Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39775580", "kind": "science-record", "revision": 3, "content_hash": "sha256:8428340556f886b901f6a3fb449262db123f857339ed1c575e3cbf935a9503fb", "created_at": "2026-11-01T20:30:06Z", "updated_at": "2026-11-01T22:13:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.", "doi": "10.1371/journal.pone.0316463", "pmid": "39775580", "authors": ["Wenlong Kuang", "Jianwu Huang", "Yulu Yang", "Yuhua Liao", "Zihua Zhou", "Qian Liu", "Hailang Wu"], "journal": "PloS one", "year": 2024, "abstract": "BACKGROUND: Myocardial infarction (MI), one of the most serious cardiovascular diseases, is also affected by altered mitochondrial metabolism and immune status, but their crosstalk is poorly understood. In this paper, we use bioinformatics to explore key targets associated with mitochondrial metabolic function in MI.\nMETHODS: The datasets (GSE775, GSE183272 and GSE236374) were from National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) in conjunction with mitochondrial gene data that were downloaded from the MitoCarta 3.0 database. Differentially expressed genes (DEGs) in the dataset were screened by ClusterGVis, Weighted Gene Co-Expression Network Analysis (WGCNA) and GEO2R, and functional enrichment was performed by Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Genomes (KEGG). Then mitochondria-associated DEGs (MitoDEGs) were obtained. Protein-protein interaction (PPI) networks were constructed to identify central MitoDEGs that are strongly associated with MI. The Cytoscape and miRWalk databases were then used to predict the transcription factors and target miRNAs of the central MitoDEG, respectively. Finally, the mouse model has been established to demonstrate the expression of MitoDEGs and their association with cardiac function.\nRESULTS: MitoDEGs in MI were mainly involved in mitochondrial function and adenosine triphosphate (ATP) synthesis pathways. The 10 MI-related hub MitoDEGs were then obtained by eight different algorithms. Immunoassays showed a significant increase in monocyte macrophage and T cell infiltration. According to animal experiments, the expression trends of the four hub MitoDEGs (Aco2, Atp5a1, Ndufs3, and Ndufv1) were verified to be consistent with the bioinformatics results.\nCONCLUSION: Our study identified key genes (Aco2, Atp5a1, Ndufs3, and Ndufv1) associated with mitochondrial function in myocardial infarction.", "claims": [{"id": "claim-method", "statement": "Student’s t-test (for comparisons between two groups) was used for the statistical analysis using IBM SPSS Statistics version 25, P<0.05 was consider as significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39775580", "locator": "sections[15] \"2.13 Statistical analysis\" paragraph 2", "quote": "Student’s t-test (for comparisons between two groups) was used for the statistical analysis using IBM SPSS Statistics version 25, P<0.05 was consider as significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Datasets were obtained from the public repository NCBI GEO (http://www.ncbi.nlm.nih.gov/ geo) [22] using \"myocardial infarction\" as the search queries.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39775580", "locator": "sections[3] \"2.1 Microarray data retrieval\" paragraph 2", "quote": "Datasets were obtained from the public repository NCBI GEO (http://www.ncbi.nlm.nih.gov/ geo) [22] using \"myocardial infarction\" as the search queries."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our study identified key genes (Aco2, Atp5a1, Ndufs3, and Ndufv1) associated with mitochondrial function in myocardial infarction.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39775580", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our study identified key genes (Aco2, Atp5a1, Ndufs3, and Ndufv1) associated with mitochondrial function in myocardial infarction."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our study identified key genes (Aco2, Atp5a1, Ndufs3, and Ndufv1) associated with mitochondrial function in myocardial infarction.", "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:39775580"], "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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Finally, the mouse model has been established to demonstrate the expr", "central MitoDEG, respectively. Finally, the mouse model has been established to demonstrate th", "ular wall to determine cardiac function. All mice were sacrificed on day 7 for histopathological examinations.", "val number No. 422023600011180. Male C57BL/6 mice were randomly divided into two groups: 1) Control"], "order_basis": "paper_text_order:1244", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["I and Control groups was further verified by Western blotting. The results showed that the protein express", "I mice; C. Protein levels of Hub MitoDEGs by western blotting; D. Correlations between Aco2, Atp5a1, Ndufs", "CON and MI mice; E. Quantitative analysis of western blotting in cardiac tissues, Numbers represent 6 inde"], "order_basis": "paper_text_order:4415", "id": "assay:2"}, {"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:3"}]}