Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Objective: The study aimed to examine the hub genes and oxidative stress-related pathways in odontogenic keratocysts (OKCs) and predict transcription factors associated with the hub genes.
Methods: The GSE38494 dataset, which includes 12 OKC tissues and 4 normal oral mucosa tissues, was retrieved from the Gene Expression Omnibus (GEO) database. The limma package in the R programming language was utilized to identify differentially expressed genes (DEGs). In addition, Gene Ontology (GO) analysis was performed specifically for genes associated with oxidative stress. Utilizing Database for Annotation, Visualization, and Integrated Discovery (DAVID), Metascape, and Gene Set Enrichment Analysis (GSEA), we comprehensively analyzed the GO terms and signaling pathways related to oxidative stress. The Degree algorithm in Cytoscape was employed to identify hub genes. The STRING database was leveraged to construct the protein-protein interaction (PPI) network. Finally, the transcription factors (TFs) of the hub genes were identified using the NetworkAnalyst web tool. scRNA data of OKC (GSE176351) was used for correlation analysis between oxidative stress-related hub genes and IL-β gene by Pearson correlation analysis.
Results: A total of 465 genes associated with oxidative stress were identified in the GSE38494 and GO databases, and 60 genes were significantly differentially expressed. The majority of these genes were involved in multiple signaling pathways, such as microRNAs in cancers, chemical carcinogenesis, reactive oxygen species, and the arachidonic acid metabolism signaling pathway. The ten most important hub genes were MAPK3, HMOX1, GPX6, GPX7, GCLM, COL1A1, TXN, PDGFRB, NQO1, and MMP2. FOXC1, HNF4A, and GATA2 may be the key regulatory factors of the hub genes. Additionally, there is a weak postitive correlation between oxidative stress-related genes and IL-1β in epithelial cells of OKC (R = 0.26).
Conclusions: Through bioinformatics analysis, we identified several oxidative stress-related hub genes and signaling pathways in OKC which was related to IL-1β expression.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.jormas.2025.102423 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Identification and prioritization of gene sets associated with schizophrenia risk by network analysis.
Psychopharmacology (Berl)
September 2025
Institute of Cardiovascular Research, Sleep Medical Center, Department of Psychiatry, Fundamental and Clinical Research on Mental Disorders Key Laboratory of Luzhou, Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province, 646000, China.
Rationale: Genome-wide association studies (GWASs) are used to identify genetic variants for association with schizophrenia (SCZ) risk; however, each GWAS can only reveal a small fraction of this association.
Objectives: This study systematically analyzed multiple GWAS data sets to identify gene subnetwork and pathways associated with SCZ.
Methods: We identified gene subnetwork using dmGWAS program by combining SCZ GWASs and a human interaction network, performed gene-set analysis to test the association of gene subnetwork with clinical symptom scores and disease state, meanwhile, conducted spatiotemporal and tissue-specific expression patterns and cell-type-specific analysis of genes in the subnetwork.
Multi-Omics and Clinical Validation Identify Key Glycolysis- and Immune-Related Genes in Sepsis.
Int J Gen Med
September 2025
Department of Geriatrics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China.
Background: Sepsis is characterized by profound immune and metabolic perturbations, with glycolysis serving as a pivotal modulator of immune responses. However, the molecular mechanisms linking glycolytic reprogramming to immune dysfunction remain poorly defined.
Methods: Transcriptomic profiles of sepsis were obtained from the Gene Expression Omnibus.
Identification of Potential Targets for EGFR-Regulated Nucleus Pulposus Degeneration Using Single-Cell RNA Sequencing and Machine Learning.
J Inflamm Res
September 2025
Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.
Introduction: While nucleus pulposus cell (NPC) degeneration is a primary driver of intervertebral disc degeneration (IVDD), the cellular heterogeneity and molecular interactions underlying NPC degeneration remain poorly characterized. Previous studies have shown that EGFR signaling plays a significant role in NPC differentiation and collagen matrix production. Consequently, this study aims to identify the critical downstream regulatory molecule of EGFR in the process of NPC degeneration.
View Article and Find Full Text PDFIdentification of GABBR2 as a diagnostic marker and its association with Aβ in Alzheimer's disease.
Biochem Biophys Rep
June 2025
Department of Public Health, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
Background: Synaptic dysfunction and synapse loss occur in Alzheimer's disease (AD). The current study aimed to identify synaptic-related genes with diagnostic potential for AD.
Methods: Differentially expressed genes (DEGs) were overlapped with phenotype-associated module selected through weighted gene co-expression network analysis (WGCNA), and synaptic-related genes.
Transcriptomic Meta-Analysis Reveals Hub Genes Integrating Multiple Abiotic Stress Responses in Wheat.
Food Sci Nutr
September 2025
Department of Biology, College of Natural and Computational Sciences Mizan-Tepi University Tepi Ethiopia.
Climatic challenges increasingly threaten global food security, necessitating crops with enhanced multi-stress resilience. Through systematic transcriptomic analysis of 100 wheat genotypes under heat, drought, cold, and salt stress, we identified 3237 differentially expressed genes (DEGs) enriched in key stress-response pathways. Core transcription factors (, , ) and two functional modules governing abiotic tolerance were characterized.
View Article and Find Full Text PDF