Identification of Key Genes and miRNAs Affecting Osteosarcoma Based on Bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36438897", "kind": "science-record", "revision": 3, "content_hash": "sha256:06f2f581d75f9d166f1e4200226805b1fa3d5db97990fe036b90d213e3695e99", "created_at": "2026-11-01T19:00:54Z", "updated_at": "2026-11-01T22:08:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes and miRNAs Affecting Osteosarcoma Based on Bioinformatics.", "doi": "10.1155/2022/1015593", "pmid": "36438897", "authors": ["Le Li", "Xin Zhou", "Wencan Zhang", "Ran Zhao"], "journal": "Disease markers", "year": 2022, "abstract": "Methods: GSE70367 and GSE69470 were obtained from the GEO database. The differentially expressed genes (DEGs) and miRNAs were analyzed using the GEO2R tool and then visualized with R software. Moreover, the targets of the miRNAs in the DEGs were screened and then used for enrichment analysis. Besides, the STRING database and Cytoscape were applied to illustrate the protein-protein interaction network. RT-qPCR was performed to measure the expression of key genes and miRNAs. Western blot was applied to detect the signaling pathway.\nResults: 9 upregulated genes and 39 downregulated genes in GSE69470 were identified as the DEGs, and 31 upregulated genes and 56 downregulated genes in GSE70367 were identified as the DEGs. Moreover, 21 common genes were found in the DEGs of GSE70367 and GSE69470. The enrichment analysis showed that the common DEGs of GSE70367 and GSE69470 were related with cell development, covalent chromatin modification, and histone modification and involve in the regulation of MAPK, mTOR, and AMPK pathways. Besides, the miRNAs including miR-543, miR-495-3p, miR-433-3p, miR-381-3p, miR-301a-3p, miR-199b-5p, and miR-125b-5p were identified as the biomarkers of osteosarcoma. In addition, the target genes including HSPA5, PPARG, MAPK14, RAB11A, RAB5A, MAPK8, LEF1, HIF1A, CAV1, GS3KB, FOXO3, IGF1, and NFKBIA were identified as hub nodes. It was found that miR-301a-3p expression was decreased and mRNA expression of RAB5A and NFKBIA was increased in the pathological tissues. The AKT-PI3K-mTOR signaling pathway was activated in pathological tissues.\nConclusion: In this study, 7 miRNAs and 13 hub genes were identified, which might be candidate markers. miR-301a-3p, RAB5A, and NFKBIA were abnormally expressed in osteosarcoma tissues.", "claims": [{"id": "claim-method", "statement": "The DEGs of the datasets were analyzed with the GEO2R tool of the GEO database to obtain the related matrix files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36438897", "locator": "sections[4] \"2.2. Identification of Differentially Expressed Genes\" paragraph 2", "quote": "The DEGs of the datasets were analyzed with the GEO2R tool of the GEO database to obtain the related matrix files."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36438897", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "9 upregulated genes and 39 downregulated genes in GSE69470 were identified as the DEGs, and 31 upregulated genes and 56 downregulated genes in GSE70367 were identified as the DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36438897", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "9 upregulated genes and 39 downregulated genes in GSE69470 were identified as the DEGs, and 31 upregulated genes and 56 downregulated genes in GSE70367 were identified as the DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "9 upregulated genes and 39 downregulated genes in GSE69470 were identified as the DEGs, and 31 upregulated genes and 56 downregulated genes in GSE70367 were identified as the DEGs.", "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:36438897"], "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:GSE69470"], "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:GSE69470"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36438897", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/1015593", "sha256": "sha256:9d86a235d31e7655bf37ed69a083dbaf6f6695030694332068fa32e8f9d66e5e", "bytes": 