Figure S5.

Basal and Peak Expression of Periodic Genes, Related to Figure 3

(A) Genes from M cluster, ranked according to their median basal expression levels. The horizontal red lines delimit expression zone 2 (0.5-2 mRNA copies/cell), and the three expression zones are indicated at right.

(B) Same as (A) for genes from G1 cluster.

(C) Same as (A) for genes from S cluster.

(D) Plot of the number of genes with median basal expression switching from expression zone 1 to expression zones 2 or 3 as a function of the assumed duration of the peak phase in percent of the cell cycle for the three gene clusters (black: M phase, red: G1 phase, green: S phase). The vertical dotted line marks a ‘peak’ phase length of 10% of the cell cycle.

(E) Cartoon showing three example transition patterns between ‘basal’ and ‘peak’ expression levels: An instantaneous change between the two expression states (red), expression level increases during 50% (gray) or 90% (dotted red) of the non-peak window. $A^i$: Amplitude of periodic variation in expression for gene i (Rustici et al., 2004).

$n_{step}$: Number of intermediate states between ‘basal’ and ‘peak’ levels.

(F) Impact of ramping time on the number of genes switching from zone 1 to zones 2-3 in three clusters of periodic genes as in (D), when either no ramping (red), ramping times between 10% and 80% (gray), or 90% (dotted red) of the ‘basal’ phase are incorporated in the model ($n_{step}$ = 1000). The vertical dotted line marks a ‘peak’ phase length of 10% of the cell cycle.