Table 1.
Differentially methylated and expressed genes.
| Gene | GDEp-value | DMR | DMRstat | DMRp-value | EnsT | DTEp-value | eQTMr | eQTMp-value |
|---|---|---|---|---|---|---|---|---|
| ENSG00000233110 | 2.53E-04 | 4:185586913-185587794 | -9.94 | 2.78E-04 | ENST00000411847.1 | 2.53E-04 | 0.88 [0.74;0.95] | 2.54E-02 |
| CD74 | 2.00E-04 | 5:150410549-150413278 | -9.48 | 3.59E-04 | ENST00000009530.11 | 1.77E-02 | -0.88 [-0.96;-0.7] | 1.00E-04 |
| CD74 | 2.00E-04 | 5:150410549-150413278 | -9.48 | 3.59E-04 | ENST00000518797.5 | 1.23E-02 | -0.9 [-0.96;-0.76] | 1.00E-04 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000637439.1 | 5.06E-03 | -0.92 [-0.96;-0.78] | 1.00E-04 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000637439.1 | 5.06E-03 | -0.92 [-0.96;-0.78] | 1.00E-04 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000575513.1 | 8.19E-04 | -0.88 [-0.96;-0.66] | 8.10E-03 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000575513.1 | 8.19E-04 | -0.88 [-0.96;-0.66] | 8.10E-03 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000572665.1 | 6.67E-03 | -0.86 [-0.94;-0.62] | 8.80E-03 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000572665.1 | 6.67E-03 | -0.86 [-0.94;-0.62] | 8.80E-03 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000576601.1 | 3.12E-02 | -0.89 [-0.96;-0.67] | 2.51E-02 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000576601.1 | 3.12E-02 | -0.89 [-0.96;-0.67] | 2.51E-02 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000381835.9 | 2.59E-02 | -0.86 [-0.95;-0.52] | 4.06E-02 |
| CIITA | 2.93E-10 | 16:10877103-10878257 | -10.23 | 2.47E-04 | ENST00000381835.9 | 2.59E-02 | -0.86 [-0.95;-0.52] | 4.06E-02 |
| CMAHP | 1.89E-04 | 6:25232404-25233193 | 10.46 | 2.24E-04 | ENST00000377993.8 | 2.12E-04 | -0.7 [-0.87;-0.25] | 1.00E-04 |
| CMAHP | 1.89E-04 | 6:25232404-25233193 | 10.46 | 2.24E-04 | ENST00000493257.5 | 2.08E-02 | -0.68 [-0.84;-0.28] | 1.00E-04 |
| COL6A1 | 1.18E-06 | 21:45978416-45978817 | 8.14 | 8.44E-04 | ENST00000361866.7 | 8.83E-08 | 0.58 [0.07;0.8] | 2.20E-03 |
| COL6A1 | 1.18E-06 | 21:45983116-45984355 | 15.46 | 2.00E-05 | ENST00000361866.7 | 8.83E-08 | 0.45 [-0.19;0.78] | 1.80E-03 |
| CYTH1 | 1.53E-04 | 17:78716750-78718002 | 12.83 | 7.40E-05 | ENST00000589296.5 | 8.32E-04 | -0.42 [-0.78;0.23] | 4.12E-02 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000342981.8 | 2.97E-02 | 0.32 [-0.28;0.72] | 1.00E-04 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000342981.8 | 2.97E-02 | 0.32 [-0.28;0.72] | 1.00E-04 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000346169.6 | 3.07E-04 | 0.68 [0.28;0.9] | 1.00E-04 