Integrated strategy of differentially expressed genes associated with ulcerative colitis

Abstract

Ulcerative colitis (UC) is a chronic inflammatory bowel disease that is associated with both genetic and environmental factors; however, the underlying pathogenesis of UC remains unclear. The present study aimed to further explore 12 microarray datasets from patients with UC obtained from the Gene Expression Omnibus repository, for potential genetic pathogenesis of UC through a global bioinformatics view, which included identification of differentially expressed genes (DEGs), functional enrichments, protein‑protein interactions, transcriptional and post‑transcriptional regulation and drug‑gene associations. This integrated analysis screened 233 DEGs that were compared between UC and normal control tissue samples; these included 173 upregulated and 60 downregulated DEGs. Subsequently, transcription factors, such as TATA‑binding protein 1 (TBP1; hsa_TATAAA_V$TATA_01) and nuclear factor-κB (NF-κB; hsa_V$NFKAPPAB_01) and microRNAs (miRNAs; such as miR‑516‑3p and miR‑23a) were revealed to be associated with 233 DEGs. Notably, further analysis indicated that these DEGs were enriched in certain diseases, including inflammation, fibrosis and immune system diseases, and were also associated with some drugs, including prednisone, collagenase and mycophenolate mofetil, which may provide choice for treatment of UC. In conclusion, this study may provide novel insights into discovering potential molecular targets involved in the pathogenesis and treatment of UC.

Figure 1.

Diagram of the chemokine signaling pathway significantly enriched in differentially expressed genes.

Figure 2.

Predicted interaction network for DEGs in ulcerative colitis. Red nodes indicate upregulated genes and green nodes indicate downregulated genes. Lines indicate interactions between DEGs, genes circled by a black ellipse are the hub genes and the gene underlined in blue is a gene of interest. DEG, differentially expressed gene.

Figure 3.

Interaction network of the top 10 miRNAs-DEGs pairs. Red nodes indicate upregulated genes and green nodes indicate downregulated genes. Diamonds indicate miRNAs and lines represent interactions between miRNAs and DEGs. Genes circled by a black ellipse are the hub genes and the gene underlined in blue is of interest. DEG, differentially expressed gene; miRNA, microRNA.

Figure 4.

Interaction network of the top 10 TFs-DEGs pairs. Red nodes indicate upregulated genes and green nodes indicate downregulated genes. Diamonds indicate TFs and lines represent interactions between TFs and DEGs. Genes circled by a black ellipse are the hub genes and the gene underlined in blue is of interest. TFs, transcription factors; DEG, differentially expressed gene.

Figure 5.

Interaction network of the top 10 drugs-DEGs pairs. Red nodes indicate upregulated genes and green nodes indicate downregulated genes. Diamonds indicate drugs and lines represent interactions between drugs and DEGs. Genes circled by a black ellipse are the hub genes and the gene underlined in blue is of interest. DEG, differentially expressed gene.