Screening and Analysis of Core Genes for Osteoporosis Based on Bioinformatics Analysis and Machine Learning Algorithms

This study aimed to identify osteoporosis-related core genes using bioinformatics analysis and machine learning algorithms.

mRNA expression profiles of osteoporosis patients were obtained from the Gene Expression Profiles (GEO) database, with GEO35958 and GEO84500 used as training sets, and GEO35957 and GSE56116 as validation sets. Differential gene expression analysis was performed using the R software “limma” package. A weighted gene co-expression network analysis (WGCNA) was conducted to identify key modules and modular genes of osteoporosis. Kyoto Gene and Genome Encyclopedia (KEGG), Gene Ontology (GO), and gene set enrichment analysis (GSEA) were performed on the differentially expressed genes. LASSO, SVM-RFE, and RF machine learning algorithms were used to screen for core genes, which were subsequently validated in the validation set. Predicted microRNAs (miRNAs) from the core genes were also analyzed, and differential miRNAs were validated using quantitative real-time PCR (qPCR) experiments.

A total of 1280 differentially expressed genes were identified. A disease key module and 215 module key genes were identified by WGCNA. Three core genes (ADAMTS5, COL10A1, KIAA0040) were screened by machine learning algorithms, and COL10A1 had high diagnostic value for osteoporosis. Four core miRNAs (has-miR-148a-3p, has-miR-195-3p, has-miR-148b-3p, has-miR-4531) were found by intersecting predicted miRNAs with differential miRNAs from the dataset (GSE64433, GSE74209). The qPCR experiments validated that the expression of has-miR-195-3p, has-miR-148b-3p, and has-miR-4531 was significantly increased in osteoporosis patients.

This study demonstrated the utility of bioinformatics analysis and machine learning algorithms in identifying core genes associated with osteoporosis.