Identification of key genes and pathways of BMP-9-induced osteogenic differentiation of mesenchymal stem cells by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33879213", "kind": "science-record", "revision": 8, "content_hash": "sha256:6fa9feadd26156f9f76a2a5e8783ec40c66bcb6e5eabfea4645559d634bed45b", "created_at": "2026-11-01T15:41:33Z", "updated_at": "2026-11-01T22:46:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes and pathways of BMP-9-induced osteogenic differentiation of mesenchymal stem cells by integrated bioinformatics analysis.", "doi": "10.1186/s13018-021-02390-w", "pmid": "33879213", "authors": ["Jia-Qi Wu", "Lin-Bo Mao", "Ling-Feng Liu", "Yong-Mei Li", "Jian Wu", "Jiao Yao", "Feng-Huan Zhang", "Ting-Yu Liu", "Ling Yuan"], "journal": "Journal of orthopaedic surgery and research", "year": 2021, "abstract": "BACKGROUND: The purpose of present study was to identify the differentially expressed genes (DEGs) associated with BMP-9-induced osteogenic differentiation of mesenchymal stem cells (MSCs) by using bioinformatics methods.\nMETHODS: Gene expression profiles of BMP-9-induced MSCs were compared between with GFP-induced MSCs and BMP-9-induced MSCs. GSE48882 containing two groups of gene expression profiles, 3 GFP-induced MSC samples and 3 from BMP-9-induced MSCs, was downloaded from the Gene Expression Omnibus (GEO) database. Then, DEGs were clustered based on functions and signaling pathways with significant enrichment analysis. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated that the identified DEGs were potentially involved in cytoplasm, nucleus, and extracellular exosome signaling pathway.\nRESULTS: A total of 1967 DEGs (1029 upregulated and 938 downregulated) were identified from GSE48882 datasets. R/Bioconductor package limma was used to identify the DEGs. Further analysis revealed that there were 35 common DEGs observed between the samples. GO function and KEGG pathway enrichment analysis, among which endoplasmic reticulum, protein export, RNA transport, and apoptosis was the most significant dysregulated pathway. The result of protein-protein interaction (PPI) network modules demonstrated that the Hspa5, P4hb, Sec61a1, Smarca2, Pdia3, Dnajc3, Hyou1, Smad7, Derl1, and Surf4 were the high-degree hub nodes.\nCONCLUSION: Taken above, using integrated bioinformatical analysis, we have identified DEGs candidate genes and pathways in BMP-9 induced MSCs, which could improve our understanding of the key genes and pathways for BMP-9-induced osteogenic of MSCs.", "claims": [{"id": "claim-method", "statement": "The raw data was downloaded and then put into the U-EDIT software to further analyses. Then, all of the differentially expressed genes (DEGs) between GFP-induced MSCs and BMP-9-induced MSCs were identified based on analyses GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) and bioconductor package limma [11]. The DEGs between the GFP-induced MSC samples and three BMP-9-induced MSC samples were selected (P < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33879213", "locator": "sections[4] \"Data processing and identification of DEGs\" paragraph 2", "quote": "The raw data was downloaded and then put into the U-EDIT software to further analyses. Then, all of the differentially expressed genes (DEGs) between GFP-induced MSCs and BMP-9-induced MSCs were identified based on analyses GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) and bioconductor package limma [11]. The DEGs between the GFP-induced MSC samples and three BMP-9-induced MSC samples were selected (P < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We state that the data will not be shared since all the raw data are present in the figures included in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33879213", "locator": "sections[19] \"notes\" paragraph 1", "quote": "We state that the data will not be shared since all the raw data are present in the figures included in the article."}], "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:33879213"], "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:GSE48882"], "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:GSE48882"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33879213", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13018-021-02390-w", "sha256": "sha256:7e57dd95879329dd4bf8c0b132057a1fdcfc5f3d3a9c268cc81df2eb8ce7d417", "bytes": 15970, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13018-021-02390-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8059242", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE48882", "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=GSE48882", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48882", "version": null, "note": "We state that the data will not be shared since all the raw data are present in the figures included in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We state that the data will not be shared since all the raw data are present in the figures included in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1186307", "GSM1186308", "GSM1186309", "GSM1186310", "GSM1186311", "GSM1186312"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "339", "taxon": "Mus musculus", "title": "Expression profiling of BMP9-stimulated mesenchymal stem cells", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33879213:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ca1c120b0cc48a0a2ccd3032c030aed05ff9aaa649e79769b3131e6f302aef68", "bytes": 1093, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#Tab1", "version": null, "note": "The differentially expressed genes (DEGs)", "structure": {"pmcid": "PMC8059242", "section_index": 8, "section_title": "Identification of DEGs", "row_count": 11, "column_count": 7}, "table": {"label": "Table 1", "caption": "The differentially expressed genes (DEGs)", "rows": [["Gene", "logFC", "AveExpr", "t", "P.Value", "adj.P.Val", "B"], ["Hspa5", "5886.413", "8805.691", "24.55842", "2.89E− 06", "0.014437", "− 4.41275"], ["Atp6v1g1", "192.8844", "1430.236", "24.16697", "3.12E− 06", "0.014437", "− 4.41281"], ["Ntan1", "849.4093", "1610.547", "22.81636", "4.11E− 06", "0.014437", "− 4.41304"], ["Ttc30b", "− 269.874", "376.4807", "− 22.6356", "4.27E− 06", "0.014437", "− 4.41307"], ["Smad7", "1291.794", "1054.716", "20.67191", "6.60E− 06", "0.017846", "− 4.4135"], ["Wars", "382.1337", "817.2169", "18.04368", "1.27E− 05", "0.024944", "− 4.41429"], ["Hif1a", "− 297.61", "791.8699", "− 17.8299", "1.34E− 05", "0.024944", "− 4.41437"], ["Fbln2", "− 2928.99", "5171.091", "− 17.4703", "1.48E− 05", "0.024944", "− 4.41452"], ["Klf10", "665.8488", "694.2806", "16.49257", "1.94E− 05", "0.029027", "− 4.41495"], ["Kat2b", "− 295.886", "399.0065", "− 15.9344", "2.29E− 05", "0.029027", "− 4.41523"]], "row_count": 11, "column_count": 7, "numeric_cells": 62, "header_rows": 1, "locator": "section[8]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:GSE48882 not downloaded", "asset:data:geo:GSE48882 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The raw data was downloaded and then put into the U-EDIT software to further analyses. 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