Identification of key genes related to heart failure by analysis of expression profiles

Abstract

Introduction: To elucidate the candidate biomarkers involved in the pathogenesis process of heart failure (HF) via analysis of differentially expressed genes (DEGs) of the dataset from the Gene Expression Omnibus (GEO).

Material and methods: The GSE76701 gene expression profiles regarding the HF and control subjects were respectively analysed. Briefly, DEGs were firstly identified and subjected to Cytoscape plug-in ClueGO + CluePedia and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A protein-protein interaction (PPI) network was then built to analyse the interaction between DEGs, followed by the construction of an interaction network by combining with hub genes with the targeted miRNA genes of DEGs to identify the key molecules of HF. In addition, potential drugs targeting key DEGs were sought using the drug-gene interaction database (DGIdb), and a drug-mRNA-miRNA interaction network was also constructed.

Results: A total of 489 DEGs were verified between HF and control, which mainly enriched in type I interferon and leukocyte migration according to molecular function. Significantly increased levels of GAPDH, GALM1, MMP9, CCL5, and GNAL2 were found in the HF setting and were identified as the hub genes based on the PPI network. Furthermore, according to the drug-mRNA-miRNA network, FCGR2B, CCND1, and NF-κb, as well as corresponding miRNA-605-5p, miRNA-147a, and miRNA-671-5p were identified as the drug targets of HF.

Conclusions: The hub genes GAPDH, GALM1, MMP9, CCL5, and GNAL2 were significantly increased in HF. miRNA-605-5p, miRNA-147a, and miRNA-671-5p were predicted as the drug target-interacted gene-miRNA of HF.

Keywords: PPI network; differentially expressed gene; drug-mRNA-miRNA network; enrichment analysis; heart failure.

Figure 1

Volcano plot (A) and Heatmap (B) of DEGs between control and heart failure (HF) samples. A – exhibit the DEGs. X-axis: log2FC; Y-axis: the log-transformed p-values. A total of 489 differential mRNAs were divided in to 271 up(red)- and 218 down(blue) regulated mRNAs in GSE76701. B – column on the top of the heatmap represents, respectively, the HF group (yellow) and the control group (blue). Upregulated and downregulated genes were respectively marked in green and red

Figure 2

Functional enrichment analysis of upregulated DEGs. A – X-axis represents the percentage of enriched genes among the functional term-related genes, and the Y-axis gives the name of the GO term and is consistent with the pie graph. The number on the right side of the bar shows the number of related genes enriched in the relevant GO function term in the list of uploaded genes. * represents a p-value between 0.01 and 0.05, while ** represents p < 0.01. B – Functionally enriched pie graph, which represents the ratio of 3 groups of GO function. C – ClueGO Functional Network Diagram of upregulated DEGs. The dot is a GO function term. The larger the p-value, the larger the size of the dot. The 2-point connection represents the correlation between the functions, and the larger the kappa coefficient, the thicker the line. Multicolour dots represent multiple GO functions

Figure 3

Functional enrichment analysis of downregulated DEGs from GSE76701. A – Downregulated DEGs between HF and control were functionally classified via GO analysis. X-axis represents the percentage of enriched genes among the functional term-related genes, and the Y-axis gives the name of the GO term and is consistent with the pie graph. The number on the right side of the bar is the number of related genes enriched in the relevant GO function term in the list of uploaded genes. * represents a p-value between 0.01 and 0.05, while ** represents p < 0.01. B – Functionally enriched pie graph, which represents the ratio of 2 groups of GO function. C – ClueGO Functional Network Diagram of downregulated genes. Red label corresponding to the dot is the enriched differential gene. The dot is a GO function term. The larger the p-value, the larger the size of the dot. The 2-point connection represents the correlation between the functions, and the larger the k coefficient, the thicker the line. Multicolour dots represent multiple GO functions

Figure 4

The bubble diagrams of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on differentially expressed mRNA. X-axis represents upregulated or downregulated enriched gene entries. Y-axis represents KEGG pathways. The size of dots represents the ratio of the number of enriched genes to the total number of uploaded genes, and the larger the ratio, the larger the dot. The colour gradation from blue to red suggests that the p-values becomes smaller, and the significance is higher

Figure 5

Sub-PPI network constructed from differential mRNA from GSE76701. Cluster 1 contains 25 genes and 146 edges with a score of 12.167; cluster 2 contains 15 genes and 53 edges with a score of 7.571; cluster 3 contains 7 genes and 21 edges with a score of 7; cluster 4 contains 15 genes and 43 edges with a score of 6.143. Pink represents upregulation, green represents downregulation. The size of the circle represents the degree of association of the node genes. The larger the dot, the greater the degree of genetic association

Figure 6

Drug-Gene-miRNA Relationship Network. The green triangle represents the miRNA, the red dot represents the gene, and the blue square represents the drug