Bioinformatics analysis of the biological changes involved in the osteogenic differentiation of human mesenchymal stem cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32463168", "kind": "science-record", "revision": 8, "content_hash": "sha256:5f57e0f17250dfbec194e66ea5188f3f2e537a129f669072b32c25d6eae82eb2", "created_at": "2026-11-01T15:41:02Z", "updated_at": "2026-11-01T22:44:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of the biological changes involved in the osteogenic differentiation of human mesenchymal stem cells.", "doi": "10.1111/jcmm.15429", "pmid": "32463168", "authors": ["Tingyu Fan", "Rongmei Qu", "Qinghe Yu", "Bing Sun", "Xin Jiang", "Yuchao Yang", "Xiaolan Huang", "Zhitao Zhou", "Jun Ouyang", "Shizhen Zhong", "Jingxing Dai"], "journal": "Journal of cellular and molecular medicine", "year": 2020, "abstract": "The mechanisms underlying the osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) remain unclear. In the present study, we aimed to identify the key biological processes during osteogenic differentiation. To this end, we downloaded three microarray data sets from the Gene Expression Omnibus (GEO) database: GSE12266, GSE18043 and GSE37558. Differentially expressed genes (DEGs) were screened using the limma package, and enrichment analysis was performed. Protein-protein interaction network (PPI) analysis and visualization analysis were performed with STRING and Cytoscape. A total of 240 DEGs were identified, including 147 up-regulated genes and 93 down-regulated genes. Functional enrichment and pathways of the present DEGs include extracellular matrix organization, ossification, cell division, spindle and microtubule. Functional enrichment analysis of 10 hub genes showed that these genes are mainly enriched in microtubule-related biological changes, that is sister chromatid segregation, microtubule cytoskeleton organization involved in mitosis, and spindle microtubule. Moreover, immunofluorescence and Western blotting revealed dramatic quantitative and morphological changes in the microtubules during the osteogenic differentiation of human adipose-derived stem cells. In summary, the present results provide novel insights into the microtubule- and cytoskeleton-related biological process changes, identifying candidates for the further study of osteogenic differentiation of the mesenchymal stem cells.", "claims": [{"id": "claim-method", "statement": "Then, the limma package was used to remove batch effect and identify DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32463168", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "Then, the limma package was used to remove batch effect and identify DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the supporting data can be downloaded.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32463168", "locator": "sections[25] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "All the supporting data can be downloaded."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32463168"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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is crucial for the arrangement of chromosomes during mitosis and is necessary for centrosomal replication"], ["CDC20", "cell division cycle 20", "Regulates the formation of synaptic vesicle clustering at active zone to the pre‐synaptic membrane in post‐mitotic neurons"], ["TOP2A", "DNA topoisomerase II α", "Is crucial for the proper separation of chromosomes"], ["PBK", "PDZ binding kinase", "The encoded protein may be involved in the activation of lymphocytes and support testicular functions"], ["NCAPG", "non‐SMC condensin I complex subunit G", "Required for chromatin condensation"]], "row_count": 11, "column_count": 3, "numeric_cells": 7, "header_rows": 1, "locator": "section[17]/table-wrap[1]#jcmm15429-tbl-0001"}}, {"id": "asset:table:pmid:32463168:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0bdc65a434cb05c39e24848b18e509e17d5b806f0476c52a132a54d8bde10824", "bytes": 1397, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#jcmm15429-tbl-0001", "version": null, "note": "Ten hub genes and their functions", "structure": {"pmcid": "PMC7348183", "section_index": 17, "section_title": "Selection and analysis of hub genes", "row_count": 11, "column_count": 3}, "table": {"label": "Table 1", "caption": "Ten hub genes and their functions", "rows": [["Gene symbol", "Description", "Function"], ["NUSAP1", "nucleolar and spindle associated protein 1", "Microtubule‐related proteins that promote the formation of mitotic spindles and microtubules"], ["KIF11", "kinesin family member 11", "Assists in spindle formation during mitosis"], ["PLK1", "polo‐like kinase 1", "Assists in spindle formation"], ["CCNB1", "cyclin B1", "Required for the control of G2/M (mitosis) of the cell cycle"], ["CDCA8", "cell division cycle associated 8", "Is essential for chromatin‐induced microtubule stabilization and spindle assembly"], ["TTK", "TTK protein kinase", "Regulates cell proliferation; 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