Identification of diagnostic model in heart failure with myocardial fibrosis and conduction block by integrated gene co-expression network analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38355637", "kind": "science-record", "revision": 4, "content_hash": "sha256:dfc4c018622c5e4a03e44c13d06292dd25d15dc57d051e5b1e5a7f0391ea6b62", "created_at": "2026-11-01T19:20:18Z", "updated_at": "2026-11-01T22:53:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of diagnostic model in heart failure with myocardial fibrosis and conduction block by integrated gene co-expression network analysis.", "doi": "10.1186/s12920-024-01814-w", "pmid": "38355637", "authors": ["Yonghua Yuan", "Yiwei Niu", "Jiajun Ye", "Yuejuan Xu", "Xuehua He", "Sun Chen"], "journal": "BMC medical genomics", "year": 2024, "abstract": "BACKGROUND: Despite the advancements in heart failure(HF) research, the early diagnosis of HF continues to be a challenging issue in clinical practice. This study aims to investigate the genes related to myocardial fibrosis and conduction block, with the goal of developing a diagnostic model for early treatment of HF in patients.\nMETHOD: The gene expression profiles of GSE57345, GSE16499, and GSE9128 were obtained from the Gene Expression Omnibus (GEO) database. After merging the expression profile data and adjusting for batch effects, differentially expressed genes (DEGs) associated with conduction block and myocardial fibrosis were identified. Gene Ontology (GO) resources, Kyoto Encyclopedia of Genes and Genomes (KEGG) resources, and gene set enrichment analysis (GSEA) were utilized for functional enrichment analysis. A protein-protein interaction network (PPI) was constructed using a string database. Potential key genes were selected based on the bioinformatics information mentioned above. SVM and LASSO were employed to identify hub genes and construct the module associated with HF. The mRNA levels of TAC mice and external datasets (GSE141910 and GSE59867) are utilized for validating the diagnostic model. Additionally, the study explores the relationship between the diagnostic model and immune cell infiltration.\nRESULTS: A total of 395 genes exhibiting differential expression were identified. Functional enrichment analysis revealed that these specific genes primarily participate in biological processes and pathways associated with the constituents of the extracellular matrix (ECM), immune system processes, and inflammatory responses. We identified a diagnostic model consisting of 16 hub genes, and its predictive performance was validated using external data sets and a transverse aortic coarctation (TAC) mouse model. In addition, we observed significant differences in mRNA expression of 7 genes in the TAC mouse model. Interestingly, our study also unveiled a correlation between these model genes and immune cell infiltration.\nCONCLUSIONS: We identified sixteen key genes associated with myocardial fibrosis and conduction block, as well as diagnostic models for heart failure. Our findings have significant implications for the intensive management of individuals with potential genetic variants associated with heart failure, especially in the context of advancing cell-targeted therapy for myocardial fibrosis.", "claims": [{"id": "claim-method", "statement": "The diagnostic model was constructed using the least absolute shrinkage and selection operator (LASSO) regression analysis and support vector machine (SVM) method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38355637", "locator": "sections[6] \"Construction and verification of HF diagnostic model\" paragraph 2", "quote": "The diagnostic model was constructed using the least absolute shrinkage and selection operator (LASSO) regression analysis and support vector machine (SVM) method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article and its supplementary information files.All R code, and input/output data for this study are available in the figshare: 10.6084/m9.figshare.24586290.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38355637", "locator": "sections[27] \"Data availability\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article and its supplementary information files.All R code, and input/output data for this study are available in the figshare: 10.6084/m9.figshare.24586290."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A diagnostic model consisting of 16 hub genes was developed and validated using external datasets and a transverse aortic coarctation mouse model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38355637", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified a diagnostic model consisting of 16 hub genes, and its predictive performance was validated using external data sets and a transverse aortic coarctation (TAC) mouse model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A diagnostic model consisting of 16 hub genes was developed and validated using external datasets and a transverse aortic coarctation mouse model.", "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:38355637"], "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:GSE141910"], "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:GSE141910"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38355637", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-024-01814-w", "sha256": 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In addition, we observed significant differ", "ces in mRNA expression of 7 genes in the TAC mouse model. Interestingly, our study also unveiled a co", "ts and a transverse aortic coarctation (TAC) mouse model. In addition, we observed significant", "ces in mRNA expression of 7 genes in the TAC mouse model. Interestingly, our study also unveile"], "order_basis": "paper_text_order:1942", "id": "assay:1"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The diagnostic model was constructed using the least absolute shrinkage and selection operator (LASSO) regression analysis and support vector machine (SVM) method."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}