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This observation was the first to draw an inverse link between methylation and transcript abundance and suggested that highly abundant messages avoid methylation to maximize stability.
A negative association between methylation and transcript level means that increased methylation levels correlate with decreased expression levels, whereas a positive correlation includes levels that both increase or decrease.
The impact of methylation on individualized gene expression was assessed in two ways, first by contrasting the amount of variance explained by CpG status, and more directly by examining the correlation between methylation and transcript abundance for each gene.
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In order to assess whether peak CpG explain the transcript abundance, we computed the correlation between methylation level and transcript abundance.
As summarized in Figure 5C, a strong correlation between methylation frequency and transcript level was found in cancer cell lines.
In this revised version, we have included an additional and earlier time point (3 days + or - Pi) in order to decipher the temporal hierarchy between changes in DNA methylation and transcript abundance.
Accordingly, in this revised manuscript we have: 1) Added an earlier time point to our extensive phosphate starvation time course experiment, enabling us to establish the temporal hierarchy between changes in DNA methylation and transcript abundance.
Firstly, as mentioned above (see Reviewer 1 section), we improved the already extensive time course experiment, allowing us to decipher the temporal relationship between changes in DNA methylation and transcript abundance.
Correlation of methylation and transcript levels of genes between memory and naïve CD4+ T cells.
The overall goal of the association analysis was to identify associations, at the genome-wide level, between age and gene expression, age and CpG methylation, and transcript expression and CpG methylation.
Season also significantly affects the methylation and transcript levels of some important genes in embryos produced from these oocytes.
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