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Two different types of data analysis were performed in order to detect methylation alterations between groups and also in individual samples, with and without previous data normalization (Supplementary material).
A χ 2 test or Fisher's exact test and an independent t test were used to compare the clinicopathological variables or the frequency of methylation alterations between the different microsatellite genotypes.
Preliminary investigations of DNA methylation mainly focused on disease-related genes, such as RELN [ 7], SOX10 [ 8], MB-COMT [ 9] and GAD1 [ 10], which exhibited methylation alterations between major psychosis and normal controls.
AXIN2 was one of these genes, which displayed a distinct level of methylation alterations between the two groups (black bar at right margins of Figure 2 and Additional file 1: Figure S2).
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We could not find any significant correlations between methylation alterations in either of the matched lymph node metastasis and clinicopathological parameters.
Differences in the average number of BAC clones that showed DNA methylation alterations (DNA hypomethylation and hypermethylation) between non-cancerous renal cortex tissue samples obtained from patients with clear cell RCCs, and the clear cell RCCs themselves, were analyzed using the Mann–Whitney U-test.
However, other studies demonstrated that epigenetic inheritance via the gametes can be more complex than the direct transmission of DNA methylation alterations, and a crosstalk might exist between different levels of epigenetic regulation across generations.
The relationship between the frequency of methylation alterations and the clinicopathological features was analyzed in 39 gastric cancers with high-level and low-level chromosomal losses (table 6).
Recently, another study confirmed the association between prenatal smoke exposure and methylation alterations.
Genome-wide surveillance of methylation alterations by MS-AFLP revealed no significant differences between the 4 groups (Table 1).
Of a total of 598 methylation alterations, 472 (79%) showed a one-level difference in methylation between the paired normal and tumor DNA and 126 (21%) showed a two- or higher-level difference with an inverse methylation status between the normal and tumor DNA [see Additional file 2].
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