Franny Jongbloed

86 CHAPTER 4 CHO-free diet. The genes corresponding to the 70 DEPS in common are listed in Table S1. Comparing 3-day 30% DR with the protective diets, a similar pattern was observed; only 15 DEPS overlapped in the three protective diets, while 47 DEPS were also present in the non-protective 3-day 30% DR diet (Figure 3B). However, both numbers of overlapping genes appeared too small to perform pathway analysis with the aim to find a common denominator of protection against renal IRI, and therefore an alternative approximation for analysis was used. Figure 2. Heat map and PCA plots of directional and cluster patterns in all dietary interventions based on the differentially expressed probe sets (DEPS) after three days of fasting compared to its control group. (A) The majority of the DEPS in the kidney after three days of fasting showed the same directionality in the other dietary interventions. The 3-day CHO-free diet was the least clustered with the other diets, followed by two weeks 30% DR and a 3-day protein-free diet. The fat-free diet, showing no significant DEPS, clustered together with a 3-day protein-free diet. Red= upregulation, blue = downregulation, white = no change. CHO-free = carbohydrate-free. (B) Principal component analysis (PCA) plot, based on the 2604 significantly regulated probe sets after three days fasting compared to the control diet fed animals. Both two weeks 30% DR and three days of 30% DR diet clustered close to each other based on the DEPS found after three days of fasting. The two control diets, control and SDS diet, clustered together with the non-protective fat-free diet. Three days of CHO-free diet positioned closely to two weeks and three days of 30% DR, but did not overlap with these diets. The protein-free diet had its own cluster, separated from the other groups on both PC axes.