Identification of Hub Genes and Pathways Associated with Oxidative Stress of Cartilage in Osteonecrosis of Femoral Head Using Bioinformatics Analysis

Cartilage. 2022 Jan-Mar;13(1):19476035221074000. doi: 10.1177/19476035221074000.


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.

Keywords: GEO; cartilage; osteonecrosis of femoral head; oxidative stress.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cartilage
  • Computational Biology*
  • Femur Head
  • Femur Head Necrosis* / genetics
  • Gene Regulatory Networks / genetics
  • Humans
  • Oxidative Stress / genetics
  • Phosphatidylinositol 3-Kinases / genetics