Screening disease feature genes and analyzing correlations with immune cell infiltration in knee osteoarthritis chondrocytes based on multiple machine learning algorithms

Jing-le Zhuge, Xi-yong Li, Yong-le Wang and Juan-fen Ma

PLOS ONE, 2026, vol. 21, issue 6, 1-21

Abstract: Objective: This study aimed to comprehensively analyze differentially expressed genes (DEGs) in chondrocytes from patients with knee osteoarthritis (OA) by integrating multiple machine learning algorithms and bioinformatics techniques, to unravel the underlying molecular mechanisms associated with OA chondrocytes, and to provide novel insights for the innovation of clinical therapeutic strategies. Methods: We downloaded the GSE117999, GSE114007, GSE169077, GSE246425, and GSE178557 datasets from the public Gene Expression Omnibus (GEO) database as the training set, while GSE57218 served as an independent validation set. To ensure data consistency and comparability, the training set was normalized, and the ComBat algorithm was applied to eliminate batch effects, yielding a merged gene expression dataset. Subsequent differential expression analysis was performed to identify genes with significant changes under disease conditions, followed by enrichment analysis. To more accurately identify genes closely linked to disease characteristics, we independently analyzed the merged dataset using three machine learning algorithms: Lasso regression, random forest, and support vector machine (SVM). The intersection of results from these three methods was used to construct a robust list of disease-related feature genes. These prominent feature genes were validated in the training set and further externally confirmed using the GSE57218 dataset. Additionally, the CIBERSORT algorithm was employed to quantify immune cell infiltration in the normalized gene expression data, selecting infiltration results with high reliability (P

Date: 2026
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0351666

DOI: 10.1371/journal.pone.0351666

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