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

Everson, Todd M.; Lyons, Genevieve; Zhang, Hongmei; Soto-Ramírez, Nelís; Lockett, Gabrielle A.; Patil, Veeresh K.; Merid, Simon K.; Sӧderhӓll, Cilla; Melén, Erik; Holloway, John W.; Arshad, S. Hasan; Karmaus, Wilfried

doi:10.1186/s13073-015-0213-8

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	%Diff_β
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

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 (%Diff_β) 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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