Bioinformatics Analysis of Differentially Expressed Genes and Protein-Protein Interaction Networks Associated with Functional Pathways in Ulcerative Colitis

Abstract

BACKGROUND This bioinformatics study aimed to identify differentially expressed genes (DEGs) and protein-protein interaction (PPI) networks associated with functional pathways in ulcerative colitis based on 3 Gene Expression Omnibus (GEO) datasets. MATERIAL AND METHODS The GSE87466, GSE75214, and GSE48958 MINiML formatted family files were downloaded from the GEO database. DEGs were identified from the 3 datasets, and volcano maps and heat maps were drawn after R language standardization and analysis, respectively. Venn diagram software was used to identify common DEGs. PPI analysis of common DEGs was performed using the Search Tool for the Retrieval of Interacting Genes. Gene modules and hub genes were visualized in the PPI network using Cytoscape. Enrichment analysis was performed for all common DEGs, module genes, and hub genes. RESULTS A total of 90 DEGs were selected, which included 3 functional modules and 1 hub gene module. CXCL8 module genes were mainly enriched in cytokine-mediated signaling pathways and interleukin (IL)-10 signaling. CCL20 module genes were mainly enriched in the IL-17 signaling pathway and cellular response to IL-1. Hub gene modules mainly involved IL-10, IL-4, and IL-13 signaling pathways. CXCL8, CXCL1, and IL-1ß were the top 3 hub genes and were mainly involved in IL-10 signaling. CONCLUSIONS Bioinformatics analysis using 3 GEO datasets identified CXCL8, CXCL1, and IL-1ß, which are involved in IL-10 signaling, as the top 3 hub genes in ulcerative colitis. The findings from this study remain to be validated, but they may contribute to the further understanding of the pathogenesis of ulcerative colitis.

Figure 1

Standardization of gene expression. Standardization of gene expression in (A) GSE87466, (B) GSE75214, and (C) GSE48958 datasets. The blue bar represents the data before normalization, and the red bar represents the data after normalization.

Figure 2

Screening results for the differentially expressed genes. (A) Volcano maps of gene expression in GSE87466, GSE75214, and GSE48958 datasets. Data points in red, green, and black represent genes with upregulated, downregulated, and not significantly different expression, respectively. (B) Heat maps of gene expression GSE87466, GSE75214, and GSE48958 datasets. (C) Venn diagram of common differentially expressed genes in GSE87466, GSE75214, and GSE48958 datasets.

Figure 3

Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis for common differentially expressed genes.

Figure 4

Protein–protein interaction (PPI) analysis. (A) PPI networks of the common differentially expressed genes. (B–D) The 3 top-scoring modules are shown from the top to bottom. (E) The PPI hub gene module.

Figure 5

Metascape enrichment analysis of the top 2 modules and reactome pathway enrichment analysis for hub gene modules. (A) Metascape analysis of the CCL20 modules. (B) Metascape analysis of the CXCL8 modules. (C) Interleukin (IL)-10 signaling pathway. (D) Heat map of the expression of all proteins involved in the IL-10 signaling pathway in the human body.