Additional file 12 of DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures

Additional file 12: Table S8. Results of gene expression analysis of CpG sites associated with metabolic measures. Displayed are the FDR (Benjamini-Hochberg, < 0.05) statistically significant associations between metabolic measure-associated CpG sites and expression transcripts in cis in whole blood (KORA F4, 480 CpG-transcript pairs examined), subcutaneous fat (TwinsUK study, 521 pairs examined) and liver (Karolinska Liver Bank cohort and the Dutch tissue cohort MORE/BBMRI obesity cohort, 271 pairs examined). FDR-adjusted p values were calculated for each tissue separately. “Probe ID” and “Transcript_annotated_gene”: transcript ID and annotated gene from the Illumina annotation files. “Distance”: distance between the CpG and the transcript according to the annotation files. CHR: chromosome; Distance: distance between the CpG and the transcript based on positions given in the annotation files; Coef: beta-coefficient; P: p value; FDR: FDR-corrected p value; Bonf_P: Bonferroni-corrected p value; N: number of observations in the model; “replicated_BIOS”: whether the association (where the CpG is matched directly, but the transcript is matched by annotated gene only), with consistent direction of effect, is found in the FDR < 0.05 significant BIOS QTL database. An “-” indicates the CpG-gene expression pair is not found in the FDR < 0.05 significant results in BIOS. All coefficients are change in log2- transformed expression intensity per unit increase in methylation (beta value on 0–1 scale), except for subcutaneous fat, which is correlation assessed using the R-package rmcorr.