Integrative Analyses of Genes Associated With Osteoporosis in CD16+ Monocyte.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33551990", "kind": "science-record", "revision": 7, "content_hash": "sha256:3a30c1cde106c826d2d951165c7e44d3c9c13008a2450f7618e483476469a481", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative Analyses of Genes Associated With Osteoporosis in CD16+ Monocyte.", "doi": "10.3389/fendo.2020.581878", "pmid": "33551990", "authors": ["Bin Hu", "Xiangan Kong", "Li Li", "Fang Dai", "Qiu Zhang", "Ruifeng Shi"], "journal": "Frontiers in endocrinology", "year": 2020, "abstract": "Background: Osteoporosis is a metabolic bone disease characterized by decreased bone mineral density and abnormal bone quality. Monocytes can secret cytokines for bone resorption, resulting in bone mass loss. However, the mechanism by which monocytes subpopulations lead to osteoporosis remains unclear. The aim of this study was to identify genes associated with osteoporosis in monocytes subsets.\nMethods: Three microarray datasets including GSE7158 (transcription of low/high-peak bone mass), GSE101489 (transcription of CD16+/CD16- monocyte) and GSE93883 (miRNA expression profile of primary osteoporosis) were derived from the Gene Expression Omnibus (GEO) database and analyzed with GEO2R tool to identify differentially expressed genes (DEGs). Functional enrichment was analyzed using Metascape database and GSEA software. STRING was utilized for the Protein-Protein Interaction Network construct. The hub genes were screened out using the Cytoscape software. Related miRNAs were predicted in miRWalk, miRDB, and TargetScan databases.\nResults: Total 368 DEGs from GSE7158 were screened out, which were mostly enriched in signaling, positive regulation of biological process and immune system process. The hub genes were clustered into two modules by PPI network analysis. We identified 15 overlapping DGEs between GSE101489 and GSE7158 microarray datasets. Moreover, all of them were up-regulated genes in both datasets. Then, nine key genes were screened out from above 15 overlapping DEGs using Cytoscape software. It is a remarkable fact that the nine genes were all in one hub gene module of GSE7158. Additionally, 183 target miRNAs were predicted according to the above nine DEGs. After cross-verification with miRNA express profile dataset for osteoporosis (GSE93883), 12 DEmiRNAs were selected. Finally, a miRNA-mRNA network was constructed with the nine key genes and 12 miRNAs, which were involved in osteoporosis.\nConclusion: Our analysis results constructed a gene expression framework in monocyte subsets for osteoporosis. This approach could provide a novel insight into osteoporosis.", "claims": [{"id": "claim-method", "statement": "The online analysis tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to detect the DEGs between HPBM and LPBM samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33551990", "locator": "sections[4] \"Data Processing\" paragraph 2", "quote": "The online analysis tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to detect the DEGs between HPBM and LPBM samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33551990", "locator": "sections[17] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding authors."}], "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:33551990"], "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:GSE101489"], "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:GSE101489"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33551990", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2020.581878", "sha256": 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inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2704854", "GSM2704855", "GSM2704856", "GSM2704857", "GSM2704858", "GSM2704859", "GSM2704860", "GSM2704861", "GSM2704862", "GSM2704863", "GSM2704864", "GSM2704865", "GSM2704866", "GSM2704867", "GSM2704868", "GSM2704869", "GSM2704870", "GSM2704871", "GSM2704872", "GSM2704873", "GSM2704874", "GSM2704875", "GSM2704876"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "10904", "taxon": "Homo sapiens", "title": "Transcriptome profiling of peripheral blood mononuclear cell subsets", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": 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"GSM172406", "GSM172407", "GSM172408", "GSM172409", "GSM172410", "GSM172411", "GSM172412", "GSM172413", "GSM172414", "GSM172415", "GSM172416", "GSM172417", "GSM172418", "GSM172419", "GSM172420", "GSM172421", "GSM172422", "GSM172423", "GSM172424", "GSM172425", "GSM172426", "GSM172427", "GSM172428", "GSM172429", "GSM172430"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Genome Wide Gene Expression Study of Circulating Monocytes in human with extremely high vs. low bone