Identified key genes related to carotid atheroma plaque from gene expression chip

Figures & data

Figure 1. The DEGs in atheroma plaque samples compared with those in normal samples. Black plots represent down- and up-regulated genes, red dots were significant differentially expressed genes.

Table 1. Most significant up and down-regulated genes in atheroma plaque.

Top 10 upregulation genes						Top 10 downregulation genes
Gene names	logFC	Ave. expr.	t	P value	Adj. P value	Gene names	logFC	Ave. expr.	t	P value	Adj. P value
CNTN1	1.933812	6.992566	6.329323	2.57E − 08	1.99E − 05	FABP4	−2.43509	5.568588	−6.08525	6.82E − 08	2.73E − 05
TPH1	1.915444	8.725099	5.535242	5.93E − 07	5.86E − 05	IGJ	−1.86047	9.888499	−4.78966	1E − 05	0.000251
CNTN4	1.816594	7.345847	6.86371	2.97E − 09	1.41E − 05	IGKC	−1.85468	8.943567	−5.51716	6.37E − 07	6.02E − 05
CASQ2	1.694836	8.551809	6.454261	1.56E − 08	1.76E − 05	IGKV3D − 11	−1.82461	7.888645	−5.11582	2.96E − 06	0.000124
MYOCD	1.655454	8.15814	6.188714	4.52E − 08	2.43E − 05	MMP7	−1.81399	7.95028	−4.36933	4.56E − 05	0.000706
FHL5	1.590583	8.029568	6.610868	8.28E − 09	1.48E − 05	MMP9	−1.78799	9.361878	−4.81926	8.96E − 06	0.000233
NBLA00301	1.524451	6.311777	5.96624	1.09E − 07	3.11E − 05	CD36	−1.77113	9.756504	−4.77631	1.05E − 05	0.000258
CARTPT	1.490325	6.493211	3.462372	0.00095	0.007282	IBSP	−1.76943	7.908648	−6.44181	1.64E − 08	1.76E − 05
CARTPT	1.490325	6.493211	3.462372	0.00095	0.007282	IGHV4 − 59	−1.71124	8.549237	−5.15228	2.58E − 06	0.000115
ATRNL1	1.464954	8.249908	5.202602	2.13E − 06	0.000104	IGHD	−1.69509	10.73476	−5.21921	2E − 06	0.000101

Figure 2. The top 13 most significantly enriched GO terms of DEGs according to the P value.

Table 2. The KEGG enriched pathways of the DEGs.

Description	Gene ratio	Bg ratio	P value	P adjust	q value	Gene ID	Count
Tryptophan metabolism	4/39	40/7017	6.45E − 05	0.005195	0.004325	TDO2/TPH1/KMO/KYNU	4
cAMP signaling pathway	7/39	199/7017	9.45E − 05	0.005195	0.004325	GRIA1/GRIA2/NPR1/NPY1R/PLN/RYR2/VAV3	7
Long-term potentiation	4/39	66/7017	0.000458	0.016812	0.013996	GRIA1/GRIA2/PLCB4/RPS6KA6	4
Circadian entrainment	4/39	95/7017	0.001804	0.049619	0.04131	GRIA1/GRIA2/PLCB4/RYR2	4

Figure 3. PPI network of DEGs obtained from the STRING database.

Table 3. Identified key genes in atheroma plaque.

Gene names	logFC	Ave. Expr	t	P value	Adj. P value
NPR1	1.100615	7.213082	5.308515	1.42E − 06	8.47E − 05
RYR2	1.265251	7.066235	5.606229	4.5E − 07	5.25E − 05
KYNU	−1.02328	7.448576	−4.63146	1.78E − 05	0.000364
MMP9	−1.78799	9.361878	−4.81926	8.96E − 06	0.000233
CD36	−1.77113	9.756504	−4.77631	1.05E − 05	0.000258

Figure 4. Structural character of kynureninase–3-hydroxyhippuric acid complex.