Identification of hub genes and potential molecular mechanisms associated with inflammatory bowel diseases using meta-analysis of gene expression data

Khaled H. Mousa, Ahmed E. Nassar


Inflammatory bowel diseases (IBDs), which primarily include Crohn's disease (CD) and ulcerative colitis (UC), are chronic recurrent diseases of the gastrointestinal tract with increasing prevalence and incidence worldwide. In this study, we aimed to identify key factor genes that control the progression of inflammatory bowel disease, identify common and unique nodal genes, examine gene-protein interactions, assess current advances in the published literature on inflammatory bowel disease, and examine the impact of various biological pathways. Gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database. We performed gene expression analysis to identify deferentially expressed genes. Subsequently, GO and KEGG pathway enrichment analyzes and protein-protein interaction network analyzes (PPI) of DEGs were performed. Text mining was used to examine the frequency of genes in the published IBD literature. Four GEO databases (GSE156044, GSE159751, GSE159008, and GSE102746) were downloaded from GEO databases. A total of 368 DEGs were identified. The results of GO term analysis showed that DEGs were mainly involved in the activity of cytokine receptors, integral components of the plasma membrane, and cytokine-mediated signaling. KEGG pathway analysis showed that DEGs were mainly enriched in bile secretion, mineral absorption, and cytokine-cytokine receptor interaction. The results of PPI analysis showed that about 10 genes were the key genes for the occurrence of CED. Text mining revealed the existence of 399 genes associated with CED. Our results suggest a possible link between CED and other diseases such as triple negative breast cancer (TNBC) and lung adenocarcinoma (LUAD), and provide new insights into the mechanisms of inflammatory bowel disease and new treatment targets.

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