Development of a novel output value for quantitative assessment in methylated DNA immunoprecipitation-CpG island microarray analysis.

ABSTRACT: In DNA methylation microarray analysis, quantitative assessment of intermediate methylation levels in samples with various global methylation levels is still difficult. Here, specifically for methylated DNA immunoprecipitation-CpG island (CGI) microarray analysis, we developed a new output value. The signal log ratio reflected the global methylation levels, but had only moderate linear correlation (r = 0.72) with the fraction of DNA molecules immunoprecipitated. By multiplying the signal log ratio using a coefficient obtained from the probability value that took account of signals in neighbouring probes, its linearity was markedly improved (r = 0.94). The new output value, Me value, reflected the global methylation level, had a strong correlation also with the fraction of methylated CpG si

SUBMITTER: Yamashita S 

PROVIDER: S-EPMC2762412 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature