Screening of key pathogenic genes in advanced knee osteoarthritis based on bioinformatics analysis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36267772", "kind": "science-record", "revision": 3, "content_hash": "sha256:7b5583f12432a32cf46fd13d42c9ad4b2c6185150a003aecee46df100a78e1ca", "created_at": "2026-11-01T18:15:39Z", "updated_at": "2026-11-01T21:29:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of key pathogenic genes in advanced knee osteoarthritis based on bioinformatics analysis.", "doi": "10.21037/atm-22-3863", "pmid": "36267772", "authors": ["Yongju Yang", "Yuqian Zhang", "Dongyu Min", "Heshan Yu", "Xuefeng Guan"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: At present, the progression mechanism of knee osteoarthritis (KOA) has not been fully elucidated, and there is a clinical need for late KOA-specific diagnostic markers to provide reference for preventive treatment. This study aimed to analyze the sequencing results of early- and late-stage KOA synovial tissue based on the key genes of late-stage KOA in combination with a machine learning algorithm.\nMethods: The whole transcriptome sequencing results of synovial tissue from KOA patients (GSE176223 and GSE32317) were downloaded from the gene expression omnibus (GEO) database. Thirty-nine early KOA synovial tissue samples and 31 late KOA synovial tissue samples were included in this study. The diagnostic criteria and baseline data balance of early and late KOA were referred to the data source literature, and the two groups of data had good baseline data balance. R software (V3.5.1) and R packages were used for screening and enrichment analysis of differentially expressed genes (DEGs). The key genes were screened by weighted correlation network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis. A receiver operating characteristic curve (ROC) curve was used to evaluate the diagnostic efficacy of key genes for advanced KOA.\nResults: A total of 211 DEGs related to knee arthritis were screened out. Compared with synovial tissue of early knee arthritis, 111 genes were upregulated and 100 genes were downregulated in the synovial tissue of late knee arthritis. Sixty-six key genes were screened out through WGCNA and 34 key genes were screened out in the LASSO analysis. The genes obtained by the two algorithms combined with three overlapping genes, namely interleukin- 6 (IL-6), C-X-C chemokine ligand 12 (CXCL12), and macrophage migration inhibitor factor (MIF). The areas under the ROC curves of CXCL12, IL-6, and MIF were 0.96, 0.944, and 0.961, respectively (P<0.001).\nConclusions: IL-6, CXCL12, and MIF are the key pathogenic genes of KOA, which have good diagnostic efficacy for advanced KOA.", "claims": [{"id": "claim-method", "statement": "A receiver operating characteristic curve (ROC) curve was used to evaluate the diagnostic efficacy of key genes for advanced KOA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36267772", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "A receiver operating characteristic curve (ROC) curve was used to evaluate the diagnostic efficacy of key genes for advanced KOA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The sequencing results of the whole transcriptome of synovial tissue from KOA patients (GSE176223 and GSE32317) were downloaded from the gene expression omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36267772", "locator": "sections[3] \"Data download\" paragraph 2", "quote": "The sequencing results of the whole transcriptome of synovial tissue from KOA patients (GSE176223 and GSE32317) were downloaded from the gene expression omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "IL-6, CXCL12, and MIF are the key pathogenic genes of KOA, which have good diagnostic efficacy for advanced KOA.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36267772", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "IL-6, CXCL12, and MIF are the key pathogenic genes of KOA, which have good diagnostic efficacy for advanced KOA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "IL-6, CXCL12, and MIF are the key pathogenic genes of KOA, which have good diagnostic efficacy for advanced KOA.", "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:36267772"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36267772", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-22-3863", "sha256": "sha256:271f9d02dae650818797f9b0c0ae548315678001c81bc90a7cbefbecdd0f50c8", "bytes": 21097, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-22-3863", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9577766", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "receiver operating characteristic curve (ROC) curve", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A receiver operating characteristic curve (ROC) curve was used to evaluate the diagnostic efficacy of key genes for advanced KOA."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (receiver operating characteristic curve (ROC) curve), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R4", "reachable": false, "accessions": ["GSE176223 and GSE32317"], "resolved_accessions": [], "statements": ["The sequencing results of the whole transcriptome of synovial tissue from KOA patients (GSE176223 and GSE32317) were downloaded from the gene expression omnibus (GEO) database."], "basis": "The paper names GSE176223 and GSE32317, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36267772"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:12:05Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 7000, "completion_tokens": 699, "cached_tokens": 256}}, "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:36267772", "type": "paper", "label": "pmid:36267772"}, {"id": "source:pmid:36267772", "type": "manuscript", "label": "PMID 36267772 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36267772", "type": "paper", "label": "pmid:36267772"}, {"id": "source:pmid:36267772", "type": "manuscript", "label": "PMID 36267772 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36267772", "type": "extraction", "used": ["source:pmid:36267772"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:36267772", "parent_hash": "sha256:a3bc9c7aaa4764b908d08caaaed8752f0ad9e42ea53d186ed5d442c126a133e3", "fork_of": null, "generation": 2}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}