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This frequency (0.86) is significantly higher than that observed in the average promoter (frequency = 0.42; p < 1.4 × 10-285) as well as promoters with increased methylation levels in abused individuals (frequency = 0.38; p < 4 × 10-138; Additional file 6: Figure S5).
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There was no significant association between RASSF1A promoter methylation frequency and the K -ras or EGFR mutation frequency.
As shown in Figure 9A the genes form two clusters based on their promoter CpG frequency (observed CpG/expected CpG) and genes with high CpG frequency promoters tend to be more highly expressed.
Figure 9B shows that the genes also form two clusters based on their promoter CpG frequency with respect to promoter methylation levels.
Although cytosine methylation was also observed in the NOS promoter, the frequency of methylation in the 35Spro region was demonstrably higher (Figure S4B).
Interestingly, non-CIMP anaplastic gliomas showed a MGMT promoter methylation frequency similar to glioblastoma.
To explore further relationships between methylation and promoter CpG frequency, promoters were divided into three groups based on their CpG ratios [ 42], that is, LCPs, ICPs, and HCPs.
Differences in the TERT promoter mutation frequency between tumors with different clinical parameters were determined using Fisher's exact test.
The relative importance of a TFBS was determined by the average ranking order of the ECR, promoter and frequency analysis.
The correlation between gene activity and DNA methylation suggests that promoter activity frequency varies among promoter classes, dependent on CpG content.
Likewise, the DAPK promoter methylation frequency in patients with p53 mutations was 25% (8/32) and not different from that in patients with wild-type p53 [35.6% (32/90), p = 0.331].
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