**5.3. Effect of white blood cells on whole blood gene expression profiles in dietary-induced hyperlipidemia**

Microarray analyses were conducted from white blood cells at the end of the dietary period to evaluate the effect of white blood cells on whole blood gene expression profiles (Figure 8). The correlation coefficients of white blood cells expression profiles within the same dietary groups were 0.94 (0.05) and 0.95 (0.03) for the control and HFCD groups at 27 weeks. The white blood cells correlation coefficients was 0.94 (0.04) between control and HFCD. The average correlation coefficients between whole blood and white blood cells were 0.83 (0.04) and 0.79 (0.05) for control and HFCD. Using Fisher's Z-transformation to normalize the correlation distributions, no significant differences in correlation coefficients of white blood cells were observed between control and HFCD groups.

Up- and down-regulated genes were identified and classified these according to function using information from the Gene Ontology (GO) Database to understand the observed differences in white blood cells gene expression profiles for the different dietary groups, as the same as whole blood gene expression profiles. Top-ranked genes with fold changes in expression greater than 2.0 (p < 0.05) and less than 0.5 (p < 0.05) were selected at 27 weeks. As a result, many genes down-regulated related oxidation-reduction process (GO:0055114) and keg pathways of steroid biosynthesis.

induced hyperlipidemia for our protocols.

**dietary-induced hyperlipidemia** 

cells were observed between control and HFCD groups.

and keg pathways of steroid biosynthesis.

respectively.

The correlation coefficients of whole blood expression profiles within the same diet groups were 0.97 (0.01) (mean (standard deviation; SD)), and 0.94 (0.05) for the control, HFCD whole blood at 10 weeks, 0.94 (0.03), and 0.93 (0.06) at 19 weeks, and 0.95 (0.02), and 0.95 (0.03) at 27 weeks, respectively. Using Fisher's Z-transformation to normalize the correlation distributions, no significant differences in correlation coefficients among dietary groups were observed at any period during the treatments. This indicates uniformity of dietary-

The whole blood correlation coefficients among the different diet groups were 0.95 (0.04) for control vs. HFCD at 10 weeks, 0.93 (0.03) at 19 weeks, and 0.95 (0.03) at 27 weeks,

**5.2. Assigning known functions to gene expression - Gene ontology annotation** 

in the GO categories related to biological adhesion (GO: 0007155, GO: 0022610).

**5.3. Effect of white blood cells on whole blood gene expression profiles in** 

Microarray analyses were conducted from white blood cells at the end of the dietary period to evaluate the effect of white blood cells on whole blood gene expression profiles (Figure 8). The correlation coefficients of white blood cells expression profiles within the same dietary groups were 0.94 (0.05) and 0.95 (0.03) for the control and HFCD groups at 27 weeks. The white blood cells correlation coefficients was 0.94 (0.04) between control and HFCD. The average correlation coefficients between whole blood and white blood cells were 0.83 (0.04) and 0.79 (0.05) for control and HFCD. Using Fisher's Z-transformation to normalize the correlation distributions, no significant differences in correlation coefficients of white blood

Up- and down-regulated genes were identified and classified these according to function using information from the Gene Ontology (GO) Database to understand the observed differences in white blood cells gene expression profiles for the different dietary groups, as the same as whole blood gene expression profiles. Top-ranked genes with fold changes in expression greater than 2.0 (p < 0.05) and less than 0.5 (p < 0.05) were selected at 27 weeks. As a result, many genes down-regulated related oxidation-reduction process (GO:0055114)

Up- and down-regulated genes were identified and classified these according to function using information from the Gene Ontology (GO) Database to understand the observed differences in whole blood gene expression profiles for the different dietary groups. Topranked genes with fold changes in expression greater than 2.0 (p < 0.05) and less than 0.5 (p < 0.05) were selected at 10, 19, and 27 weeks. As a result, the GO categories of many genes up-regulated at the end of the 19-week dietary period were related to nucleotide binding (GO: 0000166, GO: GO: 0005524, 0005525, GO: 0017076, GO: 0019001, GO: 00032553, GO: 00032555, GO: 0032561), and catabolic processes (GO: 0009057, GO: 0019941, GO: 0030163, GO: 0043632, GO: 0044257, GO: 0044265,). Many genes down-regulated after 27 weeks were

**Figure 7. Correlation matrix of dietary-related gene expression profiles of whole blood**. This colorcoded correlation matrix illustrates pairwise correlations between the levels of gene expression in individuals. Probe sets with normalized signals (log-transformed and scaled) were used to calculate correlations between 23 arrays using Pearson correlation coefficient; signals flagged as "absent" were excluded. The color scale at the bottom indicates the strengths of the correlations.

**Figure 8. Correlation matrix of dietary-related gene expression profiles of whole blood and white blood cells.** This color-coded correlation matrix illustrates pairwise correlations between the levels of gene expression in individual at feeding period at week 27. Probe sets with normalized signals (logtransformed and scaled) were used to calculate correlations between 15 arrays using Pearson correlation coefficient; signals flagged as "absent" were excluded. The color scale at the bottom indicates the strengths of the correlations.