26400, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/1015593", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9683959", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE69470", "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=GSE69470", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE69470", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1701622", "GSM1701623", "GSM1701624", "GSM1701625", "GSM1701626", "GSM1701627", "GSM1701628", "GSM1701629", "GSM1701630", "GSM1701631", "GSM1701632", "GSM1701633", "GSM1701634", "GSM1701635", "GSM1701636", "GSM1701637", "GSM1701638", "GSM1701639", "GSM1701640", "GSM1701641", "GSM1701642", "GSM1701643", "GSM1701644", "GSM1701645", "GSM1701646", "GSM1701647", "GSM1701648", "GSM1701649", "GSM1701650", "GSM1701651", "GSM1701652", "GSM1701653", "GSM1701654", "GSM1701655", "GSM1701656", "GSM1701657", "GSM1701658", "GSM1701659", "GSM1701660", "GSM1701661", "GSM1701662", "GSM1701663", "GSM1701664", "GSM1701665", "GSM1701666", "GSM1701667", "GSM1701668", "GSM1701669", "GSM1701670", "GSM1701671", "GSM1701672", "GSM1701673", "GSM1701674", "GSM1701675", "GSM1701676", "GSM1701677", "GSM1701678", "GSM1701679", "GSM1701680", "GSM1701681", "GSM1701682", "GSM1701683", "GSM1701684", "GSM1701685", "GSM1701686", "GSM1701687", "GSM1701688", "GSM1701689", "GSM1701690", "GSM1701691", "GSM1701692", "GSM1701693", "GSM1701694", "GSM1701695", "GSM1701696", "GSM1701697", "GSM1701698"], "sample_count": 77, "group_sizes": null, "group_sizes_basis": null, "platform": "20275", "taxon": "Homo sapiens", "title": "microRNA expression  profiling of human sarcoma cell lines (~68)  in the Molecular Pharmacology Branch, DTP, DCTD NCI collection of human cell lines", "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:GSE70367", "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=GSE70367", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70367", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1725892", "GSM1725893", "GSM1725894", "GSM1725895", "GSM1725896", "GSM1725897"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "16384", "taxon": "synthetic construct; Homo sapiens", "title": "miRNA Expression data from human osteosarcoma (OS)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE69470 not downloaded", "asset:data:geo:GSE69470 licence not read", "asset:data:geo:GSE70367 not downloaded", "asset:data:geo:GSE70367 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DEGs of the datasets were analyzed with the GEO2R tool of the GEO database to obtain the related matrix files."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE69470", "GSE70367"], "resolved_accessions": ["GSE69470", "GSE70367"], "statements": ["The data used to support the findings of this study are included within the article."], "basis": "The paper names GSE69470, GSE70367 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:36438897", "data:geo:GSE69470"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE69470"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:16:55Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9155, "completion_tokens": 972, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36438897", "type": "paper", "label": "pmid:36438897"}, {"id": "source:pmid:36438897", "type": "manuscript", "label": "PMID 36438897 full text"}, {"id": "data:geo:GSE69470", "type": "dataset", "label": "GEO GSE69470"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36438897", "type": "paper", "label": "pmid:36438897"}, {"id": "source:pmid:36438897", "type": "manuscript", "label": "PMID 36438897 full text"}, {"id": "data:geo:GSE69470", "type": "dataset", "label": "GEO GSE69470"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36438897", "type": "extraction", "used": ["source:pmid:36438897"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE69470", "type": "accession_resolution", "used": ["data:geo:GSE69470"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:36438897", "parent_hash": "sha256:cd29fc14cb12835a7106758f973f220a1113ebf8dd324f7233136bdee58875e7", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE69470 licence not read", "asset:data:geo:GSE69470 not downloaded", "asset:data:geo:GSE70367 licence not read", "asset:data:geo:GSE70367 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ate the protein-protein interaction network. RT-qPCR was performed to measure the expression of k", "the protein-protein interaction network. RT-qPCR was performed to measure the expression of k"], "order_basis": "paper_text_order:447", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["sure the expression of key genes and miRNAs. Western blot was applied to detect the signaling pathway."], "order_basis": "paper_text_order:520", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}