The relationship between methylation and mRNA expression was then analyzed. There was no effect of average methylation on mRNA expression as determined by either primer probeset. However, since the inter-CpG residue methylation correlation coefficients were not strong across the entire island and since some residues, particularly those near the transcription start site, may be more important than others, we then examined the relationship between methylation at each residue and mRNA expression. With respect to the exon 1 probe, before correction for multiple comparison, methylation at CpG 7 and CpG 62 was significantly associated (P < 0.05, ANOVA), and with respect to the exon 8 probe, before correction for multiple comparison, methylation at CpG 30–33 and CpG 62 (P < 0.05, ANOVA) was significantly associated with mRNA production. In each case, increased amounts of methylation at these residues were associated with decreased mRNA transcription. No other significant relationships were observed.
