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We found, however, no obvious relationship between the methylation pattern and the phenotype.
We further confirmed the association between the methylation pattern and downregulation of 14-3-3 14-3-3 14-3-3DNA demethylating agent, 5-aza-2'-deoxycytidine.
No significant association between the methylation pattern of the other CpG sites and the levels of IL-8 expression was found.
Our recent study also showed a significant association between the methylation pattern in HCC tumors and major risk factors, including HBV infection and alcohol intake [ 66].
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These results suggest us to further build the association between the methylation patterns and the phenotypic variations, and explore the possibility of the region as a biomarker in resistant breeding.
Although Jaligot et al. (2004) found poor correlation between somaclonal variations and the methylation pattern using methylation-sensitive amplified polymorphism (MSAP), this method can still reveal changes in methylation levels in small regions that are masked in global measurements (Smýkml et al. 2007).
First, we checked the homogeneity of the methylation pattern between the cells of each individual on the 2 (5mCpG/CpG) x number of cells contingency table.
However, with such a scheme, some false positive gene loci will actually arise due to differences in the methylation pattern between colorectal adenocarcinoma and leukocyte cells.
The excess of mutations in CpG sites might reflect subtle differences in the methylation pattern between the AVs and the reconstructed mutation group although problems with the parsimony reconstruction, such as excess of multiple parallel mutations in CpG codons in chimp and gorilla, cannot be ruled out.
Finally, the selected 13 CpG sites may not represent the methylation pattern of the whole APOE, but the usual highly correlated methylation status of the nearby CpG sites (Shoemaker et al., 2010) and the consistent methylation patterns between our observation and previous publication with higher coverage may ameliorate this limitation to some extent.
We looked for similarities in the methylation patterns between genes by performing an analysis of correlations between QUMSP readings on the genes across all samples.
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