Open AccessIdentification of Hub Genes and Pathways Associated with Oxidative Stress of Cartilage in Osteonecrosis of Femoral Head Using Bioinformatics Analysis
Author(s) -
Wei Shi,
Xinglong Zhang,
Chengcheng Xu,
Ran Pang,
Zhen-Qi Fan,
Xin Wan,
Z. Jiang,
Hui Li,
Zhijun Li,
Hua-feng Zhang
Publication year - 2022
Publication title -
cartilage
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.705
H-Index - 33
eISSN - 1947-6043
pISSN - 1947-6035
DOI - 10.1177/19476035221074000
Subject(s) - gene , biology , foxo3 , transcription factor , genetics , gene regulatory network , bioinformatics , signal transduction , kegg , computational biology , gene expression , transcriptome
Objective This study aimed to identify the hub genes and pathways of genes related to oxidative stress of cartilage in osteonecrosis of femoral head (ONFH), and to predict the transcription factors of the hub genes.Methods The GSE74089 was obtained from the Gene Expression Omnibus (GEO) database, including 4 necrotic tissues and 4 normal tissues, and the differentially expressed genes (DEGs) were identified by limma package in R language. Simultaneously, we searched for the genes related to oxidative stress in the Gene Ontology (GO) database. GO and signaling pathways analysis were performed using DAVID, Metascape, and GSEA. Protein-protein interaction (PPI) network was constructed using the STRING database, and the Degree algorithm of Cytoscape software was used to screen for hub genes. Finally, the NetworkAnalyst web tool was used to find the hub genes’ transcriptional factors (TFs).Results In total, 440 oxidative stress–related genes were found in GSE74089 and GO database, and 88 of them were significantly differentially expressed. These genes were mainly involved in several signaling pathways, such as MAPK signaling pathway, PI3K-AKT-mTOR signaling pathway, FOXO signaling pathway. The top 10 hub genes were JUN, FOXO3, CASP3, JAK2, RELA, EZH2, ABL1, PTGS2, FBXW7, MCL1. Besides, TFAP2A, GATA2, SP1, and E2F1 may be the key regulatory factors of hub genes.Conclusions We identified some hub genes and signaling pathways associated with oxidative stress in ONFH through a series of bioinformatics analyses.