mass", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE93883", "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=GSE93883", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE93883", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2464440", "GSM2464441", "GSM2464442", "GSM2464443", "GSM2464444", "GSM2464445", "GSM2464446", "GSM2464447", "GSM2464448", "GSM2464449", "GSM2464450", "GSM2464451", "GSM2464452", "GSM2464453", "GSM2464454", "GSM2464455", "GSM2464456", "GSM2464457"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "18058", "taxon": "Homo sapiens; Mus musculus; Rattus norvegicus", "title": "Gene expression-based, individualized outcome prediction for osteoporosis with vertebral fracture", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33551990:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:960edd771350fa13b1103b3f2b92774d8f8bebbd33b76fee2e27b686d3025898", "bytes": 2319, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "Top 20 enriched terms for differentially expressed genes in monocytes of low peak bone mass (LPBM).", "structure": {"pmcid": "PMC7859337", "section_index": 9, "section_title": "Identification and Enrichment of Differentially Expressed Genes in Low-Peak Bone Mass Monocytes", "row_count": 21, "column_count": 7}, "table": {"label": "Table 1", "caption": "Top 20 enriched terms for differentially expressed genes in monocytes of low peak bone mass (LPBM).", "rows": [["GO", "Category", "Description", "Count", "%", "Log10(P)", "Log10(q)"], ["GO:0070528", "GO Biological Processes", "protein kinase C signaling", "7", "1.98", "–6.5", "–2.14"], ["GO:0002385", "GO Biological Processes", "mucosal immune response", "6", "1.69", "–4.92", "–1.21"], ["GO:0001906", "GO Biological Processes", "cell killing", "11", "3.11", "–4.23", "–0.82"], ["GO:0098552", "GO Cellular Components", "side of membrane", "22", "6.21", "–4.13", "–0.77"], ["GO:0031225", "GO Cellular Components", "anchored component of membrane", "10", "2.82", "–3.76", "–0.58"], ["GO:0043025", "GO Cellular Components", "neuronal cell body", "19", "5.37", "–3.72", "–0.57"], ["GO:0043114", "GO Biological Processes", "regulation of vascular permeability", "5", "1.41", "–3.67", "–0.54"], ["GO:0010810", "GO Biological Processes", "regulation of cell-substrate adhesion", "11", "3.11", "–3.48", "–0.5"], ["GO:0048762", "GO Biological Processes", "mesenchymal cell differentiation", "11", "3.11", "–3.43", "–0.5"], ["GO:0002068", "GO Biological Processes", "glandular epithelial cell development", "4", "1.13", "–3.29", "–0.47"], ["GO:0003678", "GO Molecular Functions", "DNA helicase activity", "6", "1.69", "–2.99", "–0.2"], ["GO:0051216", "GO Biological Processes", "cartilage development", "10", "2.82", "–2.95", "–0.18"], ["GO:1901611", "GO Molecular Functions", "phosphatidylglycerol binding", "3", "0.85", "–2.92", "–0.16"], ["GO:0042623", "GO Molecular Functions", "ATPase activity, coupled", "12", "3.39", "–2.9", "-0.16"], ["GO:0030011", "GO Biological Processes", "maintenance of cell polarity", "3", "0.85", "–2.75", "-0.04"], ["GO:0071634", "GO Biological Processes", "regulation of transforming growth factor beta production", "4", "1.13", "–2.75", "–0.04"], ["GO:0005938", "GO Cellular Components", "cell cortex", "12", "3.39", "–2.58", "0"], ["GO:0060541", "GO Biological Processes", "respiratory system development", "9", "2.54", "–2.55", "0"], ["GO:0061640", "GO Biological Processes", "cytoskeleton-dependent cytokinesis", "6", "1.69", "–2.49", "0"], ["GO:0016853", "GO Molecular Functions", "isomerase activity", "8", "2.26", "–2.49", "0"]], "row_count": 21, "column_count": 7, "numeric_cells": 102, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33551990:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:86051115b05d703a16388b3260feff1ce318dc6dac9d92a176387347512b1b40", "bytes": 741, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "The hub genes for DEGs in monocytes of LPBM.", "structure": {"pmcid": "PMC7859337", "section_index": 11, "section_title": "Protein–Protein Interaction Network Analysis and Hub Gene Identification of Differentially Expressed Genes in Low-Peak Bone Mass Monocytes", "row_count": 11, "column_count": 4}, "table": {"label": "Table 2", "caption": "The hub genes for DEGs in monocytes of LPBM.", "rows": [["Rank", "Gene Symbol", "Gene Name", "MMC Score"], ["1", "RHOH", "Ras homolog family member H", "104"], ["2", "RHOJ", "Ras Homolog Family Member J", "102"], ["2", "RHOBTB2", "Rho Related BTB Domain Containing 2", "102"], ["4", "FN1", "Fibronectin 1", "68"], ["5", "PRF1", "Perforin 1", "67"], ["6", "CFL1", "Cofilin 1", "58"], ["7", "KLRD1", "Killer Cell Lectin Like Receptor D1", "56"], ["8", "DOCK1", "Dedicator of Cytokinesis 1", "51"], ["9", "NCR1", "Natural Cytotoxicity Triggering Receptor 1", "43"], ["10", "SLAMF1", "Signaling Lymphocytic Activation Molecule Family Member 1", "38"]], "row_count": 11, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE7158", "GSE101489", "GSE93883"], "resolved_accessions": ["GSE7158", "GSE101489", "GSE93883"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE7158, GSE101489, GSE93883 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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