RNA-Seq Data Mining: Downregulation of NeuroD6 Serves as a Possible Biomarker for Alzheimer’s Disease Brains

Table 4

The set of 12 DEGs downregulated in the hippocampus of Japanese AD patients identified by microarray data analysis of GSE36980 corresponding to RNA-Seq data analysis of SRA060752.

Entrez Gene; ID	Gene symbol	Gene name	Fold change; (AD versus non-AD)	value
63974	NeuroD6	Neurogenic differentiation 6	0.433171474	0.001616741
10368	CACNG3	Calcium channel, voltage-dependent, gamma subunit 3	0.496685808	0.004499281
5176	SERPINF1	Serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	0.522226034	0.00019849
348980	HCN1	Hyperpolarization activated cyclic nucleotide-gated potassium channel 1	0.523810594	0.004508668
5774	PTPN3	Protein tyrosine phosphatase, nonreceptor type 3	0.54910964	0.001537752
8507	ENC1	Ectodermal-neural cortex (with BTB-like domain)	0.559652363	0.003288053
266722	HS6ST3	Heparan sulfate 6-O-sulfotransferase 3	0.560440342	0.001753288
2903	GRIN2A	Glutamate receptor, ionotropic, N-methyl D-aspartate 2A	0.581203611	0.002390123
51299	NRN1	Neuritin 1	0.590013553	0.001828335
125113	KRT222	Keratin 222 pseudogene	0.592296133	0.004941811
1428	CRYM	Crystallin, mu	0.594516424	0.002824762
221692	PHACTR1	Phosphatase and actin regulator 1	0.597310446	0.002464967

The set of 31 DEGs downregulated in the hippocampus of Japanese AD patients satisfying value <0.005 by two-tailed -test and fold change smaller than 0.6 were extracted by microarray data analysis of GSE36980. Among them, the set of 12 genes corresponding to the core set of 522 DEGs identified by RNA-Seq data analysis of SRA060572 are listed with Entrez Gene ID, gene symbol, gene name, fold change, and value. NeuroD6 is italicized. The complete list of 31 DEGs are shown in Supplementary Table  5.