Identification of ROCK1 as a novel biomarker for postmenopausal osteoporosis and pan-cancer analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37683138", "kind": "science-record", "revision": 5, "content_hash": "sha256:25f150a83bca0ddef34967f51524f6af719164801002b48b07dece2affd34d57", "created_at": "2026-11-01T19:02:29Z", "updated_at": "2026-11-01T22:52:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of ROCK1 as a novel biomarker for postmenopausal osteoporosis and pan-cancer analysis.", "doi": "10.18632/aging.205004", "pmid": "37683138", "authors": ["Bowen Lai", "Heng Jiang", "Yuan Gao", "Xuhui Zhou"], "journal": "Aging", "year": 2023, "abstract": "BACKGROUND: Postmenopausal osteoporosis (PMOP) is a prevalent bone disorder with significant global impact. The elevated risk of osteoporotic fracture in elderly women poses a substantial burden on individuals and society. Unfortunately, the current lack of dependable diagnostic markers and precise therapeutic targets for PMOP remains a major challenge.\nMETHODS: PMOP-related datasets GSE7429, GSE56814, GSE56815, and GSE147287, were downloaded from the GEO database. The DEGs were identified by \"limma\" packages. WGCNA and Machine Learning were used to choose key module genes highly related to PMOP. GSEA, DO, GO, and KEGG enrichment analysis was performed on all DEGs and the selected key hub genes. The PPI network was constructed through the GeneMANIA database. ROC curves and AUC values validated the diagnostic values of the hub genes in both training and validation datasets. xCell immune infiltration and single-cell analysis identified the hub genes' function on immune reaction in PMOP. Pan-cancer analysis revealed the role of the hub genes in cancers.\nRESULTS: A total of 1278 DEGs were identified between PMOP patients and the healthy controls. The purple module and cyan module were selected as the key modules and 112 common genes were selected after combining the DEGs and module genes. Five Machine Learning algorithms screened three hub genes (KCNJ2, HIPK1, and ROCK1), and a PPI network was constructed for the hub genes. ROC curves validate the diagnostic values of ROCK1 in both the training (AUC = 0.73) and validation datasets of PMOP (AUC = 0.81). GSEA was performed for the low-ROCK1 patients, and the top enriched field included protein binding and immune reaction. DCs and NKT cells were highly expressed in PMOP. Pan-cancer analysis showed a correlation between low ROCK1 expression and SKCM as well as renal tumors (KIRP, KICH, and KIRC).\nCONCLUSIONS: ROCK1 was significantly associated with the pathogenesis and immune infiltration of PMOP, and influenced cancer development, progression, and prognosis, which provided a potential therapy target for PMOP and tumors. However, further laboratory and clinical evidence is required before the clinical application of ROCK1 as a therapeutic target.", "claims": [{"id": "claim-method", "statement": "With the criteria of the adjusted p-value (FDR method) <0.05 and |log fold change value| >0.03, we identified the differentially expressed genes (DEGs) between controls and the PMOP patients by “limma” package [81].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37683138", "locator": "sections[17] \"Identification of differentially expressed genes\" paragraph 2", "quote": "With the criteria of the adjusted p-value (FDR method) <0.05 and |log fold change value| >0.03, we identified the differentially expressed genes (DEGs) between controls and the PMOP patients by “limma” package [81]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets GSE7429, GSE56814, GSE56815, and GSE174287 for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data for this study can be found in the TCGA database TARGET database (https://ocg.cancer.gov/programs/target/), and the GTEx database (https://gtexportal.org/home/). Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37683138", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "The datasets GSE7429, GSE56814, GSE56815, and GSE174287 for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data for this study can be found in the TCGA database TARGET database (https://ocg.cancer.gov/programs/target/), and the GTEx database (https://gtexportal.org/home/). Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Totally 1278 DEGs were identified with 715 up-regulated genes and 563 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37683138", "locator": "sections[3] \"Identification of the DEGs in PMOP\" paragraph 2", "quote": "Totally 1278 DEGs were identified with 715 up-regulated genes and 563 down-regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Totally 1278 DEGs were identified with 715 up-regulated genes and 563 down-regulated genes.", "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:37683138"], "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:GSE147287"], "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:GSE147287"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37683138", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.205004", "sha256": "sha256:e3ff4b031610b227e8d6c755f281eba91500c28d32377e3e9c32d807d3e36b3f", "bytes": 82708, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.205004", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10522383", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE147287", "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=GSE147287", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE147287", "version": null, "note": "The datasets GSE7429, GSE56814, GSE56815, and GSE174287 for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data for this study can be found in the TCGA database TARGET database (https://ocg.cancer.gov/programs/target/), and the GTEx database (https://gtexportal.org/home/). Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets GSE7429, GSE56814, GSE56815, and GSE174287 for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data for this study can be found in the TCGA database TARGET database (https://ocg.cancer.gov/programs/target/), and the GTEx database (https://gtexportal.org/home/). 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