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This interaction is modulated by methylation of arginine residues within and proximal to the NLS (Dormann et al., 2012).
The advantage of the iBAG unified model is that it can identify the genes with effects modulated by methylation, and thus the results are more biologically interpretable.
Of the 22 genes identified by effects modulated by methylation, 14 are negatively associated with survival, whereas eight genes are positively associated with survival.
Data suggest that CTCF binding to enhancer blocking sequences within the DMR is modulated by methylation status, which results in differential interference of enhancer-promoter communication.
We use an asterisk to show the genes significantly modulated by methylation, as identified by the iBAG unified model (within the list provided in Supplementary Table S1).
Furthermore, our data suggest that MMP-2 expression in ameloblastomas may not be modulated by methylation because the methylation profile for this gene did not correlate with MMP-2 transcript levels in this odontogenic tumour.
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Finally, we utilized the GOLDN population to explore (i) whether age is associated with APOE methylation, (ii) whether the effects of age on APOE methylation leads to changes in plasma lipids, the main functional phenotype of APOE, and (iii) whether the effect of age on APOE methylation can be modulated by methylation-related genetic variants in the APOE locus.
Since multiple single-nucleotide polymorphisms (SNPs) associated with poor activity to clopidogrel [ 11] did not appear to directly affect P2Y12 expression, the altered expression of P2Y12 was likely to be modulated by methylations of promoters or other epigenetic changes.
A similar trend was previously noticed for the HSP70 gene, which has genomic methylation, but is not transcriptionally modulated by DNA methylation [ 18].
By uncovering DNA methylation patterns on individual genes, some genes accurately modulated by DNA methylation were found to be associated with cancers and virus infection, e.g., AKT1 and CTNNB1.
Interestingly, miRNAs expression can be modulated by DNA methylation and histone modifications and they can modulate the DNA methylation machinery leading to a "loop" of epigenetic regulation [ 57– 57].
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