Machine learning analysis of gene expression profile reveals a novel diagnostic signature for osteoporosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33722258", "kind": "science-record", "revision": 8, "content_hash": "sha256:18050ba6eb6bfcdbece10f6fb95540badf6f29295c6a62fca01c94688cee62ed", "created_at": "2026-11-01T15:41:28Z", "updated_at": "2026-11-01T22:03:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Machine learning analysis of gene expression profile reveals a novel diagnostic signature for osteoporosis.", "doi": "10.1186/s13018-021-02329-1", "pmid": "33722258", "authors": ["Xinlei Chen", "Guangping Liu", "Shuxiang Wang", "Haiyang Zhang", "Peng Xue"], "journal": "Journal of orthopaedic surgery and research", "year": 2021, "abstract": "BACKGROUND: Osteoporosis (OP) is increasingly prevalent with the aging of the world population. It is urgent to identify efficient diagnostic signatures for the clinical application.\nMETHOD: We downloaded the mRNA profile of 90 peripheral blood samples with or without OP from GEO database (Number: GSE152073). Weighted gene co-expression network analysis (WGCNA) was used to reveal the correlation among genes in all samples. GO term and KEGG pathway enrichment analysis was performed via the clusterProfiler R package. STRING database was applied to screen the interaction pairs among proteins. Protein-protein interaction (PPI) network was visualized based on Cytoscape, and the key genes were screened using the cytoHubba plug-in. The diagnostic model based on these key genes was constructed, and 5-fold cross validation method was applied to evaluate its reliability.\nRESULTS: A gene module consisted of 176 genes predicted to be associated with the occurrence of OP was identified. A total of 16 significantly enriched GO terms and 1 significantly enriched KEGG pathway were obtained based on the 176 genes. The top 50 key genes in the PPI network were identified. Then 22 genes were screened based on stepwise regression analysis from the 50 key genes. Of which, 9 genes were further screened out by multivariate regression analysis with the significant threshold of P value < 0.01. The diagnostic model was established based on the optimal 9 key genes, which efficiently separated the normal samples and OP samples.\nCONCLUSION: A diagnostic model established based on nine key genes could reliably separate OP patients from healthy subjects, which provided novel lightings on the diagnostic research of OP.", "claims": [{"id": "claim-method", "statement": "The mRNA profile GSE152073 was downloaded from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) which includes 90 peripheral blood samples of 44 OP patients and 46 healthy subjects. Meanwhile, the 5-fold cross validation method was used to verify the accuracy of the logistic regression model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33722258", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The mRNA profile GSE152073 was downloaded from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) which includes 90 peripheral blood samples of 44 OP patients and 46 healthy subjects."}, {"asset": "source:pmid:33722258", "locator": "sections[7] \"The construction of logistic regression model\" paragraph 2", "quote": "Meanwhile, the 5-fold cross validation method was used to verify the accuracy of the logistic regression model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA profile GSE152073 was downloaded from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) which includes 90 peripheral blood samples of 44 OP patients and 46 healthy subjects. The mRNA profiles of GSE152073 were detected by using Affymetrix Human Transcriptome Array 2.0.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33722258", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The mRNA profile GSE152073 was downloaded from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) which includes 90 peripheral blood samples of 44 OP patients and 46 healthy subjects. The mRNA profiles of GSE152073 were detected by using Affymetrix Human Transcriptome Array 2.0."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33722258"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE152073"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE152073"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33722258", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13018-021-02329-1", "sha256": "sha256:59e889bef973ce486dc065feeb790e8bcc31fe7fafe262c720e7fa675d87ba85", "bytes": 31241, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13018-021-02329-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7958453", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE152073", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152073", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE152073", "version": null, "note": "The mRNA profile GSE152073 was downloaded from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) which includes 90 peripheral blood samples of 44 OP patients and 46 healthy subjects. 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