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000346169.6 | 3.07E-04 | 0.68 [0.28;0.9] | 1.00E-04 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000411531.5 | 1.71E-02 | 0.7 [0.33;0.9] | 1.00E-04 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000411531.5 | 1.71E-02 | 0.7 [0.33;0.9] | 1.00E-04 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000435046.6 | 1.78E-06 | 0.53 [-0.05;0.8] | 1.00E-04 |
| EIF4G1 | 4.11E-07 | 3:184319325-184320192 | 7.83 | 1.09E-03 | ENST00000435046.6 | 1.78E-06 | 0.53 [-0.05;0.8] | 1.00E-04 |
| EVL | 2.46E-05 | 14:100132409-100133139 | 9.08 | 4.52E-04 | ENST00000556921.1 | 3.54E-02 | 0.89 [0.73;0.97] | 3.04E-02 |
| FASTK | 1.23E-06 | 7:151081348-151082120 | 11.88 | 1.10E-04 | ENST00000460980.5 | 2.32E-03 | -0.21 [-0.76;0.52] | 1.00E-04 |
| FMN1 | 1.83E-04 | 15:33154437-33154950 | -7.96 | 9.88E-04 | ENST00000320930.7 | 2.49E-02 | -0.82 [-0.94;-0.59] | 1.26E-02 |
| GPR132 | 3.80E-05 | 14:105055190-105056414 | 9.09 | 4.48E-04 | ENST00000329797.7 | 6.12E-03 | 0.9 [0.62;0.99] | 1.00E-04 |
| GPR132 | 3.80E-05 | 14:105063870-105066425 | -11.52 | 1.36E-04 | ENST00000549990.1 | 2.60E-02 | -0.38 [-0.72;0.44] | 3.57E-02 |
| IKZF1 | 6.58E-06 | 7:50305276-50312367 | -11.26 | 1.55E-04 | ENST00000471793.1 | 1.04E-02 | -0.8 [-0.92;-0.33] | 1.00E-04 |
| IKZF1 | 6.58E-06 | 7:50305276-50312367 | -11.26 | 1.55E-04 | ENST00000492119.1 | 3.29E-02 | -0.88 [-0.94;-0.7] | 1.00E-04 |
| IKZF1 | 6.58E-06 | 7:50305276-50312367 | -11.26 | 1.55E-04 | ENST00000413698.5 | 1.30E-02 | -0.9 [-0.95;-0.72] | 2.55E-02 |
| IL4I1 | 2.32E-04 | 19:49895253-49897628 | -7.97 | 9.82E-04 | ENST00000391826.6 | 2.32E-04 | -0.96 [-0.98;-0.74] | 1.00E-04 |
| ITGB2 | 7.75E-05 | 21:44898213-44900097 | 8.96 | 4.89E-04 | ENST00000498666.5 | 5.07E-03 | 0.91 [0.67;0.98] | 1.00E-04 |
| ITGB2 | 7.75E-05 | 21:44911555-44912533 | -11.65 | 1.24E-04 | ENST00000397852.5 | 5.15E-03 | -0.94 [-0.98;-0.72] | 1.00E-04 |
| ITGB2 | 7.75E-05 | 21:44911555-44912533 | -11.65 | 1.24E-04 | ENST00000498666.5 | 5.07E-03 | -0.93 [-0.98;-0.81] | 2.00E-03 |
| ITGB2 | 7.75E-05 | 21:44911555-44912533 | -11.65 | 1.24E-04 | ENST00000522688.5 | 3.04E-02 | -0.9 [-0.97;-0.63] | 3.80E-03 |
| ITGB2 | 7.75E-05 | 21:44911555-44912533 | -11.65 | 1.24E-04 | ENST00000320216.10 | 6.78E-03 | -0.79 [-0.93;-0.57] | 4.08E-02 |
