Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Macartney-Coxson, Donia; Benton, Miles C.; Blick, Ray; Stubbs, Richard S.; Hagan, Ronald D.; Langston, Michael A.

doi:10.1186/s13148-017-0344-4

Table 2 Top 20 CpG sites by magnitude of DNA methylation difference between subcutaneous and omental adipose tissue at each time point

From: Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Illumina probe ID	T statistic	Adjusted P value	AB mean beta	OM mean beta	Δbeta	CpG site chromosome and position^a	UCSC gene name^a ^b	Location	Rank P value^c	Rank biomarker^d
Before weight loss
cg02245004	−14.92	2.32E−04	0.12	0.64	−0.51	15:76634887	Intergenic		318	1
cg20540209	−13.61	7.74E−04	0.06	0.53	−0.48	15:76633981	ISL2	Body	557	NA
cg17446010	−16.17	7.97E−05	0.13	0.58	−0.45	15:76633627	ISL2	Body	192	NA
cg00838040	−18.85	1.02E−05	0.53	0.96	−0.43	16:84446919	ATP2C2	Body	66	NA
cg03923561	23.49	5.10E−07	0.45	0.04	0.41	12:54447220	HOXC4	5′UTR;TSS1500	12	2
cg09400037	−17.63	2.50E−05	0.42	0.82	−0.40	16:84822801	Intergenic		102	4
cg22747076	20.83	2.62E−06	0.42	0.02	0.40	12:54447873	HOXC4	1stExon;Body	31	3
cg15233062	22.19	1.11E−06	0.48	0.09	0.39	12:54447349	HOXC4	5′UTR;TSS1500	18	NA
cg00108351	−16.19	7.79E−05	0.23	0.61	−0.39	16:86529658	Intergenic		191	NA
cg01184975	23.53	4.97E−07	0.44	0.06	0.39	12:114852091	Intergenic		11	NA
cg12984729	−13.17	1.19E−03	0.12	0.50	−0.38	15:76633817	ISL2	Body	668	13
cg08307030	−10.46	2.27E−02	0.14	0.52	−0.38	15:76634380	ISL2	3′UTR	2336	16
cg20291855	−20.02	4.48E−06	0.02	0.40	−0.38	4:13524143	Intergenic		41	NA
cg11797364	−14.85	2.46E-04	0.59	0.97	−0.38	6:436969	Intergenic		329	6
cg01697719	12.27	2.97E-03	0.38	0.01	0.37	22:19754125	TBX1	Body	986	NA
cg07266404	28.62	3.38E−08	0.43	0.07	0.37	12:54447584	HOXC4	5′UTR;TSS200	4	NA
cg24864887	−13.27	1.07E−03	0.14	0.50	−0.36	15:76635638	Intergenic		644	NA
cg21215550	18.67	1.15E−05	0.55	0.20	0.36	9:969544	Intergenic		70	NA
cg06800235	16.38	6.67E−05	0.56	0.20	0.35	1:7692367	CAMTA1	Body	176	NA
cg08036309	−21.31	1.92E−06	0.17	0.52	−0.35	4:13536991	Intergenic		24	NA
After weight loss
cg00838040	−38.29	6.04E−10	0.34	0.97	−0.64	16:84446919	ATP2C2	Body	2	1
cg09400037	−34.83	2.24E−09	0.33	0.92	−0.59	16:84822801	Intergenic		3	NA
cg02245004	−11.25	9.01E−03	0.07	0.65	−0.58	15:76634887	Intergenic		4290	NA
cg20540209	−10.86	1.41E−02	0.02	0.59	−0.56	15:76633981	ISL2	Body	4998	NA
cg22747076	17.06	3.89E−05	0.59	0.06	0.53	12:54447873	HOXC4	1stExon;Body	517	NA
cg24145118	11.73	5.30E−03	0.84	0.31	0.52	10:2777041	Intergenic		3554	NA
cg17446010	−12.37	2.68E−03	0.09	0.61	−0.52	15:76633627	ISL2	Body	2760	NA
cg03923561	14.78	2.62E−04	0.60	0.09	0.51	12:54447220	HOXC4	5′UTR;TSS1500	1131	NA
cg21917524	−28.43	3.70E−08	0.31	0.81	−0.51	11:74200334	Intergenic		19	2
cg00108351	−11.97	4.11E−03	0.17	0.67	−0.51	16:86529658	Intergenic		3233	NA
cg12984729	−11.88	4.50E−03	0.09	0.58	−0.49	15:76633817	ISL2	Body	3338	4
cg15233062	14.15	4.63E−04	0.62	0.14	0.49	12:54447349	HOXC4	5′UTR;TSS1500	1400	NA
cg00319661	17.95	1.96E−05	0.92	0.43	0.49	5:2632178	Intergenic		381	NA
cg11797364	−21.71	1.49E−06	0.47	0.93	−0.47	6:436969	Intergenic		122	NA
cg13593391	12.35	2.74E−03	0.94	0.47	0.47	11:132582488	OPCML	Body	2783	NA
cg08307030	−10.93	1.30E−02	0.14	0.60	−0.46	15:76634380	ISL2	3′UTR	4855	NA
cg08773462	−11.52	6.65E−03	0.10	0.56	−0.46	16:17107610	Intergenic		3864	NA
cg01697719	16.48	6.15E−05	0.49	0.03	0.45	22:19754125	TBX1	Body	622	NA
cg20249252	15.65	1.22E−04	0.60	0.15	0.45	12:114852308	Intergenic		837	NA
cg17185060	−17.72	2.34E−05	0.27	0.72	−0.45	3:193990712	Intergenic		415	NA

Illumina probe IDs in bold indicate probes unique to the analysis at that time point
^aGene symbol and map position as Illumina manifest, GRCh37/hg19
^b‘Intergenic’, no gene loci annotation in Illumina manifest
^c P value in ‘traditional’ differential methylation analysis
^dIndicates ranking in combinatorial analysis if applicable. NA indicates that the CpG site was not seen in this analysis

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