Identification of Key Genes and miRNAs in Osteosarcoma Patients with Chemoresistance by Bioinformatics Analysis.

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The present study aims to identify Chemoresistance-regulated gene signatures and microRNAs (miRNAs) in Gene Expression Omnibus (GEO) database. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) included positive regulation of transcription, DNA-templated, tryptophan metabolism, and the like. Then differentially expressed genes (DEGs) were uploaded to Search Tool for the Retrieval of Interacting Genes (STRING) to construct protein-protein interaction (PPI) networks, and 9 hub genes were screened, such as fucosyltransferase 3 (Lewis blood group) (FUT3) whose expression in chemoresistant samples was high, but with a better prognosis in osteosarcoma patients. Furthermore, the connection between DEGs and differentially expressed miRNAs (DEMs) was explored. GEO2R was utilized to screen out DEGs and DEMs. A total of 668 DEGs and 5 DEMs were extracted from GSE7437 and GSE30934 differentiating samples of poor and good chemotherapy reaction patients. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform GO and KEGG pathway enrichment analysis to identify potential pathways and functional annotations linked with osteosarcoma chemoresistance. The present study may provide a deeper understanding about regulatory genes of osteosarcoma chemoresistance and identify potential therapeutic targets for osteosarcoma.", "claims": [{"id": "claim-method", "statement": "GEO2R, an R-associated web application, was applied to filtrate DEGs between good chemotherapy reaction samples and poor chemotherapy reaction samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29850522", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "GEO2R, an R-associated web application, was applied to filtrate DEGs between good chemotherapy reaction samples and poor chemotherapy reaction samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset of GSE87437, gene expression array, and GSE30934, miRNA expression array, included 10 and 8 samples from poor chemotherapy reaction patients and 11 and 16 samples from good ones, respectively. Moreover, the former dataset was based on GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and the latter one was based on GPL10312 platform (3D-Gene Human miRNA Oligo chip v12-1.00).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29850522", "locator": "sections[3] \"2.1. Microarray Data\" paragraph 2", "quote": "The dataset of GSE87437, gene expression array, and GSE30934, miRNA expression array, included 10 and 8 samples from poor chemotherapy reaction patients and 11 and 16 samples from good ones, respectively. Moreover, the former dataset was based on GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and the latter one was based on GPL10312 platform (3D-Gene Human miRNA Oligo chip v12-1.00)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used GEO2R analysis of GEO series GSE87437 and GSE30934, with cutoffs of P < 0.05 and |logFC| ≥ 1, to identify 668 differentially expressed genes and 5 differentially expressed miRNAs associated with osteosarcoma chemotherapy response.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "The P < 0.05 and |log⁡FC|⩾ 1 were considered as cutoff criterion."}, "evidence": [{"asset": "source:pmid:29850522", "locator": "sections[1] \"1. Introduction\" paragraph 5", "quote": "In the present study, we analyzed the data of GSE87437 and GSE30934 submitted by Serra Mand and Kobayashi E. et al., respectively, to get 668 differentially expressed genes (DEGs) and 5 differentially expressed miRNA (DEMs) between samples of poor and good chemotherapy reaction patients in GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/)."}, {"asset": "source:pmid:29850522", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "The P < 0.05 and |log⁡FC|⩾ 1 were considered as cutoff criterion."}, {"asset": "source:pmid:29850522", "locator": "sections[10] \"3.1. Identification of DEGs\" paragraph 2", "quote": "A total of 668 DEGs were obtained from GSE87437 in the poor chemotherapy response samples and compared with those of good response with the criteria of P < 0.05 and |log⁡FC|⩾ 1.0, comprising 422 upregulated genes and 246 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used GEO2R analysis of GEO series GSE87437 and GSE30934, with cutoffs of P < 0.05 and |logFC| ≥ 1, to identify 668 differentially expressed genes and 5 differentially expressed miRNAs associated with osteosarcoma chemotherapy response.", "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:29850522"], "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. 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A run that reproduces the effect is judged against this threshold."}], "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": ["hierarchical_cluster"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: hierarchical."}, "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": ["GSE87437", "GSE30934", "GSE21257", "GSE7437"], "resolved_accessions": ["GSE87437", "GSE30934", "GSE21257", "GSE7437"], "statements": ["The dataset of GSE87437, gene expression array, and GSE30934, miRNA expression array, included 10 and 8 samples from poor chemotherapy reaction patients and 11 and 16 samples from good ones, respectively. Moreover, the former dataset was based on GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and the latter one was based on GPL10312 platform (3D-Gene Human miRNA Oligo chip v12-1.00)."], "basis": "The paper names GSE87437, GSE30934, GSE21257, GSE7437 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["hierarchical_cluster"], "assets": ["source:pmid:29850522", "data:geo:GSE21257", "asset:table:pmid:29850522:1", "asset:table:pmid:29850522:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21257"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:39Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 76780, "completion_tokens": 6096, "cached_tokens": 2104}}, "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:29850522", "type": "paper", "label": "pmid:29850522"}, {"id": "source:pmid:29850522", "type": "manuscript", "label": "PMID 29850522 full text"}, {"id": "data:geo:GSE21257", "type": "dataset", "label": "GEO GSE21257"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29850522", "type": "paper", "label": "pmid:29850522"}, {"id": "source:pmid:29850522", "type": "manuscript", "label": "PMID 29850522 full text"}, {"id": "data:geo:GSE21257", "type": "dataset", "label": "GEO GSE21257"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29850522", "type": "extraction", "used": ["source:pmid:29850522"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21257", "type": "accession_resolution", "used": ["data:geo:GSE21257"], "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:29850522", "parent_hash": "sha256:ff4ab2c710cddb8ff665de51caa47e516b634c09ae0fbb8775b694fcbd6d97df", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE21257 licence not read", "asset:data:geo:GSE21257 not downloaded", "asset:data:geo:GSE30934 licence not read", "asset:data:geo:GSE30934 not downloaded", "asset:data:geo:GSE7437 licence not read", "asset:data:geo:GSE7437 not downloaded", "asset:data:geo:GSE87437 licence not read", "asset:data:geo:GSE87437 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "clustering", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["hierarchical_cluster"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Hierarchical Clustering"], "order_basis": "analysis_only", "id": "assay:1"}]}