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. 2022 Dec 29:2022:5437560.
doi: 10.1155/2022/5437560. eCollection 2022.

Identification of Differentially Expressed Genes Particularly Associated with Immunity in Uremia Patients by Bioinformatic Analysis

Guixia Li #  1 , Shijun Wang #  2 , Jing Huo  1
Affiliations

Identification of Differentially Expressed Genes Particularly Associated with Immunity in Uremia Patients by Bioinformatic Analysis

Guixia Li et al. Anal Cell Pathol (Amst). .

Abstract

Uremia is a common syndrome that happens to nearly all end-stage kidney diseases, which profound have changes in human gene expressions, but the related pathways are poorly understood. Gene Ontology categories and Kyoto Encyclopedia of Genes and Genomes pathways enriched in the differentially expressed genes (DEGs) were analyzed by using clusterProfiler, org.Hs.eg.db, and Pathview, and protein-protein interaction (PPI) network was built by Cytoscape. We identified 3432 DEGs (including 3368 down- and 64 up-regulated genes), of which there were 52 different molecular functions, and 178 genes were identified as immune genes controlled by the four transcription factors (POU domain class 6 transcription factor 1 (POU6F1), interferon regulator factor 7 [IRF7], forkhead box D3 (FOXD3), and interferon-stimulated response element [ISRE]). In the gender research, no significant difference was observed. The top 15 proteins of 178 immune-related genes were identified with the highest degree in PPI network. The DEG analysis of uremia patients was expected to provide fundamental information to relieve pain and add years to their life.

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Conflict of interest statement

The author(s) declare(s) that they have no conflicts of interest.

Figures

Figure 1
Figure 1
Heatmap of the top 3432 significant DEGs. Red and green indicate up-regulated and down-regulated gene expression.
Figure 2
Figure 2
The volcano plot shows the DEGs. The red dots represent up-regulated genes, the green dots represent down-regulated genes, but the black dots represent genes that are non-significantly differentially expressed.
Figure 3
Figure 3
GO and KEGG pathway enrichment analyses of DEGs. (a) Top 15 GO enrichment analysis. (b) Top 10 pathways enrichment analysis.
Figure 4
Figure 4
Immune-related genes. (a) Venn diagram for the overlapping comparison of immune-related genes and DEGs. (b) Immune infiltration. (c) Nine types of immune cells with significant differences in normal and uremic samples.
Figure 5
Figure 5
The regulatory network of transcription factor. The lines between two nodes mean that they have a subordinate relationship or can interact with each other.
Figure 6
Figure 6
The exploration of PPI with 178 target genes using String. The area of the circle is proportional to the size of the degree.
Figure 7
Figure 7
Venn diagram of DEGs. The DEGs were identified from the three microarray datasets showed overlaps of 3053 in both male and female.
See this image and copyright information in PMC

References

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