Identification of hub genes and potential molecular mechanisms associated with inflammatory bowel diseases using meta-analysis of gene expression data
Open Access
- 15 July 2022
- journal article
- review article
- Published by International Library of Science in Highlights in BioScience
Abstract
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.Keywords
This publication has 56 references indexed in Scilit:
- Gain-of-function mutations in granulocyte colony–stimulating factor receptor (CSF3R) reveal distinct mechanisms of CSF3R activationOnline Journal of Public Health Informatics, 2018
- ViDGER: An R package for integrative interpretation of differential gene expression results of RNA-seq dataPublished by Cold Spring Harbor Laboratory ,2018
- A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstractsPLoS Computational Biology, 2018
- The function of macromolecular complex of CFTR-NHERF2-LPA2 in inflammatory responses of intestinal epithelial cellsPublished by Cold Spring Harbor Laboratory ,2017
- Understanding the Genomic Structure of Copy-Number Variation of the Low-Affinity Fcγ Receptor Region Allows Confirmation of the Association ofFCGR3BDeletion with Rheumatoid ArthritisHuman Mutation, 2017
- Low-FODMAP diet reduces irritable bowel symptoms in patients with inflammatory bowel diseaseWorld Journal of Gastroenterology, 2017
- ESPEN guideline: Clinical nutrition in inflammatory bowel diseaseClinical Nutrition, 2016
- TIMP1 is a prognostic marker for the progression and metastasis of colon cancer through FAK-PI3K/AKT and MAPK pathwayJournal of Experimental & Clinical Cancer Research, 2016
- The Gene Expression Omnibus DatabasePublished by Springer Science and Business Media LLC ,2016
- Proton pump inhibitors affect the gut microbiomeGut, 2015