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Fig. 1 | BMC Research Notes

Fig. 1

From: Changes in DNA methylation in naïve T helper cells regulate the pathophysiological state in minimal-change nephrotic syndrome

Fig. 1

Three sets of comparisons with microarray-based integrated analysis of methylation by isoschizomers (MIAMI). The 3 sets of comparisons are indicated schematically: comparison between a relapse and remission, d relapse and controls, and g remission and controls. Scatter plots of the signals obtained with each probe in MIAMI analysis are represented; comparisons between relapse and remission in monocytes (b) and in naïve T helper cells (Th0s) (c), between relapse and controls in monocytes (e) and in Th0s (f), and between remission and controls in monocytes (h) and Th0s (i) are shown. The y-axis represents the signal intensity ratios of each probe between 2 samples digested with HpaII, a methyl-sensitive restriction enzyme that indicates the differences in DNA methylation between the 2 samples. The x-axis represents the ratios between the same set of samples digested with MspI, which is a methyl-insensitive isoschizomer of HpaII. Thus, the x-axis indicates the digestion efficiency or accessibility of restriction enzymes. For statistical analysis, we used the Mahalanobis distance, which is a simplistic approach for estimating the standard deviation of distance between each sample point and the center of mass. The threshold values were determined at a 99% CI of the Mahalanobis distance from the center of the mass (solid line) and 99% CI of the MspI treatment signal plotted on the x-axis (dash line). The probes in the upper area of the 99% CI of Mahalanobis distance and concomitantly within 99% CI of MspI digestion corresponded to significantly less methylated in relapse (b, c, e, and f) and in remission (h and i) than each comparative. In contrast, the probes in the lower area indicated significantly more methylated in the relapse (b, c, e, and f) or in remission (h and i). The numbers in each figure indicate detected probe numbers in each area; (minus) indicates less methylated probes, while (plus) indicates more methylated probes. The number of probes detected is shown in Table 2

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