Microarray analysis for differentially expressed genes of patients undergoing total knee arthroplasty with ischemia preconditioning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25496472", "kind": "science-record", "revision": 9, "content_hash": "sha256:0a888707cdab7cba4776c829137e2cba536386c246c5fe473fabd03b2049c354", "created_at": "2026-11-01T15:40:07Z", "updated_at": "2026-11-01T22:42:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microarray analysis for differentially expressed genes of patients undergoing total knee arthroplasty with ischemia preconditioning.", "doi": "10.1186/s13018-014-0133-0", "pmid": "25496472", "authors": ["Jianguang Wang", "Zhengdong Cai", "Junjian Liu"], "journal": "Journal of orthopaedic surgery and research", "year": 2014, "abstract": "BACKGROUND: Ischemia preconditioning (IPC) has been proved as a powerful method of protecting tissues against ischemia reperfusion insults. We aimed to elucidate the mechanism of IPC in ischemia reperfused tissues.\nMETHODS: GSE21164 containing 16 muscle biopsies taken from the operative knee of four IPC-treated patients and four control at the onset of surgery (T¿=¿0) and 1 h into surgery (T¿=¿1) undergoing primary total knee arthroplasty was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between IPC group and control were screened with Limma package in R language. KEGG pathway enrichment analysis was performed by the DAVID online tool. Meanwhile, potential regulatory microRNAs (miRNAs) for downregulated DEGs and targets of transcription factors for upregulated DEGs were screened out. Based on the above DEGs, protein-protein interaction (PPI) networks were constructed by the STRING software.\nRESULTS: Significantly upregulated DEGs at T1 were mainly enriched in asthma and p53 signaling pathway. Meanwhile, significantly enriched transcriptional factor NOTCH1 at T1 and GABP at T0 were obtained. Moreover, miRNA analysis showed that targets of miR141/200a were enriched in downregulated DEGs both at T0 and T1. Mostly, RPA1 and JAK2 in PPI network at T1 were with higher degree.\nCONCLUSIONS: In our study, obtained DEGs, regulatory transcriptional factors, and miRNA might play a vital role in the protection of ischemia reperfusion injury. This finding will provide a deeper understanding to the mechanism of IPC.", "claims": [{"id": "claim-method", "statement": "To identify DEGs between the IPC group and the control, the empirical Bayes test (implemented in Linear Models for Microarray Data (Limma) package [25]) was applied in our analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25496472", "locator": "sections[4] \"Date preprocessing and DEGs screening\" paragraph 2", "quote": "To identify DEGs between the IPC group and the control, the empirical Bayes test (implemented in Linear Models for Microarray Data (Limma) package [25]) was applied in our analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE21164 containing 16 muscle biopsies taken from the operative knee of four IPC-treated patients and four control at the onset of surgery (T = 0) and 1 h into surgery (T = 1) undergoing primary total knee arthroplasty was downloaded from the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25496472", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "GSE21164 containing 16 muscle biopsies taken from the operative knee of four IPC-treated patients and four control at the onset of surgery (T = 0) and 1 h into surgery (T = 1) undergoing primary total knee arthroplasty was downloaded from the Gene Expression Omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GSE21164 downloaded from the Gene Expression Omnibus, the authors screened differentially expressed genes with the Limma package in R; the headline biological result was that significantly upregulated DEGs at T1 were mainly enriched in asthma and the p53 signaling pathway.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25496472", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "GSE21164 containing 16 muscle biopsies taken from the operative knee of four IPC-treated patients and four control at the onset of surgery (T = 0) and 1 h into surgery (T = 1) undergoing primary total knee arthroplasty was downloaded from the Gene Expression Omnibus (GEO) database."}, {"asset": "source:pmid:25496472", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes (DEGs) between IPC group and control were screened with Limma package in R language."}, {"asset": "source:pmid:25496472", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Significantly upregulated DEGs at T1 were mainly enriched in asthma and p53 signaling pathway."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GSE21164 downloaded from the Gene Expression Omnibus, the authors screened differentially expressed genes with the Limma package in R; the headline biological result was that significantly upregulated DEGs at T1 were mainly enriched in asthma and the p53 signaling pathway.", "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:25496472"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:25496472", "data:geo:GSE21164", "asset:table:pmid:25496472:1", "asset:table:pmid:25496472:2", "asset:table:pmid:25496472:3", "asset:table:pmid:25496472:4", "asset:table:pmid:25496472:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21164"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:23:26Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 46011, "completion_tokens": 3241, "cached_tokens": 6680}}, "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:25496472", "type": "paper", "label": "pmid:25496472"}, {"id": "source:pmid:25496472", "type": "manuscript", "label": "PMID 25496472 full text"}, {"id": "data:geo:GSE21164", "type": "dataset", "label": "GEO GSE21164"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25496472", "type": "paper", "label": "pmid:25496472"}, {"id": "source:pmid:25496472", "type": "manuscript", "label": "PMID 25496472 full text"}, {"id": "data:geo:GSE21164", "type": "dataset", "label": "GEO GSE21164"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25496472", "type": "extraction", "used": ["source:pmid:25496472"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21164", "type": "accession_resolution", "used": ["data:geo:GSE21164"], "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:25496472", "parent_hash": "sha256:e79afee3bc1bac00483523f2353e3918bddee2f650bc954b0bf088cc66743fcb", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE21164 licence not read", "asset:data:geo:GSE21164 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Microarray analysis for differentially expressed genes"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To identify DEGs between the IPC group and the control, the empirical Bayes test (implemented in Linear Models for Microarray Data (Limma) package [25]) was applied in our analysis."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}