Scientific Reports

Table 2 Utilized gene expression microarrays/RNA-sequencing for the differential gene expression analysis of the target genes of ASD with 16p11.2 deletion and CHD8 variants.

From: LINE-1 and Alu methylation signatures in autism spectrum disorder and their associations with the expression of autism-related genes

Methylome data				Transcriptome data
Probe ID	Elements	Delta	P_FDR	GSE	Gene ID	Gene	log₂FC	q-value
ASD with 16p11.2 deletion
cg22062537	L1MB3	− 0.079	0.0002	GSE25507	1553515_at	MYEOV2	0.107	0.0496
cg13749477	L1MB3	− 0.038	0.0004	GSE25507	1553515_at	MYEOV2	0.107	0.0496
cg07628769	L1MB3	− 0.101	0.0028	GSE25507	1553515_at	MYEOV2	0.107	0.0496
cg01772945	AluSq	− 0.048	0.0003	GSE18123	205739_x_at	ZNF107	0.382	0.0017
cg09168728	HAL1	0.042	0.0039	GSE18123	202651_at	LPGAT1	0.16	0.0038
cg21300361	AluY	0.024	0.0139	GSE18123	1553640_at	XKR6	− 0.949	0.0206
cg21300361	AluY	0.024	0.0139	GSE25507	1553640_at	XKR6	0.134	0.0112
ASD with *CHD8* variant
cg06421197	AluJo	− 0.034	0.0266	GSE18123	206011_at	CASP1	0.14	0.0122
cg06421197	AluJo	− 0.034	0.0266	GSE42133	ILMN_2326509	CASP1	− 0.16	0.0258
cg06421197	AluJo	− 0.034	0.0266	GSE42133	ILMN_2326512	CASP1	− 0.17	0.0213
cg06421197	AluJo	− 0.034	0.0266	GSE42133	ILMN_1727762	CASP1	− 0.25	< 0.0001
cg06421197	AluJo	− 0.034	0.0266	GSE59288	834	CASP1	0.61	0.0096
cg09604414	AluSx	− 0.067	0.0336	GSE25507	229079_at	EHMT2	0.09	0.0471
cg22706070	L1MC5	− 0.008	0.0496	GSE25507	229079_at	EHMT2	0.09	0.0471
cg02169692	AluSx	− 0.109	0.0275	GSE42133	ILMN_3240420	USP18	− 0.31	0.025
cg02169692	AluSx	− 0.109	0.0275	GSE42133	ILMN_3240420	USP18	− 0.31	0.025
cg18699242	AluSx	− 0.106	0.0448	GSE42133	ILMN_3240420	USP18	− 0.31	0.025
cg18699242	AluSx	− 0.106	0.0448	GSE42133	ILMN_3240420	USP18	− 0.31	0.025

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