Comprehensive Analysis of Novel Genes and Pathways Associated with Osteogenic Differentiation of Adipose Stem Cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36133435", "kind": "science-record", "revision": 5, "content_hash": "sha256:68c2d1f06d276322e29359e0a3a855b52b496111599a78c4c0b8411295aead1b", "created_at": "2026-11-01T18:15:24Z", "updated_at": "2026-11-01T22:50:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Analysis of Novel Genes and Pathways Associated with Osteogenic Differentiation of Adipose Stem Cells.", "doi": "10.1155/2022/4870981", "pmid": "36133435", "authors": ["Qiuni Gao", "Xiaorong Ma", "Zuoliang Qi"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Adipose-derived stem cells (ADSCs) are an important alternative source of mesenchymal stem cells (MSCs) and show great promise in tissue engineering and regenerative medicine applications. However, identifying the novel genes and pathways and finding the underlying mechanisms regulating ADSCs osteogenic differentiation remain urgent.\nMethods: We downloaded the gene expression profiles of GSE63754 and GSE37329 from the Gene Expression Omnibus (GEO) Database. We derived differentially expressed genes (DEGs) before and after ADSC osteogenic differentiation, followed by Gene Ontology (GO) functional and KEGG pathway analysis and protein-protein interaction (PPI) network analysis. 211 differentially expressed genes (142 upregulated genes and 69 downregulated genes) were aberrantly expressed. GO analysis revealed that these DEGs were associated with extracellular matrix organization, protein extracellular matrix, and semaphorin receptor binding.\nConclusions: Our study provides novel genes and pathways that play important roles in regulating ADSC osteogenic differentiation, which may have potential therapeutic targets for clinic.", "claims": [{"id": "claim-method", "statement": "The Limma package was subsequently used for identifying DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36133435", "locator": "sections[4] \"2.2. Identification of Differentially Expressed Gene\" paragraph 2", "quote": "The Limma package was subsequently used for identifying DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data in this manuscript can be acquired by request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36133435", "locator": "sections[15] \"Data Availability\" paragraph 2", "quote": "All the data in this manuscript can be acquired by request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "211 differentially expressed genes (142 upregulated genes and 69 downregulated genes) were aberrantly expressed.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36133435", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "211 differentially expressed genes (142 upregulated genes and 69 downregulated genes) were aberrantly expressed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "211 differentially expressed genes (142 upregulated genes and 69 downregulated genes) were aberrantly expressed.", "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:36133435"], "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:GSE37329"], "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:GSE37329"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36133435", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/4870981", "sha256": "sha256:5bef9c41872b65084903d338ab8f33ff0401bfb38b4d9fbe3e23b54e2d715776", "bytes": 30413, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/4870981", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9484926", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37329", "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=GSE37329", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37329", "version": null, "note": "All the data in this manuscript can be acquired by request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data in this manuscript can be acquired by request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM916203", "GSM916204", "GSM916205", "GSM916206", "GSM916207", "GSM916208", "GSM916209"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "11532", "taxon": "Homo sapiens", "title": "Genome-wide gene expression during osteogenic and myogenic differentiation from adipose- derived stem cells.", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63754", "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=GSE63754", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63754", "version": null, "note": "All the data in this manuscript can be acquired by request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data in this manuscript can be acquired by request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1556693", "GSM1556694", "GSM1556695", "GSM1556696", "GSM1556697", "GSM1556698"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Gene expression profile of osteogenically differentiated human adipose-derived stem cells", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE37329 not downloaded", "asset:data:geo:GSE37329 licence not read", "asset:data:geo:GSE63754 not downloaded", "asset:data:geo:GSE63754 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 Limma package was subsequently used for identifying DEGs."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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