Research Article

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

Table 3

The set of 25 DEGs downregulated in the hippocampal CA1 region during progression of AD identified by microarray data analysis of GSE1297 corresponding to RNA-Seq data analysis of SRA060752.

Entrez Gene
ID
Gene symbolGene nameFold change
(severe AD versus NC)
value

57172CAMK1GCalcium/calmodulin-dependent protein kinase IG0.1197912160.00015044
7447VSNL1Visinin-like 10.1766595560.003811085
10368CACNG3Calcium channel, voltage-dependent, gamma subunit 30.2129069420.000645324
55711FAR2Fatty acyl CoA reductase 20.2300908290.00066547
10769PLK2Polo-like kinase 20.2643294820.001588852
9331B4GALT6UDP-Gal: betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 60.2842468710.005450676
55312RFKRiboflavin kinase0.3263515610.000250327
5274SERPINI1Serpin peptidase inhibitor, clade I (neuroserpin), member 10.3375269150.006332563
9079LDB2LIM domain binding 20.3409992250.003326867
1268CNR1Cannabinoid receptor 1 (brain)0.3446535890.008057005
5579PRKCBProtein kinase C, beta0.3450048890.002186833
63982ANO3Anoctamin 30.3720849360.008600399
81831NETO2Neuropilin (NRP) and tolloid- (TLL-) like 20.3939775660.000965658
440270GOLGA8BGolgin A8 family, member B0.4225388730.004711934
23236PLCB1Phospholipase C, beta 1 (phosphoinositide-specific)0.435899040.001873881
27324TOX3TOX high mobility group box family member 30.4504257350.002724595
6000RGS7Regulator of G-protein signaling 70.4519715330.006045425
138046RALYLRALY RNA binding protein-like0.4534630380.001029166
5530PPP3CAProtein phosphatase 3, catalytic subunit, alpha isozyme0.4617270970.001385837
1020CDK5Cyclin-dependent kinase 50.4647425790.00340998
3751KCND2Potassium voltage-gated channel, Shal-related subfamily, member 20.4897872980.004105453
29114TAGLN3Transgelin 30.5364812180.00215522
7534YWHAZTyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide0.5561676190.006101886
63974 NeuroD6 Neurogenic differentiation 6 0.5685494760.007199422
2744GLSGlutaminase0.5916601350.007897416

The set of 131 DEGs downregulated in the hippocampal CA1 region among incipient, moderate, and severe AD and NC groups by one-way ANOVA satisfying value <0.01 and fold change of severe AD versus NC smaller than 0.6 were extracted by microarray data analysis of GSE1297. Among them, the set of 25 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 131 DEGs are shown in Supplementary Table  4.