Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping

BMC Medical Genomics

Table 2 Statistical test for DEG enrichment in eQTL genes

Dataset	Brain region	Samples	Significant DEG Count	DEG Count	FER	P-value
syn5550404	TC	160	61	122	1.245	0.006
syn5550404	CBE	159	47	122	1.080	0.060
GSE44770	PFC	230	44	96	1.097	0.059
	VC	230	45	96	1.208	0.022
	CBE	230	27	96	1.114	0.074
GSE5281	EC	23	39	118	1.419	0.004
	HIP	23	31	118	1.212	0.041
	MTG	28	44	118	1.125	0.048
	PC	22	43	118	1.187	0.031
	SFG	34	7	118	1.115	0.148
	VC	31	2	118	1.982	0.187

“Brain region” includes the following regions; TC Temporal cortex, CBE Cerebellum, PFC Prefrontal cortex, VC Visual cortex, EC Entorhinal cortex, HIP Hippocampus, MTG Medial temporal gyrus, SFG Superior frontal gyrus, PC Posterior cingulate. “Samples” indicates the number of samples in each dataset. “Significant DEG Count” indicates the number of signficantly differentially expressed genes in eQTL genes analyzed in each dataset (FDR<0.05). “DEG Count” indicates the number of eQTL genes analyzed in each dataset. “FER” indicates the number of the observed genes to the expected value. “P-value” were calculated from hypergeometic distribution test

ISSN: 1755-8794