Identification of potential molecular mechanisms and small molecule drugs in myocardial ischemia/reperfusion injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32696819", "kind": "science-record", "revision": 6, "content_hash": "sha256:56dacbddaee7062d1a150d6aa392b36fbc1555685a3dc0d0e74571b6f620dd66", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:01:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential molecular mechanisms and small molecule drugs in myocardial ischemia/reperfusion injury.", "doi": "10.1590/1414-431x20209717", "pmid": "32696819", "authors": ["Tao Jiang", "Yingcun Liu", "Biao Chen", "Liangyi Si"], "journal": "Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologica", "year": 2020, "abstract": "Myocardial ischemia/reperfusion (MI/R) injury is a complex phenomenon that causes severe damage to the myocardium. However, the potential molecular mechanisms of MI/R injury have not been fully clarified. We identified potential molecular mechanisms and therapeutic targets in MI/R injury through analysis of Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were found between MI/R injury and normal samples, and overlapping DEGs were found between GSE61592 and GSE67308. Gene Ontology (GO) and pathway analysis were performed for overlapping DEGs by Database for Annotation, Visualization and Integration Discovery (DAVID). Then, a network of protein-protein interaction (PPI) was constructed through the Search Tool for the Retrieval of Interacting Genes (STRING) database. Potential microRNAs (miRNAs) and therapeutic small molecules were screened out using microRNA.org database and the Comparative Toxicogenomics database (CTD), respectively. Finally, we identified 21 overlapping DEGs related to MI/R injury. These DEGs were significantly enriched in IL-17 signaling pathway, cytosolic DNA-sensing pathway, chemokine signaling, and cytokine-cytokine receptor interaction pathway. According to the degree in the PPI network, CCL2, LCN2, HP, CCL7, HMOX1, CCL4, and S100A8 were found to be hub genes. Furthermore, we identified potential miRNAs (miR-24-3p, miR-26b-5p, miR-2861, miR-217, miR-4251, and miR-124-3p) and therapeutic small molecules like ozone, troglitazone, rosiglitazone, and n-3 polyunsaturated fatty acids for MI/R injury. These results identified hub genes and potential small molecule drugs, which could contribute to the understanding of molecular mechanisms and treatment for MI/R injury.", "claims": [{"id": "claim-method", "statement": "After data preprocessing, the fold change (FC) of gene expression and the false discovery rate (FDR) was calculated between MI/R and normal samples. DEGs were identified with a |log FC| ≥2 and an FDR <0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32696819", "locator": "sections[4] \"Identification of overlapping DEGs and enrichment analysis\" paragraph 2", "quote": "After data preprocessing, the fold change (FC) of gene expression and the false discovery rate (FDR) was calculated between MI/R and normal samples. DEGs were identified with a |log FC| ≥2 and an FDR <0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE61592 and GSE67308 datasets were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The GSE61592 dataset included three normal heart samples and three MI/R injury samples. The MI/R injury samples of two datasets were obtained from mice subjected to I/R involving left anterior descending coronary artery occlusion followed by reperfusion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32696819", "locator": "sections[3] \"Datasets and data preprocessing\" paragraph 2", "quote": "The GSE61592 and GSE67308 datasets were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/)."}, {"asset": "source:pmid:32696819", "locator": "sections[3] \"Datasets and data preprocessing\" paragraph 2", "quote": "The GSE61592 dataset included three normal heart samples and three MI/R injury samples."}, {"asset": "source:pmid:32696819", "locator": "sections[3] \"Datasets and data preprocessing\" paragraph 2", "quote": "The MI/R injury samples of two datasets were obtained from mice subjected to I/R involving left anterior descending coronary artery occlusion followed by reperfusion."}], "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:32696819"], "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:GSE61592"], "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:GSE61592"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32696819", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1590/1414-431x20209717", "sha256": "sha256:36f3597d6046b9b62f3f9c489c0af93483fe202910da935e2b613b72d556e8fe", "bytes": 33575, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1590/1414-431x20209717", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7372942", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE61592", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61592", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61592", "version": null, "note": "The GSE61592 and GSE67308 datasets were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). 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count", "Target genes"], ["miR-24-3p", "1.93E-02", "4", "S100A8, CCL2, CCL4, HMOX1"], ["miR-26b-5p", "1.93E-02", "5", "CCL2, CCL7, PLAC8, HMOX1, CH25H"], ["miR-2861", "2.91E-02", "3", "AIF1, ANGPTL4, LCN2"], ["miR-217", "3.60E-02", "4", "CLEC4D, CYP1B1, CCL4, HMOX1"], ["miR-4251", "3.61E-02", "4", "CLEC4D, CCL7, PLAC8, LCN2"], ["miR-124-3p", "3.85E-02", "4", "CYP1B1, CCL2, ANGPTL4, HMOX1"]], "row_count": 7, "column_count": 4, "numeric_cells": 20, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t03"}}, {"id": "asset:table:pmid:32696819:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5a18c8ab4d88cf53939355650afcd553d7cffb8c5109c2f345707a574bc4e3a6", "bytes": 2056, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#t04", "version": null, "note": "Top 20 potential small molecules of the overlapping DEGs.", "structure": 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AIF1, S100A9, CYP1B1, CCL2, CCL4, CCL7, PLAC8, G0S2, HMOX1, LCN2, CH25H"], ["Troglitazone", "7.00E-08", "11", "HP, CYP1B1, CCL2, CCL4, IL33, CCL7, G0S2, ANGPTL4, HMOX1, LCN2, CH25H"], ["Naphthalene", "8.36E-08", "8", "S100A8, S100A9, CYP1B1, CCL2, CCL7, ANGPTL4, HMOX1, CH25H"], ["Isoproterenol", "1.26E-07", "10", "CLEC4D, S100A8, AIF1, S100A9, CYP1B1, CCL2, CCL7, HMOX1, LCN2, CH25H"], ["Cobalt", "2.36E-07", "7", "CYP1B1, CCL2, CCL4, CCL7, G0S2, ANGPTL4, HMOX1"], ["Rosiglitazone", "2.92E-07", "11", "AIF1, HP, CYP1B1, CCL2, CCL4, CCL7, G0S2, ANGPTL4, HMOX1, LCN2, CH25H"], ["Tesaglitazar", "3.13E-07", "8", "AIF1, CCL2, CCL4, IL33, G0S2, ANGPTL4, HMOX1, CH25H"], ["1-Naphthylisothiocyanate", "6.76E-07", "9", "S100A8, AIF1, S100A9, CCL2, IL33, PLAC8, G0S2, HMOX1, LCN2"], ["CI 1044", "6.76E-07", "5", "S100A8, S100A9, CYP1B1, HMOX1, LCN2"], ["Trimethyltin", "6.76E-07", "5", "AIF1, CCL2, CCL4, HMOX1, LCN2"], ["Chloroprene", "1.22E-06", "10", "S100A8, AIF1, S100A9, CYP1B1, IL33, PLAC8, G0S2, 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