| ITGB2 | 7.75E-05 | 21:44911555-44912533 | -11.65 | 1.24E-04 | ENST00000302347.9 | 4.31E-02 | -0.9 [-0.97;-0.62] | 4.71E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000397852.5 | 5.15E-03 | -0.96 [-0.98;-0.88] | 1.00E-04 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000397852.5 | 5.15E-03 | -0.96 [-0.98;-0.88] | 1.00E-04 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000498666.5 | 5.07E-03 | -0.92 [-0.98;-0.79] | 1.14E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000498666.5 | 5.07E-03 | -0.92 [-0.98;-0.79] | 1.14E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000302347.9 | 4.31E-02 | -0.92 [-0.97;-0.72] | 2.00E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000302347.9 | 4.31E-02 | -0.92 [-0.97;-0.72] | 2.00E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000522688.5 | 3.04E-02 | -0.87 [-0.96;-0.61] | 3.08E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000522688.5 | 3.04E-02 | -0.87 [-0.96;-0.61] | 3.08E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000320216.10 | 6.78E-03 | -0.79 [-0.95;-0.45] | 3.97E-02 |
| ITGB2 | 7.75E-05 | 21:44913899-44915246 | -12.34 | 9.60E-05 | ENST00000320216.10 | 6.78E-03 | -0.79 [-0.95;-0.45] | 3.97E-02 |
| ITGB2 | 7.75E-05 | 21:44918461-44921815 | -18.22 | 9.00E-06 | ENST00000498666.5 | 5.07E-03 | -0.9 [-0.98;-0.55] | 1.00E-04 |
| ITGB2 | 7.75E-05 | 21:44918461-44921815 | -18.22 | 9.00E-06 | ENST00000498666.5 | 5.07E-03 | -0.9 [-0.98;-0.55] | 1.00E-04 |
| ITGB2 | 7.75E-05 | 21:44918461-44921815 | -18.22 | 9.00E-06 | ENST00000320216.10 | 6.78E-03 | -0.85 [-0.93;-0.69] | 3.35E-02 |
| ITGB2 | 7.75E-05 | 21:44918461-44921815 | -18.22 | 9.00E-06 | ENST00000320216.10 | 6.78E-03 | -0.85 [-0.93;-0.69] | 3.35E-02 |
| KLC1 | 7.08E-05 | 14:103696092-103697307 | 8.07 | 9.05E-04 | ENST00000246489.11 | 1.93E-08 | 0.62 [0.28;0.84] | 2.73E-02 |
| LAIR1 | 6.55E-07 | 19:54375122-54375966 | -8.84 | 5.29E-04 | ENST00000440716.5 | 9.38E-03 | -0.93 [-0.98;-0.73] | 3.80E-03 |
| LCP2 | 1.90E-08 | 5:170295513-170298924 | -13.19 | 6.10E-05 | ENST00000046794.9 | 1.23E-03 | -0.9 [-0.97;-0.66] | 1.00E-04 |
| LCP2 | 1.90E-08 | 5:170295513-170298924 | -13.19 | 6.10E-05 | ENST00000519149.1 | 8.96E-03 | -0.82 [-0.9;-0.62] | 1.00E-04 |
| LCP2 | 1.90E-08 | 5:170295513-170298924 | -13.19 | 6.10E-05 | ENST00000628092.2 | 6.87E-03 | -0.92 [-0.97;-0.74] | 1.00E-04 |
| LCP2 | 1.90E-08 | 5:170295513-170298924 | -13.19 | 6.10E-05 | ENST00000519594.5 | 2.89E-02 | -0.87 [-0.93;-0.72] | 3.70E-03 |
| LCP2 | 1.90E-08 | 5:170295513-170298924 | -13.19 | 6.10E-05 | ENST00000522760.5 | 7.55E-03 | -0.93 [-0.97;-0.8] | 8.10E-03 |
| OSM | 4.92E-04 | 22:30266011-30268071 | -13.63 | 5.10E-05 | ENST00000215781.2 | 3.59E-04 | -0.68 [-0.95;-0.13] | 1.00E-04 |
| OSM | 4.92E-04 | 22:30266011-30268071 | -13.63 | 5.10E-05 | ENST00000215781.2 | 3.59E-04 | -0.68 [-0.95;-0.13] | 1.00E-04 |
| PPP6R1 | 5.34E-04 | 19:55251330-55251959 | -11.33 | 1.51E-04 | ENST00000592242.1 | 4.83E-02 | -0.86 [-0.94;-0.6] | 4.22E-02 |
