Integrative analyses of genetic characteristics associated with skeletal endothelial cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38656074", "kind": "science-record", "revision": 5, "content_hash": "sha256:2823a45a275e35e0015eba03b37b3d3b2932c13fcdf19784976848cdba148528", "created_at": "2026-11-01T19:20:37Z", "updated_at": "2026-11-01T22:54:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analyses of genetic characteristics associated with skeletal endothelial cells.", "doi": "10.1590/1414-431X2024e13339", "pmid": "38656074", "authors": ["Zhanhui Wang", "Bowen Hu", "Xiaoming Chen", "Zheng Zhang", "Lu Liu", "Nan Li", "Chun Liang"], "journal": "Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologica", "year": 2024, "abstract": "The osseous vascular endothelium encompasses a vast intricate framework that regulates bone remodeling. Osteoporosis, an age-associated systemic bone disease, is characterized by the degeneration of the vascular architecture. Nevertheless, the precise mechanisms underpinning the metamorphosis of endothelial cells (ECs) with advancing age remain predominantly enigmatic. In this study, we conducted a systematic analysis of differentially expressed genes (DEGs) and the associated pathways in juvenile and mature femoral ECs, utilizing data sourced from the Gene Expression Omnibus (GEO) repositories (GSE148804) and employing bioinformatics tools. Through this approach, we successfully discerned six pivotal genes, namely Adamts1, Adamts2, Adamts4, Adamts14, Col5a1, and Col5a2. Subsequently, we constructed a miRNA-mRNA network based on miRNAs displaying differential expression between CD31hiEMCNhi and CD31lowEMCNlow ECs, utilizing online repositories for prediction. The expression of miR-466i-3p and miR-466i-5p in bone marrow ECs exhibited an inverse correlation with age. Our in vivo experiments additionally unveiled miR-466i-5p as a pivotal regulator in osseous ECs and a promising therapeutic target for age-related osteoporosis.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were identified using the Limma package by comparing the mRNA profile of juvenile and adult mouse femoral capillaries (GSE148804). Moreover, differentially expressed miRNAs (DEmiRNAs) between type H and type L ECs were obtained by the Limma package (GSE95196; https://bioconductor.org/packages/release/bioc/html/limma.html). An adjusted P-value of 0.05 and a fold-change of 1 were set as criteria of DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38656074", "locator": "sections[4] \"Identification and functional analyses of DEGs\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were identified using the Limma package by comparing the mRNA profile of juvenile and adult mouse femoral capillaries (GSE148804). Moreover, differentially expressed miRNAs (DEmiRNAs) between type H and type L ECs were obtained by the Limma package (GSE95196; https://bioconductor.org/packages/release/bioc/html/limma.html). An adjusted P-value of 0.05 and a fold-change of 1 were set as criteria of DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All gene expression datasets were obtained from GEO (https://www.ncbi.nlm.nih.gov/geo/). The investigation (GSE148804), based on GPL19057Illumina NextSeq 500 (Mus musculus), was conducted on capillaries from the ossification front of the juvenile (5 samples) and adult (4 samples) mouse femurs (18).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38656074", "locator": "sections[3] \"Sample collection\" paragraph 2", "quote": "All gene expression datasets were obtained from GEO (https://www.ncbi.nlm.nih.gov/geo/). The investigation (GSE148804), based on GPL19057Illumina NextSeq 500 (Mus musculus), was conducted on capillaries from the ossification front of the juvenile (5 samples) and adult (4 samples) mouse femurs (18)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified six pivotal genes: Adamts1, Adamts2, Adamts4, Adamts14, Col5a1, and Col5a2.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38656074", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Through this approach, we successfully discerned six pivotal genes, namely Adamts1, Adamts2, Adamts4, Adamts14, Col5a1, and Col5a2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified six pivotal genes: Adamts1, Adamts2, Adamts4, Adamts14, Col5a1, and Col5a2.", "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:38656074"], "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:GSE148804"], "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:GSE148804"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38656074", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1590/1414-431X2024e13339", "sha256": "sha256:9aff87f4ecc1198752b07b3456315955e6d8ffe1b2955f53fd8fc2182f6fb5c1", "bytes": 25144, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1590/1414-431X2024e13339", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11027181", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE148804", "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=GSE148804", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE148804", "version": null, "note": "All gene expression datasets were obtained from GEO (https://www.ncbi.nlm.nih.gov/geo/). 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Our in vivo experiments additionally unveiled miR-466i-5", "(n=6), and 12-month-old (n=21) C57BL/6 male mice were bought from Shanghai Jihui Laboratory Animal", "val Medical University (SYXK 2017-0004). The mice were housed under specific pathogen-free (SPF) co", "±5% humidity and 12-h light/dark cycle). The mice were fed with standard chow (corn (40%), bran (25"], "order_basis": "paper_text_order:1133", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["les) mouse femurs (18). The miRNA expression microarray GSE95196 included 6 samples of ECs (3 sample", "based on GPL21265 Agilent-070155 Mouse miRNA Microarray (miRBase Release 21.0, miRNA ID version) (17"], "order_basis": "paper_text_order:1650", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) were identified using the Limma package by comparing the mRNA profile of juvenile and adult mouse femoral capillaries (GSE148804). Moreover, differentially expressed miRNAs (DEmiRNAs) between type H and type L ECs were obtained by the Limma package (GSE95196; https://bioconductor.org/packages/release/bioc/html/limma.html). An adjusted P-value of 0.05 and a fold-change of 1 were set as criteria of DEGs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}