Bioinformatics-based screening of genes associated with dilated cardiomyopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40529774", "kind": "science-record", "revision": 3, "content_hash": "sha256:4c20e2ca5162b1d736d3379d0253c03ab8302db88a17c23b1ac80999ff0faadd", "created_at": "2026-11-01T20:30:37Z", "updated_at": "2026-11-01T22:14:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics-based screening of genes associated with dilated cardiomyopathy.", "doi": "10.21037/jtd-2025-132", "pmid": "40529774", "authors": ["Yanghua Liu", "Qingshan Wu", "Fangni Mo", "Ye Mai", "Shengyuan Zhang", "Xiang Wu"], "journal": "Journal of thoracic disease", "year": 2025, "abstract": "Background: Due to the lack of appropriate diagnostic biomarkers and intervention targets, the diagnosis and treatment of dilated cardiomyopathy (DCM) in clinical practice are considerably challenging. Therefore, this study aimed to identify reliable biomarker genes using bioinformatics methods to improve the clinical management of DCM.\nMethods: Three DCM gene datasets, GSE120895, GSE42955, and GSE3586, were downloaded from the Gene Expression Omnibus (GEO). Differential gene analysis was used to screen for differentially expressed genes in these datasets, and weighted gene coexpression network analysis (WGCNA) was used to screen for the gene coexpression modules most relevant to DCM. Machine learning algorithms and a Protein-protein interaction (PPI) network were used to screen for the core DCM genes in the gene coexpression module.\nResults: WGCNA identified the turquoise module as the most relevant gene module for DCM disease. Subsequently, machine learning algorithms identified 8 core genes while PPI screening identified 10 core genes. HSPA8 was found in both machine learning algorithms and PPI screening.\nConclusions: In this study, the HSPA8 gene was found to be a core gene in DCM, demonstrating the closest association with this disease. Further research on HSPA8 is expected to provide a target for the diagnosis and treatment of DCM.", "claims": [{"id": "claim-method", "statement": "Subsequently, based on five external datasets (GSE57338, GSE5406, GSE116250, GSE42955, and GSE19303), we employed receiver operating characteristic (ROC) curve analysis to evaluate the diagnostic efficacy of HSPA8 for DCM.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40529774", "locator": "sections[18] \"The diagnostic efficacy of HSPA8 for DCM\" paragraph 2", "quote": "Subsequently, based on five external datasets (GSE57338, GSE5406, GSE116250, GSE42955, and GSE19303), we employed receiver operating characteristic (ROC) curve analysis to evaluate the diagnostic efficacy of HSPA8 for DCM."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three datasets were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/), along with their expression profiles and sample information (GSE120895, GSE42955, and GSE3586).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40529774", "locator": "sections[4] \"Gene Expression Omnibus (GEO) datasets\" paragraph 2", "quote": "Three datasets were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/), along with their expression profiles and sample information (GSE120895, GSE42955, and GSE3586)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "HSPA8 had high diagnostic value for dilated cardiomyopathy, with an ROC area under the curve of 0.954.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40529774", "locator": "sections[18] \"The diagnostic efficacy of HSPA8 for DCM\" paragraph 2", "quote": "This yielded an area under the ROC curve of 0.954, indicating that HSPA8 has extremely high diagnostic value for DCM (Figure 6B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "HSPA8 had high diagnostic value for dilated cardiomyopathy, with an ROC area under the curve of 0.954.", "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:40529774"], "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:GSE116250"], "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:GSE116250"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40529774", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jtd-2025-132", "sha256": 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313, "group_sizes": null, "group_sizes_basis": null, "platform": "11532", "taxon": "Homo sapiens", "title": "RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [microarray]", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE116250 not downloaded", "asset:data:geo:GSE116250 licence not read", "asset:data:geo:GSE120895 not downloaded", "asset:data:geo:GSE120895 licence not read", "asset:data:geo:GSE19303 not downloaded", "asset:data:geo:GSE19303 licence not read", "asset:data:geo:GSE3586 not downloaded", "asset:data:geo:GSE3586 licence not read", "asset:data:geo:GSE42955 not downloaded", "asset:data:geo:GSE42955 licence not read", "asset:data:geo:GSE5406 not downloaded", "asset:data:geo:GSE5406 licence not read", "asset:data:geo:GSE57338 not downloaded", "asset:data:geo:GSE57338 licence not read"]}, 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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": ["GSE120895", "GSE42955", "GSE3586", "GSE57338", "GSE5406", "GSE116250", "GSE19303"], "resolved_accessions": ["GSE120895", "GSE42955", "GSE3586", "GSE57338", "GSE5406", "GSE116250", "GSE19303"], "statements": ["Three datasets were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/), along with their expression profiles and sample information (GSE120895, GSE42955, and GSE3586)."], "basis": "The paper names GSE120895, GSE42955, GSE3586, GSE57338, GSE5406, GSE116250, GSE19303 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:40529774", "data:geo:GSE116250"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116250"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:54:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 7484, "completion_tokens": 2320, "cached_tokens": 264}}, "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:40529774", "type": "paper", "label": "pmid:40529774"}, {"id": "source:pmid:40529774", "type": "manuscript", "label": "PMID 40529774 full text"}, {"id": "data:geo:GSE116250", "type": "dataset", "label": "GEO GSE116250"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40529774", "type": "paper", "label": "pmid:40529774"}, {"id": "source:pmid:40529774", "type": "manuscript", "label": "PMID 40529774 full text"}, {"id": "data:geo:GSE116250", "type": "dataset", "label": "GEO GSE116250"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40529774", "type": "extraction", "used": ["source:pmid:40529774"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116250", "type": "accession_resolution", "used": ["data:geo:GSE116250"], "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:40529774", "parent_hash": "sha256:44a11d68979e06f534087d7f0f36c562619380a54aac84a7163dcbafb617d3d3", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE116250 licence not read", "asset:data:geo:GSE116250 not downloaded", "asset:data:geo:GSE120895 licence not read", "asset:data:geo:GSE120895 not downloaded", "asset:data:geo:GSE19303 licence not read", "asset:data:geo:GSE19303 not downloaded", "asset:data:geo:GSE3586 licence not read", "asset:data:geo:GSE3586 not downloaded", "asset:data:geo:GSE42955 licence not read", "asset:data:geo:GSE42955 not downloaded", "asset:data:geo:GSE5406 licence not read", "asset:data:geo:GSE5406 not downloaded", "asset:data:geo:GSE57338 licence not read", "asset:data:geo:GSE57338 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": "analysis_only", "id": "assay:1"}]}