Study on differentially expressed genes and pattern recognition receptors in osteoporosis based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40854963", "kind": "science-record", "revision": 4, "content_hash": "sha256:79dcf618a0e21959e0eff9969d92532cfd60003e3a5d7a9bb2ccf5e131c46560", "created_at": "2026-11-01T20:30:57Z", "updated_at": "2026-11-01T22:57:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Study on differentially expressed genes and pattern recognition receptors in osteoporosis based on bioinformatics analysis.", "doi": "10.1038/s41598-025-16891-9", "pmid": "40854963", "authors": ["Songbo Mao", "Yanbiao Wang", "Mingyong Gu", "Kai Liu", "Jibin Ma", "Jun Miao", "Fang Zhao"], "journal": "Scientific reports", "year": 2025, "abstract": "Osteoporosis is a common skeletal disorder characterized by low bone mass and structural deterioration, leading to an increased risk of fractures. This study aimed to explore the molecular mechanisms underlying osteoporosis using bioinformatics approaches, with a focus on pattern recognition receptor-related differentially expressed genes (PRR-related DEGs). Two gene expression datasets (GSE7429 and GSE56815) were retrieved from the GEO database, comprising 30 osteoporosis samples and 30 matched controls. Data integration and batch effect correction were performed using the GEOquery and sva packages, followed by differential expression analysis with limma. A total of 1,052 pattern recognition receptor-related genes (PRR-related genes) were obtained from GeneCards, and 98 PRR-related DEGs were identified. GO and KEGG enrichment analyses revealed that these genes are primarily involved in the MAPK cascade, calcium ion homeostasis, leukocyte migration, and the regulation of inflammatory responses. A protein-protein interaction (PPI) network was constructed using STRING, and six hub genes (MDM2, AKT1, ESR1, NCOR1, CCND1, and NCOA2) were identified via CytoHubba. Regulatory networks involving miRNAs and transcription factors were constructed using ENCORI and ChIPBase. ROC curve analysis showed that ESR1 exhibited moderate diagnostic potential (AUC > 0.7). In conclusion, this study systematically identifies PRR-related DEGs and hub genes associated with osteoporosis through integrated bioinformatics analysis. These findings may contribute to a better understanding of immune-related molecular mechanisms and lay the groundwork for future research on potential diagnostic markers or therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed on the integrated GSE7429 and GSE56815 dataset using the limma package (version 3.54.2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40854963", "locator": "sections[4] \"Identification of PRR-related DEGs in osteoporosis\" paragraph 2", "quote": "Differential expression analysis was performed on the integrated GSE7429 and GSE56815 dataset using the limma package (version 3.54.2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40854963", "locator": "sections[26] \"Data availability\" paragraph 2", "quote": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 1,347 DEGs met the screening criteria of |logFC| > 0 and p-value < 0.05, of which 742 genes were upregulated (logFC > 0) and 605 genes were downregulated (logFC < 0).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "The integrated GEO dataset was divided into osteoporosis and control groups. To identify differentially expressed genes (DEGs) between the two groups, differential expression analysis was conducted using the limma package in R. A total of 1,347 DEGs met the screening criteria of |logFC| > 0 and p-value < 0.05, of which 742 genes were upregulated (logFC > 0) and 605 genes were downregulated (logFC < 0)."}, "evidence": [{"asset": "source:pmid:40854963", "locator": "sections[15] \"Differentially expressed pattern recognition receptor-related genes in osteoporosis\" paragraph 2", "quote": "The integrated GEO dataset was divided into osteoporosis and control groups. To identify differentially expressed genes (DEGs) between the two groups, differential expression analysis was conducted using the limma package in R. A total of 1,347 DEGs met the screening criteria of |logFC| > 0 and p-value < 0.05, of which 742 genes were upregulated (logFC > 0) and 605 genes were downregulated (logFC < 0)."}, {"asset": "source:pmid:40854963", "locator": "sections[15] \"Differentially expressed pattern recognition receptor-related genes in osteoporosis\" paragraph 4", "quote": "To identify PRR-related DEGs, the list of DEGs was intersected with pattern recognition receptor-related genes obtained from the GeneCards database. A Venn diagram (Fig. 3b) was used to visualize the intersection, resulting in a total of 98 PRR-related DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 1,347 DEGs met the screening criteria of |logFC| > 0 and p-value < 0.05, of which 742 genes were upregulated (logFC > 0) and 605 genes were downregulated (logFC < 0).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40854963"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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