Comprehensive Analysis of ceRNA Regulation Network Involved in the Development of Coronary Artery Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33511207", "kind": "science-record", "revision": 4, "content_hash": "sha256:aaa2a83612f5ffde3b6d38fcd79a7b4b0f3815ea2da2add74bd69ff75f40ebb1", "created_at": "2026-11-01T15:41:23Z", "updated_at": "2026-11-01T22:03:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Analysis of ceRNA Regulation Network Involved in the Development of Coronary Artery Disease.", "doi": "10.1155/2021/6658115", "pmid": "33511207", "authors": ["Jiabei He", "Xinglong Li", "Yao Zhang", "Qingqing Zhang", "Lianhong Li"], "journal": "BioMed research international", "year": 2021, "abstract": "BACKGROUND: Coronary artery disease (CAD) is one of the most common causes of sudden death with high morbidity in recent years. This paper is aimed at exploring the early peripheral blood biomarkers of sudden death and providing a new perspective for clinical diagnosis and forensic pathology identification by integrated bioinformatics analysis.\nMETHODS: Two microarray expression profiling datasets (GSE113079 and GSE31568) were downloaded from the Gene Expression Omnibus (GEO) database, and we identified differentially expressed lncRNAs, miRNAs, and mRNAs in CAD. Gene Ontology (GO) and KEGG pathway analyses of DEmRNAs were executed. A protein-protein interaction (PPI) network was constructed, and hub genes were identified. Finally, we constructed a competitive endogenous RNA (ceRNA) regulation network among lncRNAs, miRNAs, and mRNAs. Also, the 5 miRNAs of the ceRNA network were verified by RT-PCR.\nRESULTS: In total, 86 DElncRNAs, 148 DEmiRNAs, and 294 DEmRNAs were dysregulated in CAD. We received 12 GO terms and 5 pathways of DEmRNAs. 31 nodes and 78 edges were revealed in the PPI network. The top 10 genes calculated by degree method were identified as hub genes. Moreover, there were a total of 26 DElncRNAs, 5 DEmiRNAs, and 13 DEmRNAs in the ceRNA regulation network. We validated the 5 miRNAs of the ceRNA network by RT-PCR, which were consistent with the results of the microarray.\nCONCLUSIONS: In this paper, a CAD-specific ceRNA network was successfully constructed, contributing to the understanding of the relationship among lncRNAs, miRNAs, and mRNAs. We identified potential peripheral blood biomarkers in CAD and provided novel insights into the development and progress of CAD.", "claims": [{"id": "claim-method", "statement": "GEO2R, an online analysis tool in GEO, was used to evaluate the differential expression in CAD and control groups from the two profile datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33511207", "locator": "sections[4] \"2.2. Data Preprocessing and Differential Expression Analysis\" paragraph 3", "quote": "GEO2R, an online analysis tool in GEO, was used to evaluate the differential expression in CAD and control groups from the two profile datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Two microarray expression profiling datasets (GSE113079 and GSE31568) were retrieved and downloaded from the Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33511207", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "Two microarray expression profiling datasets (GSE113079 and GSE31568) were retrieved and downloaded from the Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33511207"], "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:GSE113079"], "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:GSE113079"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33511207", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/6658115", "sha256": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE113079", "GSE31568"], "resolved_accessions": ["GSE113079", "GSE31568"], "statements": ["Two microarray expression profiling datasets (GSE113079 and GSE31568) were retrieved and downloaded from the Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/geo)."], "basis": "The paper names GSE113079, GSE31568 in Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information (NCBI) 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:33511207", "data:geo:GSE113079"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE113079"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 17935, "completion_tokens": 1797, "cached_tokens": 392}}, "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:33511207", "type": "paper", "label": "pmid:33511207"}, {"id": "source:pmid:33511207", "type": "manuscript", "label": "PMID 33511207 full text"}, {"id": "data:geo:GSE113079", "type": "dataset", "label": "GEO GSE113079"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33511207", "type": "paper", "label": "pmid:33511207"}, {"id": "source:pmid:33511207", "type": "manuscript", "label": "PMID 33511207 full text"}, {"id": "data:geo:GSE113079", "type": "dataset", "label": "GEO GSE113079"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33511207", "type": "extraction", "used": ["source:pmid:33511207"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE113079", "type": "accession_resolution", "used": ["data:geo:GSE113079"], "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:33511207", "parent_hash": "sha256:1a6a36ce2311d258f1eb941197779b9ed04fe1e3e6266584e47cda77dae0a8f6", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE113079 licence not read", "asset:data:geo:GSE113079 not downloaded", "asset:data:geo:GSE31568 licence not read", "asset:data:geo:GSE31568 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.99, "evidence": ["grated bioinformatics analysis. METHODS: Two microarray expression profiling datasets (GSE113079 and", "hich were consistent with the results of the microarray. CONCLUSIONS: In this paper, a CAD-specific"], "order_basis": "paper_text_order:422", "id": "assay:1"}, {"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:2"}]}