the repressilator can also be determined in many cases. The default switch parameter values in the parameter setting GUI are used, with the prior mRNA degradation rate set by choosing Arabidopsis