DNA methylation of insulin signaling pathways is associated with HOMA2-IR in primary myoblasts from older adults

Burton, Mark A.; Garratt, Emma S.; Hewitt, Matthew O.; Sharkh, Hanan Y.; Antoun, Elie; Westbury, Leo D.; Dennison, Elaine M.; Harvey, Nicholas C.; Cooper, Cyrus; MacIsaac, Julia L.; Kobor, Michael S.; Patel, Harnish P.; Godfrey, Keith M.; Lillycrop, Karen A.

doi:10.1186/s13395-023-00326-y

Skeletal Muscle

Table 2 HOMA2-IR-associated dmCpGs (FDR < 0.05) in skeletal muscle myoblast cells from elderly individuals

From: DNA methylation of insulin signaling pathways is associated with HOMA2-IR in primary myoblasts from older adults

No	Cg ID	logFC	_P	FDR	UCSC Name	UCSC Grp	Location	Chr
1	cg08944484	− 0.093	4.51E-09	0.00327	SCCPDH	3′UTR	OpenSea	chr1
2	cg01351409	0.169	1.38E-08	0.00337			OpenSea	chr7
3	cg20625334	− 0.0343	1.40E − 08	0.00337	STAM2	Body	OpenSea	chr2
4	cg00623421	− 0.173	2.95E − 08	0.00534			OpenSea	chr10
5	cg19423170	− 0.104	4.42E − 08	0.00641	APP	Body	OpenSea	chr21
6	cg10703001	− 0.118	6.36E − 08	0.00769			OpenSea	chr6
7	cg13357714	− 0.102	1.57E − 07	0.0162	SGCD	Body	OpenSea	chr5
8	cg15926784	− 0.0682	2.49E − 07	0.0226	SEMA4G	1stExon	S_Shelf	chr10
9	cg13451048	0.112	3.40E − 07	0.027	ERI3	Body	N_Shore	chr1
10	cg14417798	0.0349	3.72E − 07	0.027	MAP3K7CL	1stExon	OpenSea	chr21
11	cg10416784	− 0.0504	4.77E − 07	0.0294			OpenSea	chr2
12	cg17612681	− 0.0395	4.99E − 07	0.0294			OpenSea	chr2
13	cg02219409	0.183	5.28E − 07	0.0294			OpenSea	chr20
14	cg20815084	− 0.0116	5.76E − 07	0.0298	BAT4	TSS1500	Island	chr6
15	cg26180255	0.122	6.61E − 07	0.032	CELSR1	Body	N_Shelf	chr22
16	cg21097491	0.046	7.47E − 07	0.0334	FAM53B	Body	OpenSea	chr10
17	cg04267098	− 0.129	7.84E − 07	0.0334	PLAG1	3′UTR	OpenSea	chr8
18	cg11409040	− 0.0275	1.04E − 06	0.04			OpenSea	chr14
19	cg09704075	0.123	1.05E − 06	0.04	CDH23	Body	OpenSea	chr10
20	cg02108897	− 0.101	1.23E − 06	0.0434			OpenSea	chr2
21	cg21781422	− 0.114	1.26E − 06	0.0434	RNF8	3′UTR	OpenSea	chr6
22	cg11040884	− 0.123	1.38E − 06	0.0436	PDLIM3	TSS1500	S_Shore	chr4
23	cg20818795	0.136	1.38E − 06	0.0436			S_Shelf	chr14
24	cg05550692	− 0.0123	1.52E − 06	0.0459	MED9	TSS200	Island	chr17
25	cg18584042	− 0.156	1.71E − 06	0.0471	MIR7853	Body	OpenSea	chr2
26	cg16072884	− 0.0963	1.72E − 06	0.0471	KIAA1462	Body	OpenSea	chr10
27	cg11893955	− 0.0196	1.83E − 06	0.0471			OpenSea	chr8
28	cg08640046	0.151	1.94E − 06	0.0471			S_Shore	chr2
29	cg08148660	0.0619	2.04E − 06	0.0471	MIR548H4	Body	N_Shore	chr15
30	cg08379995	0.105	2.16E − 06	0.0471	RBM19	Body	OpenSea	chr12
31	cg12331505	− 0.185	2.2E − 06	0.0471			OpenSea	chr5
32	cg12713159	0.11	2.21E − 06	0.0471			OpenSea	chr19
33	cg08800761	− 0.041	2.23E − 06	0.0471	UGGT2	Body	OpenSea	chr13
34	cg21554704	0.0275	2.37E − 06	0.0471			OpenSea	chr2
35	cg18185665	0.0743	2.4E − 06	0.0471	CENPV	TSS1500	Island	chr17
36	cg07635735	− 0.121	2.42E − 06	0.0471			S_Shelf	chr2
37	cg04349455	− 0.139	2.45E − 06	0.0471	PARK2	Body	OpenSea	chr6
38	cg16388983	− 0.0443	2.47E − 06	0.0471	PTPN14	5′UTR	N_Shelf	chr1

Log fold change was calculated as the log change in methylation per one unit of HOMA-IR to demonstrate effect size
LogFC log fold change, FDR false discovery rate, Chr chromosome

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ISSN: 2044-5040

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