<p>Identification of Hub Genes in Type 2 Diabetes Mellitus Using Bioinformatics Analysis</p>

Abstract

Background: Type 2 diabetes mellitus (T2DM) is one of the most common chronic diseases in the world with complicated pathogenesis. This study aimed to identify differentially expressed genes (DEGs) and molecular pathways in T2DM using bioinformatics analysis. Materials and Methods: To explore potential therapeutic targets for T2DM, we analyzed three microarray datasets (GSE50397, GSE38642, and GSE44035) acquired from the Gene Expression Omnibus (GEO) database. DEGs between T2DM islet and normal islet were picked out by the GEO2R tool and Venn diagram software. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to identify the pathways and functional annotation of DEGs. Then, protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Results: In total, we identified 36 DEGs in the three datasets, including 32 up-regulated genes and four down-regulated genes. The improved functions and pathways of the DEGs enriched in cytokine-cytokine receptor interaction, pathways in cancer, PI3K-Akt signaling pathway, and Rheumatoid arthritis. Among them, ten hub genes with a high degree of connectivity were selected. Furthermore, via the re-analysis of DAVID, four genes (IL6, MMP3, MMP1, and IL11) were significantly enriched in the Rheumatoid arthritis pathway. Conclusion: Our study, based on the GEO database, identified four significant up-regulated DEGs and provided novel targets for diagnosis and treatment of T2DM.

Integrated Analysis of Key Genes and Pathways Involved in Nonalcoholic Steatohepatitis Improvement After Roux-en-Y Gastric Bypass Surgery

“…Hub genes were identified using CytoHubba plug-in APP in Cytoscape with the cut-off value degree value >10. Vital modules in the PPI network were clustered using the Molecular Complex Detection (MCODE) plug-in APP in Cytoscape ( 17 ). The cut-off value was MCODE score ≥ 5.…”

Highly perturbed genes and hub genes associated with type 2 diabetes in different tissues of adult humans: a bioinformatics analytic workflow

“…Yet, to date, no comprehensive evidence synthesis study has been performed to identify highly perturbed genes and hub genes associated with T2D in human adults using an extensive bioinformatics analytic pipeline. Prior studies were limited to identifying hub genes in a few ( n = 3) microarrays from a single tissue type (pancreatic islets) (Lin et al 2020 ) or performing an ad hoc gene expression meta-analysis of all diabetes phenotypes ( n = 13) (Mei et al 2017 ). In this study, we aimed to identify highly perturbed genes and hub genes associated with T2D in different tissues of adult humans via a pre-defined and extensive bioinformatics analytic workflow consisting of systematic review, meta-analysis, identification and classification of differentially expressed genes (DEGs), network analysis, and downstream analysis.…”

Comprehensive analysis of key m5C modification-related genes in type 2 diabetes

“…The 10th edition of the International Diabetes Federation Diabetes Atlas revealed that the prevalence of diabetes worldwide reached 10.5% in 2021 and would rise to 12.2% by 2045 (Sun et al, 2022). In China, the number of T2D patients has been increasing annually, and the disease has become an important public health issue (Li Y. et al, 2020). T2D is a heterogeneous complex disorder.…”