Identification of a Potential MiRNA-mRNA Regulatory Network for Osteoporosis by Using Bioinformatics Methods: A Retrospective Study Based on the Gene Expression Omnibus Database.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35620387", "kind": "science-record", "revision": 4, "content_hash": "sha256:87c582e5cf468c2728beff226a33fc1e2e09116a2f843e559c62f1195c12abab", "created_at": "2026-11-01T18:14:32Z", "updated_at": "2026-11-01T22:06:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Potential MiRNA-mRNA Regulatory Network for Osteoporosis by Using Bioinformatics Methods: A Retrospective Study Based on the Gene Expression Omnibus Database.", "doi": "10.3389/fendo.2022.844218", "pmid": "35620387", "authors": ["Shi Lin", "Jianjun Wu", "Baixing Chen", "Shaoshuo Li", "Hongxing Huang"], "journal": "Frontiers in endocrinology", "year": 2022, "abstract": "Introduction: As a systemic skeletal dysfunction, osteoporosis (OP) is characterized by low bone mass, impairment of bone microstructure, and a high global morbidity rate. There is increasing evidence that microRNAs (miRNAs) are associated with the pathogenesis of OP. Weighted gene co-expression network analysis (WGCNA) is a systematic method for identifying clinically relevant genes involved in disease pathogenesis. However, the study of the miRNA-messenger RNA (mRNA) regulatory network in combination with WGCNA in OP is still lacking.\nMethods: The GSE93883 and GSE7158 microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DE-miRNAs) and differentially expressed genes (DEGs) were analyzed with the limma package. OP-related miRNAs from the most clinically relevant module were identified by the WGCNA method. The overlap of DE-miRNAs and OP-related miRNAs was identified as OP-related DE-miRNAs. Both upstream transcription factors and downstream targets of OP-related DE-miRNAs were predicted by FunRich. An intersection of predicted target genes and DEGs was confirmed as downstream target genes of OP-related DE-miRNAs. With the use of clusterProfiler in R, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed on target genes. Finally, both the protein-protein interaction (PPI) network and miRNA-mRNA network were constructed and analyzed.\nResults: A total of 79 OP-related DE-miRNAs were obtained, most of which were predicted to be regulated by specificity protein 1 (SP1). Subsequently, 197 downstream target genes were screened out. The target genes were enriched in multiple pathways, including signaling pathways closely related to the onset of OP, such as Ras, PI3K-Akt, and ErbB signaling pathways. Through the construction of the OP-related miRNA-mRNA regulatory network, a hub network that may play a prominent role in the formation of OP was documented.\nConclusion: By using WGCNA, we constructed a potential OP-related miRNA-mRNA regulatory network, offering a novel perspective on miRNA regulatory mechanisms in OP.", "claims": [{"id": "claim-method", "statement": "A weighted gene co-expressed network of miRNAs using the “WGCNA” package in R generates a scale-free weighted gene co-expressed network (26).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35620387", "locator": "sections[5] \"Identification of Osteoporosis-Related MiRNAs by Weighted Gene Co-Expression Network Analysis\" paragraph 2", "quote": "A weighted gene co-expressed network of miRNAs using the “WGCNA” package in R generates a scale-free weighted gene co-expressed network (26)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/, GSE93883; GSE7158.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35620387", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/, GSE93883; GSE7158."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 79 OP-related DE-miRNAs were obtained, most of which were predicted to be regulated by specificity protein 1 (SP1).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35620387", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 79 OP-related DE-miRNAs were obtained, most of which were predicted to be regulated by specificity protein 1 (SP1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 79 OP-related DE-miRNAs were obtained, most of which were predicted to be regulated by specificity protein 1 (SP1).", "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:35620387"], "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:GSE7158"], "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:GSE7158"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35620387", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2022.844218", "sha256": "sha256:68acee3b5fc7cb6bc43bf06d01b1a58fa200af25b1092c944ee1f45b6815485d", "bytes": 26445, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2022.844218", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9128237", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE7158", "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=GSE7158", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7158", "version": null, "note": "Publicly available datasets were analyzed in this study. 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This data can be found here: https://www.ncbi.nlm.nih.gov/, GSE93883; GSE7158.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. 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