Figure 7.

Change rates with respect to chromosomal location. By comparing change rates of the top 200 regulating genes and their respective chromosome positions, it becomes obvious that strongly regulating genes during early phases of the IDC are enriched in the periphery of the chromosomes (telomeres/sub-telomeres), whereas expression of central genes runs counter to telomeric regions. Genes are represented by red and/or blue lines, which refer to the time of up- (red) or down-regulation (blue). A threshold had to be applied for clarity of the figure and to focus on the strongest regulating genes. Here the threshold consists of an absolute slope degree larger than 3.5 (with respect to a cycle length of 2π; see also "Definitions" within Materials and Methods). The length of a line represents the duration wherein the expression rate strongly continuously increases or decreases. If the gene is only represented by a red line it means that the up-regulation was strong and above the threshold, but the down-regulation was too weak to be included in the graph. Note the four circled regions: A, with strong up-regulation at the subtelomeres (equivalent to class C1 in Figure 8); B, strongly down-regulated genes (belonging to classes C5 and C6 in Figure 8); C, genes that are localized throughout the genome and up-regulated around trophozoite stages (Figure 8, classes C2 and C3); D, second burst of up-regulation that mainly takes place in subtelomeric areas (Figure 8, class C5). This figure illustrates similar information as depicted in Figure 6, with the data now resolved over time. On the right-hand side the weighted density plot of Figure 6 is drawn as a reference. Again, the area of low gene activity is observed.