Table 3.
Top differentially methylated sites based on metabolic syndrome.
| CpG probe ID | Gene | Chromosome | Position | CpG type | Fold changea | Raw p value | FDR-corrected p value |
|---|---|---|---|---|---|---|---|
| cg04640913 | Cadherin-like 22 (CDH22) | 20 | 44880515 | South shore | 0.123 | 9.26 × 10−07 | 0.02∗ |
| cg12501957 | Family with sequence similarity 19 (chemokine- (C-C motif-) like), member A2 (FAM19A2) | 12 | 62629234 | Open sea | −0.0266 | 1.05 × 10−06 | 0.04∗ |
| cg05086443 | Cadherin-like 22 (CDH5) | 16 | 66437349 | South shore | −0.0215 | 3.45 × 10−06 | 0.04∗ |
| cg16653173 | Casein kinase 1 (CSNK1E) | 22 | 38713453 | South shore | 0.0675 | 3.83 × 10−06 | 0.04∗ |
| cg16656316 | Delta/notch-like EGF repeat (DNER) | 2 | 230280621 | Open sea | −0.0764 | 7.85 × 10−06 | 0.04∗ |
| cg06378976 | Transcription factor EB (TFEB) | 6 | 41703613 | South shore | 0.135 | 1.05 × 10−05 | 0.08 |
| cg04457354 | E2F transcription factor 3 (E2F2) | 6 | 20447442 | Open sea | −0.0221 | 2.03 × 10−05 | 0.08 |
| cg04953503 | Melanophilin (MLPH) | 2 | 238420656 | Open sea | −0.00763 | 2.24 × 10−05 | 0.08 |
| Cg05434957 | Islet autoantigen 1 (ICA1) | 7 | 8301435 | Island | 0.118 | 2.26 × 10−05 | 0.09 |
| cg08464505 | ATPase, class VI, type 11A (ATP11A) | 13 | 113425982 | South shore | −0.0113 | 2.87 × 10−05 | 0.09 |
| Cg22158175 | Proteosome subunit, beta type, 8 (PSMB8) | 6 | 32809475 | North sea | −0.0162 | 3.10 × 10−05 | 0.09 |
| Cg17492940 | Protein phosphatase 1, regulatory subunit 12B (PPP1R12B) | 1 | 202407102 | Open sea | −0.00380 | 3.30 × 10−05 | 0.1 |
| Cg04033559 | Pyruvate dehydrogenase kinase, isozyme 1 (PDK1) | 2 | 173461819 | Open sea | −0.312 | 3.46 × 10−05 | 0.1 |
Top differentially methylated sites based on metabolic syndrome status with an FDR p value < 0.1. Only FDR < 0.05 was considered statistically significant in this study. Columns 1 and 2 give the probe ID and associated gene name. Columns 3 and 4 give the genomic location (GRCh37/hg19) of the CpG site and CpG classification of the probe with respect to CpG islands (i.e., island versus shore versus sea). The final columns give the fold change with direction, unadjusted, and FDR-corrected p values. aFold change calculated by log2 of the quotient in methylation in subjects with metabolic syndrome compared to subjects without metabolic syndrome. Positive fold change indicates an increase in methylation (hypermethylation) in the metabolic syndrome group. ∗ indicates statistical significance based on an FDR cutoff below 0.05