TABLE 2.
Details for markers showing significant (FDR adjusted P-value), substantial differences in mean methylation (Δβ) between case and control groups in the discovery phase.
| Locus | Sequence position | Cytogenetic location | Symbol | Role from Entrez Gene | Δβ DN vs. DC | P DN vs. DC | Δβ ESRD vs. DC | P ESRD vs. DC |
| cg04861640 | 28234605 | 6p21.31 | ZNF187 (ZSCAN26) | Transcriptional regulation | 0.23 | 3.70E-24 | 0.22 | 3.80E-13 |
| cg16203607 | 62500946 | 17q21 | DDX5 | Transcriptional regulation, differentiation, apoptosis | 0.21 | 2.10E-23 | 0.21 | 1.90E-13 |
| cg21829265 | 56911139 | 6p12.1 | KIAA1586 | Nucleic acid binding | 0.21 | 4.10E-23 | 0.21 | 5.50E-13 |
| cg20419181 | 38063874 | 4p14 | TBC1D1 | Regulation of cell growth, differentiation, protein organization | 0.26 | 5.20E-23 | 0.27 | 9.00E-14 |
| cg21935083 | 131892314 | 5q31 | RAD50 | Multiple including telomere maintenance and DNA repair/recombination | 0.22 | 5.40E-23 | 0.23 | 3.10E-14 |
| cg21739208 | 80280621 | 6 | NA | NA | 0.22 | 6.80E-23 | 0.22 | 8.10E-13 |
| cg07242860 | 140739522 | 5q31 | PCDHG@ | Calcium ion binding | 0.22 | 7.20E-23 | 0.23 | 1.20E-13 |
| cg07979357 | 14142353 | 19p13.11 | IL27RA | Immunity | 0.2 | 1.80E-22 | Not significant | Not significant |
| cg24115040 | 96652375 | 7q22 | DLX5 | Multiple, including transcriptional regulation, positive regulation of canonical Wnt receptor signaling pathway, and cell proliferation/differentiation | 0.22 | 2.10E-22 | 0.23 | 4.70E-13 |
| cg02339392 | 28234615 | 6p21.31 | ZNF187 (ZSCAN26) | Transcriptional regulation | 0.21 | 2.20E-22 | 0.21 | 7.90E-13 |
| cg10463299 | 54987330 | 20q13.31 | CASS4 | Cell adhesion, cytoskeletal organization | 0.23 | 2.30E-22 | 0.24 | 2.40E-13 |
| cg00618312 | 41556559 | 13q13 | ELF1 | Protein acts as both an enhancer and a repressor to regulate transcription | 0.2 | 2.40E-22 | 0.2 | 3.20E-12 |
| cg15189015 | 72707255 | 17q25.1 | RAB37;CD300LF | GTP binding; receptor activity | 0.22 | 3.00E-22 | 0.23 | 6.40E-13 |
| cg25418748 | 178977236 | 5q35.3 | RUFY1 | Endocytosis/protein transport | 0.21 | 5.00E-22 | 0.21 | 1.20E-12 |
| cg02399570 | 156877196 | 3q25.31 | CCNL1 | Transcription/RNA processing. | 0.21 | 8.60E-22 | 0.21 | 3.30E-12 |
| cg10905876 | 56716656 | 6p12.1 | DST | Cell adhesion, cytoskeletal organization | 0.22 | 8.90E-22 | 0.21 | 9.80E-12 |
| cg16595484 | 122512170 | 3q21.1 | HSPBAP1 | Cell growth and differentiation | 0.22 | 2.40E-21 | 0.22 | 1.30E-11 |
| cg01667324 | 34392045 | 13q13.2 | RFC3 | Multiple including telomere maintenance and DNA repair/replication | 0.2 | 5.30E-21 | Not significant | Not significant |
| cg08779777 | 106505772 | 7q22.3 | PIK3CG | Multiple. Associated with blood pressure variation (PMID: 21909110) | 0.26 | 1.50E-20 | 0.25 | 6.10E-11 |
| cg03037561 | 16459464 | 7p21.2 | ISPD (CRPPA) | Nucleotidyltransferase activity, isoprenoid biosynthetic process | 0.2 | 3.20E-18 | 0.24 | 1.50E-09 |
| cg11671265 | 78722517 | 4q13.3 | CNOT6L | Gene expression, RNA metabolic processing | 0.24 | 5.00E-18 | 0.22 | 6.30E-09 |
| cg26399113* | 70752639 | Xq13 | OGT | Multiple, including response to insulin | 0.22 | 1.00E-12 | 0.23 | 2.30E-07 |
Differential methylation between individuals with DKD (DN, n = 150) compared to controls (DC, n = 100) with diabetes but no evidence of renal disease are highlighted, alongside differential methylation and significance values for the smaller ESRD versus control dataset. * Results presented from female cases compared to female controls.