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Published on: November 30, 2016
Candidate Biomarkers for Crohn's Disease: Hub Genes and Regulatory miRNAs Identified by Bioinformatics Analysis
1Department of Gynecology and Obstetrics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China, zju.edu.cn.
Background:
Crohn's disease (CD) is a chronic, complex inflammatory condition that can affect the entire digestive tract, most commonly the terminal ileum. The exact cause of CD remains unknown. Bioinformatics was used in this study to identify the differentially expressed genes (DEGs) and microRNAs (miRNAs) that show potential as diagnostic and therapeutic agents in treating CD.
Materials And Methods:
Datasets were downloaded from the Gene Expression Omnibus database and filtered. DEGs between CD samples and healthy control samples were identified using the GEO2R tool (including GEOquery and Linear Models for Microarray Analysis), and Kyoto Encyclopedia of Genes and Genomes/Gene Ontology enrichment analyses were conducted as part of the study to gain deeper insights into the data. A network depicting protein-protein interactions was established and visualized using the STRING database and Cytoscape software, and hub genes were identified and extracted utilizing the cytoHubba program. Cytoscape and miRTarBase were used to construct the miRNA-hub gene regulatory network and predict the potential miRNAs associated with the DEGs. The hub genes were analyzed further using ROC curves and combined ROC curve analyses of the GSE179285, GSE186582, and GSE112366 datasets. A regularized LASSO regression model was constructed to reduce the risk of overfitting.
Results:
Three datasets (GSE179285, GSE186582, and GSE112366) were selected. A comprehensive analysis of the three datasets revealed 60 DEGs that showed significantly altered expression levels, including 44 upregulated genes and 16 downregulated genes. Ten different algorithms were randomly used, and three hub genes (CXCL1, CXCL2, and CXCR2) were identified. Based on the miRNA-hub gene regulatory network, hsa-miR-1-3p and hsa-miR-335-5p were recognized as potentially vital miRNAs.
Conclusion:
Three hub genes (CXCL1, CXCL2, and CXCR2) and two miRNAs (hsa-miR-1-3p and hsa-miR-335-5p) are postulated to play a role in the initiation and progression of CD, thereby offering potential as biomarkers for this condition.
