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Table 4 Stage 1 – Assessment of the influence of cell type on CpG selection in stage 1 analyses (n = 245)

From: DNA methylation loci associated with atopy and high serum IgE: a genome-wide application of recursive Random Forest feature selection

CpG Site Crude β1 Crude P-value Adjusted β1 Adjusted P-value %Diffβ
cg00155310 2.24 0.00066 2.24 0.0011 −0.26
cg00528600 1.66 0.0038 1.68 0.0043 1.11
cg00854799 1.23 0.0062 1.25 0.0067 1.29
cg01097406 0.25 0.0050 0.27 0.0042 5.08
cg01190915 2.43 0.00020 2.61 0.00011 7.49
cg01203365 −1.25 0.0051 −1.19 0.0087 −4.59
cg01777765 −1.51 0.0030 −1.69 0.0015 11.76
cg01847596 −2.62 0.0015 −2.65 0.0019 1.49
cg02201050 2.08 0.0012 2.10 0.0017 0.87
cg02366798 0.84 0.0097 0.85 0.014 0.46
cg02775369 −1.55 0.00072 −1.53 0.0011 −1.37
cg03131171 −1.21 0.0064 −1.28 0.0049 5.47
cg03468115 1.68 0.0017 1.58 0.0052 −5.88
cg03553407 1.54 0.00037 1.50 0.00060 −2.44
cg04085542 1.00 0.00033 0.95 0.00094 −5.15
cg04162999 0.92 0.030 1.05 0.016 14.72
cg04342090 −1.55 0.0086 −1.46 0.014 −5.58
cg04775941 −1.67 0.020 −1.54 0.034 −7.5
cg04798929 2.20 0.0024 2.14 0.0034 −2.98
cg04983687 −1.18 0.000010 −1.43 0.0000017 21.45
cg05048002 −1.91 0.00074 −1.75 0.0036 −8.1
cg05104993 2.89 0.0018 3.18 0.0012 10.1
cg05560165 1.37 0.0011 1.55 0.00062 13.84
cg05652668 −1.15 0.00068 −1.27 0.00031 10.57
cg06816054 −1.37 0.0081 −1.49 0.0068 9.25
cg06824199 −2.11 0.000029 −2.45 0.000011 16.35
cg06851336 −1.78 0.00099 −1.76 0.0011 −0.86
cg07765167 −2.47 0.000065 −2.52 0.000095 1.94
cg07880854 1.21 0.014 1.43 0.0070 18.16
cg07908654 −1.67 0.000013 −1.80 0.0000099 7.96
cg07970948 −1.26 0.000027 −1.42 0.000014 12.22
cg08397758 0.84 0.043 1.90 0.0032 125.56
cg09249800 −1.14 0.000016 −1.27 0.0000094 11.06
cg09332506 −1.97 0.0000097 −2.10 0.0000078 6.38
cg09570585 0.85 0.064 0.82 0.082 −3.88
cg09635874 1.96 0.00037 1.90 0.0010 −3.11
cg10016610 −0.57 0.098 −0.63 0.085 9.8
cg11182893 1.81 0.00032 1.64 0.0015 −9.47
cg11372831 2.62 0.00018 2.63 0.00029 0.2
cg11569718 −1.54 0.011 −1.44 0.021 −6.64
cg12578575 −0.58 0.012 −0.59 0.014 1.49
cg12819826 −1.90 0.000087 −1.93 0.00029 1.67
cg12819873 −2.36 0.0000045 −2.47 0.0000051 4.97
cg13168187 1.65 0.0024 2.79 0.000043 69.09
cg13197551 −1.84 0.000062 −1.77 0.00016 −3.49
cg13233042 −1.64 0.000032 −1.74 0.000031 6.21
cg13713293 −1.43 0.00039 −1.40 0.00070 −1.67
cg14322298 −1.53 0.0031 −1.57 0.0052 2.77
cg14478663 1.81 0.00020 1.91 0.00017 5.64
cg14574726 1.75 0.0058 1.91 0.0037 9.54
cg15281774 −1.91 0.0014 −2.13 0.00076 11.37
cg17041511 −1.97 0.000021 −2.25 0.000027 14.69
cg17549513 1.62 0.0094 1.82 0.0051 12.16
cg17594242 1.72 0.000035 1.71 0.000071 −0.93
cg17971837 −3.38 0.000061 −3.64 0.000069 7.85
cg23527183 −0.83 0.0048 −0.92 0.0034 10.38
cg24077454 1.33 0.0056 1.27 0.012 −4.29
cg24836822 −1.09 0.000020 −1.17 0.000014 8.19
cg25854298 −1.40 0.000042 −1.51 0.000037 7.39
cg27202913 −0.67 0.010 −0.69 0.0094 2.01
cg27468224 −1.83 0.00013 −1.85 0.00019 1.29
cg27469152 −1.99 0.00021 −2.21 0.000094 11.21
  1. Results of 62 logistic regressions between methylation M-values and atopy for each selected CpG. We present crude associations as well as associations adjusted for predicted cell proportions of CD8+ T cells, CD4+ T cells, natural killer cells, B-cells, monocytes, and granulocytes. β1 represents the value of the regression coefficient for the CpG site in that statistical model. The percent change in β-values (%Diffβ) was calculated as [(crude β1 – adjusted β1)/crude β1] and was used to evaluate whether cell type influenced the selection of each CpG site
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Genome Medicine

ISSN: 1756-994X

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