Bioinformatics Analysis and Identification of Genes and Pathways in Ischemic Cardiomyopathy

Figures & data

Table 1 The Top 10 Differential Expressed Genes (DEGs) in the Left Ventricular Myocardial Tissue of Patients with Ischemic Cardiomyopathy in GSE116250, GSE46224, GSE5406

GSE116250			GSE46224			GSE5406
Gene	Log2 FC	Adjust P	Gene	Log2 FC	Adjust P	Gene	Log2 FC	Adjust P
MTATP6P1	−16.93972	0.00065	HBB	5.03998	0.00078	ASPN	2.44397	0.00000
MTATP8P1	−16.50207	0.00055	NPPB	4.67375	0.02280	MYOT	−2.27140	0.00000
GCSHP3	13.86860	0.01736	HBA1	4.66989	0.00149	LUM	2.06227	0.00000
NDUFS1	11.21495	0.02041	HBA2	4.45526	0.00100	NPPA	1.76952	0.00000
RN7SKP232	10.83579	0.00000	MYH6	−2.9162	0.00100	MXRA5	1.63951	0.00000
TRBV5-4	10.08304	0.00000	TUBA3E	−2.8583	0.00078	HBB	1.50740	0.00004
RP11-777B9.5	−9.87759	0.00029	COMP	2.65490	0.01899	FKBP5	−1.49216	0.00000
CUX1	9.40378	0.04378	FMOD	2.63632	0.00896	NRAP	−1.49200	0.00462
ACTA1	7.81456	0.00576	LUM	2.41298	0.00710	HOPX	−1.48882	0.00000
RP5-857K21.11	−7.33930	0.03388	SFRP4	2.40590	0.01113	RPS4Y1	1.42053	0.00121

Abbreviations: Log2 FC, Log2 fold change; adjust P, adjust P value; MTATP6P1, MT-ATP6 pseudogene 1; MTATP8P1, MT-ATP8 pseudogene 1; GCSHP3, glycine cleavage system protein H pseudogene 3; NDUFS1, NADH, Ubiquinone Oxidoreductase Core Subunit S1; RN7SKP232, RN7SK pseudogene 232; TRBV5-4, T cell receptor beta variable 5-4; CUX1, Cut Like Homeobox 1; ACTA1, Actin alpha 1, skeletal muscle; HBB, Hemoglobin subunit beta; NPPB, Natriuretic peptide B; HBA1, Hemoglobin subunit alpha 1; HBA2, Hemoglobin subunit alpha 2; MYH6, Myosin heavy chain 6; TUBA3E, Tubulin alpha 3e; COMP, Cartilage oligomeric matrix protein; FMOD, Fibromodulin; LUM, lumican; SFRP4, secreted frizzled related protein 4; ASPN, Asporin; MYOT, myotilin; NPPA, Natriuretic peptide A; MXRA5, Matrix remodeling associated 5; HBB, Hemoglobin subunit beta; FKBP5, FKBP prolyl isomerase 5; NRAP, Nebulin related anchoring protein; HOPX, HOP homeobox; RPS4Y1, ribosomal protein S4 Y-linked 1.

Table 2 Co-Expressed Differential Expressed Genes (co-DEGs)

Gene	GSE116250		GSE46224		GSE5406
	Log2 FC	Adjust P value	Log2 FC	Adjust P value	Log2 FC	Adjust P value
LUM	2.06461371	0.00040205	2.41298228	0.00710086	2.06226548	3.48E-15
FCN3	−1.65780841	0.00115544	−1.58296821	0.01053148	−1.33651814	8.47E-16
MXRA5	1.91960666	0.00116672	1.61809866	0.00455141	1.63950658	9.47E-09
HBB	2.67938588	0.00132138	5.03998253	0.00077615	1.50739663	3.77E-05
SERPINA3	−2.15000927	0.00367814	−1.79533725	0.02799646	−1.29892016	2.03E-14
ASPN	1.54437120	0.01250974	2.09911174	0.00339544	2.44397193	1.20E-14
COL1A2	1.31286048	0.01716398	1.56899182	0.02778214	1.23113629	0.00150730
COL3A1	1.38917275	0.03254463	1.52824442	0.03899465	1.22361165	0.002995064

Abbreviations: Log2 FC, Log2 fold change; LUM, lumican; FCN3, Ficolin 3; MXRA5, Matrix remodeling associated 5; HBB, Hemoglobin subunit beta; SERPINA3, Serpin family A member 3; ASPN, Asporin; COL1A2, collagen alpha-2(I) chain; COL3A1, protein Collagen alpha-1(III) chain.

Figure 1 Volcano plot and heat map of all the differentially expressed genes (DEGs) between Non-failure patients and heart failure patients in cardiac tissues. (A), volcano plot of DEGs in GSE116250 dataset; (B), volcano plot of DEGs in GSE46224 dataset; (C), volcano plot of DEGs in GSE5406 dataset; Green dot represent DEGs with fold change <-1, red dot represents DEGs with fold change >1, adjust P <0.05. (D), heat map of DEGs in GSE116250 dataset; (E), heat map of DEGs in GSE46224 dataset; (F), heat map of DEGs in GSE5406 dataset; The gradient colour change from blue to red represents the changing process from downregulation to upregulation.

Figure 2 Functional enrichment analysis of common differentially expressed genes (co-DEGs). (A), Venn diagram of co-DEGs; (B), Gene Ontology (GO) analysis of co-DEGs regard to biological process (BP), cellular component (CC), and molecular function (MF).

Figure 3 Gene Ontology (GO) analysis of all DEGs. (A) the top 10 enriched GO terms in biological process (BP), cellular component (CC), and molecular function (MF) of GSE116250 dataset; (B), the top 10 enriched GO terms in biological process (BP), cellular component (CC), and molecular function (MF) of GSE462224 dataset; (C), the top 10 enriched GO terms in biological process (BP), cellular component (CC), and molecular function (MF) of GSE5406 dataset.

Figure 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis of all DEGs. (A), the enriched KEGG pathways in co-DEGs; (B), the enriched KEGG pathways of DEGs in GSE116250 dataset; (C), the enriched KEGG pathways of DEG in GSE46224 dataset; (D), the enriched KEGG pathways in GSE5406 dataset.

Figure 5 Protein–protein interaction (PPI) network analysis. (A), PPI network of co-DEGs identified by Cytoscape; (B and C), PPI network and hub gene of DEGs in GSE116250; (D and E), PPI network and hub gene of DEGs in GSE46224; (G and H), PPI network and hub gene of DEGs in GSE5406.

Figure 6 Relative gene expression verification of eight co-DEGs. The expression of SERPINA3 (A), FCN3 (B), LUM (C), COL1A2 (D), ASPN (E), HBB (F), COL3A1 (G), MXRA5 (H) were measured by real time-qPCR. *P < 0.05; **P < 0.01.