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

Table 1

Top 20 DEGs in the frontal cortex of AD overlapping between two cohorts identified by RNA-Seq data analysis of SRA060752.

Entrez Gene; ID	Gene symbol	Gene name	Chromosome locus	Fold change (AD versus NC: EMU)	-value; (EMU)	Fold change (AD versus NC: UKY)	-value; (UKY)
6863	TAC1	Tachykinin, precursor 1	chr7: 97361270–97369784	0.028013577	0.00232257	0.189297859	0.000638422
5121	PCP4	Purkinje cell protein 4	chr21: 41239346–41301322	0.060477403	0.00232257	0.263070248	0.000638422
793	CALB1	Calbindin 1, 28 kDa	chr8: 91070837–91095107	0.068756027	0.00232257	0.229478357	0.000638422
54112	GPR88	G protein-coupled receptor 88	chr1: 101002397–101008223	0.083735314	0.00232257	0.380695653	0.000638422
143162	FRMPD2	FERM and PDZ domain containing 2	chr10: 49364156–49482941	0.086014876	0.00232257	0.344904773	0.00248927
6588	SLN	Sarcolipin	chr11: 107578100–107582787	0.091647542	0.00398798	0.110806929	0.00396642
6750	SST	Somatostatin	chr3: 187386693–187388201	0.094938693	0.00232257	0.042406817	0.000638422
63974	NeuroD6	Neurogenic differentiation 6	chr7: 31377079–31380538	0.095418314	0.00232257	0.159354316	0.000638422
3358	HTR2C	5-Hydroxytryptamine (serotonin) receptor 2C	chrX: 113818550–114144627	0.09625865	0.00232257	0.211803744	0.000638422
771	CA12	Carbonic anhydrase XII	chr15: 63615729–63674075	0.104187926	0.00232257	0.453231488	0.0218249
845	CASQ2	Calsequestrin 2 (cardiac muscle)	chr1: 116242519–116345204	3.491410523	0.00962874	5.322706439	0.000638422
23704	KCNE4	Potassium voltage-gated channel, Isk-related family, member 4	chr2: 223916861–223920355	4.436801472	0.00232257	4.699574041	0.000638422
6279	S100A8	S100 calcium binding protein A8	chr1: 153362507–153363664	5.018965399	0.00232257	2.142150734	0.0151369
871	SERPINH1	Serpin peptidase inhibitor, clade H (heat shock protein 47), member 1 (collagen binding protein 1)	chr11: 75273100–75283870	5.437863735	0.00232257	2.129345418	0.0101566
6275	S100A4	S100 calcium binding protein A4	chr1: 153516094–153518282	5.52659158	0.00232257	4.606560625	0.000638422
26266	SLC13A4	Solute carrier family 13 (sodium/sulfate symporters), member 4	chr7: 135365246–135412933	6.580968881	0.00232257	2.996233377	0.000638422
3303	HSPA1A	Heat shock 70 kDa protein 1A	chr6: 31777395–31785719	6.599057552	0.00232257	3.8880048	0.000638422
3304	HSPA1B	Heat shock 70 kDa protein 1B	chr6: 31795511–31798031	6.599057552	0.00232257	2.366327899	0.000638422
375061	FAM89A	Family with sequence similarity 89, member A	chr1: 231154703–231175995	8.186858725	0.00232257	2.253222839	0.00248927
100500849	MIR3916	MicroRNA 3916	chr1: 247342111–247374105	17.2291545	0.00762148	2.127294836	0.00287725

The core set of 522 DEGs in the frontal cortex of AD overlapping between EMU and UKY satisfying -value (FDR-corrected value) <0.05 and fold change greater than 2.0 or smaller than 0.5 were extracted by RNA-Seq data analysis of SRA060572. Top 10 downregulated and top 10 upregulated genes based on fold change in EMU are listed with Entrez Gene ID, gene symbol, gene name, chromosomal locus, fold change, and -value. NeuroD6 is italicized. The complete list of 522 DEGs is shown in Supplementary Table  1.