Bioinformatics Analysis Identified miR-584-5p and Key miRNA-mRNA Networks Involved in the Osteogenic Differentiation of Human Periodontal Ligament Stem Cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34646313", "kind": "science-record", "revision": 5, "content_hash": "sha256:9fa41829dc2d226194416197d6f2ff8ccdc02a16665a0182501b7a77bdadd973", "created_at": "2026-11-01T17:36:18Z", "updated_at": "2026-11-01T22:47:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis Identified miR-584-5p and Key miRNA-mRNA Networks Involved in the Osteogenic Differentiation of Human Periodontal Ligament Stem Cells.", "doi": "10.3389/fgene.2021.750827", "pmid": "34646313", "authors": ["Chengze Wang", "Lingling Dong", "Ying Wang", "Zhiwei Jiang", "Jing Zhang", "Guoli Yang"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "Human periodontal ligament cells (PDLCs) play an important role in periodontal tissue stabilization and function. In the process of osteogenic differentiation of PDLSCs, the regulation of molecular signal pathways are complicated. In this study, the sequencing results of three datasets on GEO were used to comprehensively analyze the miRNA-mRNA network during the osteogenic differentiation of PDLSCs. Using the GSE99958 and GSE159507, a total of 114 common differentially expressed genes (DEGs) were identified, including 62 up-regulated genes and 52 down-regulated genes. GO enrichment analysis was performed. The up-regulated 10 hub genes and down-regulated 10 hub genes were screened out by protein-protein interaction network (PPI) analysis and STRING in Cytoscape. Similarly, differentially expressed miRNAs (DEMs) were selected by limma package from GSE159508. Then, using the miRwalk website, we further selected 11 miRNAs from 16 DEMs that may have a negative regulatory relationship with hub genes. In vitro RT-PCR verification revealed that nine DEMs and 18 hub genes showed the same trend as the RNA-seq results during the osteogenic differentiation of PDLSCs. Finally, using miR-584-5p inhibitor and mimics, it was found that miR-584-5p negatively regulates the osteogenic differentiation of PDLSCs in vitro. In summary, the present results found several potential osteogenic-related genes and identified candidate miRNA-mRNA networks for the further study of osteogenic differentiation of PDLSCs.", "claims": [{"id": "claim-method", "statement": "For the dataset GSE99958, without biological replicates, CORNAS (default 1.5-fold count change) was used to obtain DEGs (Hu et al., 2018). The DEGs of 3, 7, and 14 days compared to 0 days were obtained and the common DEGs were determined. For the dataset GSE159507, the limma package was used to identify DEGs. LogFC > 1 or LogFC < −1 and P-value < 0.05 were considered to indicate statistical significance. At last, the common up-regulated genes and down-regulated genes between GSE99958 and GSE159507 were selected. For the dataset GSE159508, the limma package was also used to identify the differentially expressed miRNAs (DEMs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34646313", "locator": "sections[4] \"Differentially Expressed Analysis\" paragraph 2", "quote": "For the dataset GSE99958, without biological replicates, CORNAS (default 1.5-fold count change) was used to obtain DEGs (Hu et al., 2018). The DEGs of 3, 7, and 14 days compared to 0 days were obtained and the common DEGs were determined. For the dataset GSE159507, the limma package was used to identify DEGs. LogFC > 1 or LogFC < −1 and P-value < 0.05 were considered to indicate statistical significance. At last, the common up-regulated genes and down-regulated genes between GSE99958 and GSE159507 were selected. 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