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* χ2 test of the difference of complementary substitution between non-CpG site and CpG site.
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Our analysis revealed that around a CGI there is an asymmetry between complementary substitution rates that is similar to the one that found around the OBR in bacteria.
In this study we have found that within intronic regions, strand asymmetries between complementary substitution rates are found in all mammals.
To check whether transcription has an additional impact on the ratios between complementary substitution rates, we preformed a sliding-window analysis also along intronic regions of genes whose TSS is inside of a tCGI and we denote them by tCGI genes (see fig. 1 and Materials and Methods).
Reverse mapping reads therefore show the complementary substitution patterns at the 3′ end to the forward mapping reads at the 5′ end.
Note that these groups are invariant with respect to the strand direction because complementary substitutions do not change the group membership.
Similarly, equal proportions of complementary substitutions were observed for DIMs.
We focused our analysis on the three most frequent substitutions (connected to its complementary substitutions): the transversion G→T (complementary to C→A) and the two transitions A→G (complementary to T→C) and C→T (complementary to G→A).
Besides their length, the blue15 and yellow18 complementary regions differ from each other by few complementary substitutions.
We determined lineage-specific substitution rates of the transcribed regions γ of human and mouse genomes and computed the rate asymmetries for the three most frequent substitutions (and its complementary substitutions): the transversion G→T (complementary to C→A) and the two transitions A→G (complementary to T→C) and C→T (complementary to G→A).
The couple of complementary substitutions A↔T followed a similar distribution in the total and cancer-associated datasets.
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CEO of Professional Science Editing for Scientists @ prosciediting.com