| PPP6R1 | 5.34E-04 | 19:55251330-55251959 | -11.33 | 1.51E-04 | ENST00000412770.6 | 2.83E-03 | -0.88 [-0.96;-0.6] | 4.54E-02 |
| RASSF4 | 4.87E-05 | 10:44977022-44977811 | 11 | 1.76E-04 | ENST00000489171.5 | 3.42E-02 | 0.93 [0.76;0.98] | 1.00E-04 |
| RPS6KA4 | 3.11E-04 | 11:64359911-64360661 | -10.55 | 2.11E-04 | ENST00000334205.8 | 1.51E-03 | -0.7 [-0.86;-0.43] | 1.00E-04 |
| RPS6KA4 | 3.11E-04 | 11:64359911-64360661 | -10.55 | 2.11E-04 | ENST00000334205.8 | 1.51E-03 | -0.7 [-0.86;-0.43] | 1.00E-04 |
| SH3TC1 | 3.47E-04 | 4:8240533-8241022 | -7.96 | 9.85E-04 | ENST00000507891.1 | 6.46E-05 | -0.7 [-0.83;-0.17] | 1.64E-02 |
| TMC6 | 6.31E-05 | 17:78126612-78127570 | -9.6 | 3.35E-04 | ENST00000590602.5 | 3.31E-02 | -0.92 [-0.98;-0.82] | 3.02E-02 |
| TMC6 | 6.31E-05 | 17:78126612-78127570 | -9.6 | 3.35E-04 | ENST00000590602.5 | 3.31E-02 | -0.92 [-0.98;-0.82] | 3.02E-02 |
| TMC6 | 6.31E-05 | 17:78126612-78127570 | -9.6 | 3.35E-04 | ENST00000591436.5 | 1.21E-02 | -0.81 [-0.91;-0.64] | 3.78E-02 |
| TMC6 | 6.31E-05 | 17:78126612-78127570 | -9.6 | 3.35E-04 | ENST00000591436.5 | 1.21E-02 | -0.81 [-0.91;-0.64] | 3.78E-02 |
| TMC6 | 6.31E-05 | 17:78126612-78127570 | -9.6 | 3.35E-04 | ENST00000593044.5 | 1.28E-02 | -0.85 [-0.93;-0.67] | 4.06E-02 |
| TMC6 | 6.31E-05 | 17:78126612-78127570 | -9.6 | 3.35E-04 | ENST00000593044.5 | 1.28E-02 | -0.85 [-0.93;-0.67] | 4.06E-02 |
| UCP2 | 7.66E-10 | 11:73979728-73982457 | -9.4 | 3.75E-04 | ENST00000545562.2 | 3.59E-02 | -0.67 [-0.83;-0.46] | 1.33E-02 |
| UCP2 | 7.66E-10 | 11:73979728-73982457 | -9.4 | 3.75E-04 | ENST00000545562.2 | 3.59E-02 | -0.67 [-0.83;-0.46] | 1.33E-02 |
| VAC14 | 2.54E-04 | 16:70691109-70693047 | 11.18 | 1.56E-04 | ENST00000261776.9 | 4.82E-03 | 0.88 [0.55;0.96] | 2.74E-02 |
| VAC14 | 2.54E-04 | 16:70746190-70746702 | 9.13 | 4.36E-04 | ENST00000261776.9 | 4.82E-03 | 0.87 [0.71;0.94] | 3.48E-02 |
Expression quantitative trait methylation (eQTM) analysis of the GDEMs representing the correlation between methylation and transcript expression. Key in table legend: Gene = HGNC gene symbol, DMR = co-ordinates of the DMR (GRCh38), DMRp-value = p-value associated to the differential methylation analysis, EnsT = Ensembl transcript ID, DTEp-value = p-value associated to the differential transcript expression analysis, eQTMr = Pearson correlation coefficient for the methylation-expression correlation and the 95% confidence intervals, eQTMp-value = p-value associated to the methylation-expression correlation. An extended parsable table including the full eQTM analysis for all GDEMs can be found in Table S6 .