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We confirmed that CpG sites have much lower methylation levels in promoter regions when compared with the genome-wide average, as previously shown (Lister et al. 2009).
Our results indicated that CHD cases have a much lower methylation level (49.77 ± 6.43%) compared with controls (54.47 ± 7.65%, P = 0.018).
When comparing non-CpG methylation across genomic regions, a pattern similar to that for CpG sites within CGIs, CGS, introns, and exons was detected, albeit at a much lower methylation level (Fig. 3b).
The 44 genistein-fed offspring were more than twice as likely as the 52 controls to have brown fur and to have much higher methylation, while they were only one-third as likely to have yellow fur and much lower methylation.
The pyrosequencing revealed much lower methylation of the 6.1 Kb promoter region (1-19% mean methylation) in the 5 CpG islands; the 6.2 Kb promoter region showed a higher percentage of mean methylation of 60-65% in all the tissues examined.
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Populations 1 and 3 displayed a profile compatible with loss of imprinting, with no major allele-specific difference in methylation and a much lower overall methylation (around 4 6%).
To accomplish this aim, we first developed an algorithm to establish regions of high fractional DNA methylation bordered by regions of much lower DNA methylation (see Materials and Methods).
MAGEA1 had high mean methylation levels in the control mammoplasty samples and adjacent samples (>80 % for both) but much lower DNA methylation levels in the cancer samples.
For instance, if we assume p 1 = 0.95 (near perfect conversion), the estimated global methylation level is much lower than fractional methylation (Table 2).
Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues.
Second, those insects that have the enzymatic machinery to perform DNA methylation, such as the honey bee Apis mellifera, show much lower overall levels of methylation (approximately 0.69% of all CpGs are methylated) than mammals, and methylation occurs primarily in exonic regions (Glastad et al. 2011; Lyko et al. 2010).
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