Table 3.
Top ten differentially methylated positions [DMPs] in patients with inflammatory bowel diseases vs controls that were tested in the Scandinavian cohort [NE Holm represents Holm-corrected p value] and replicated across UK [UK Holm represents p value] and Spain [SE Holm]. The highlighted probe remains significant across all cohorts
| Probe ID | Chr | Gene | Region | Relation to CpG island | Log FC | NE p value | NE Holm | UK Holm | SE Holm |
|---|---|---|---|---|---|---|---|---|---|
| cg17501210 | 6 | RPS6KA2 | Body | OpenSea | −0.04 | 4.61E-09 | 1.57E-03 | 5.26E-08 | 2.51E-02 |
| cg12992827 | 3 | ZLPD1 | OpenSea | −0.05 | 1.81E-09 | 6.18E-04 | 9.89E-04 | 2.13E-01 | |
| cg02464912 | 14 | SYNE2 | TSS200 | N_Shore | −0.01 | 7.46E-08 | 2.55E-02 | 1.00E-01 | 3.28E-01 |
| cg12054453 | 17 | VMP1 | Body | OpenSea | −0.07 | 2.02E-13 | 6.89E-08 | 2.37E-04 | 5.08E-01 |
| cg01101459 | 1 | LINC01132 | OpenSea | 0.03 | 3.78E−08 | 1.29E-02 | 5.72E-02 | 5.08E-01 | |
| cg02782634 | 17 | VMP1 | Body | OpenSea | −0.02 | 1.04E-07 | 3.56E-02 | 1.00E-01 | 5.55E-01 |
| cg18942579 | 17 | VMP1 | Body | OpenSea | −0.05 | 1.77E-08 | 6.03E-03 | 8.90E-05 | 5.55E-01 |
| cg09349128 | 22 | CRELD2 | N_Shore | −0.04 | 3.80E-17 | 1.30E-11 | 3.07E-03 | 6.88E-01 | |
| cg18608055 | 19 | SBNO2 | Body | OpenSea | −0.03 | 7.08E-09 | 2.42E-03 | 5.21E-06 | 6.88E-01 |
| cg16936953 | 17 | VMP1 | Body | OpenSea | −0.07 | 3.43E-11 | 1.17E-05 | 2.23E-04 | 8.08E-01 |
Positive values indicate increased methylation in cases compared to controls; negative values indicate hypomethylation in IBD cases vs controls. TSS200: 200 bp from transcription start site. Body: within body of the gene.