Bioinformatics analysis to identify potential biomarkers and therapeutic targets for ST-segment-elevation myocardial infarction-related ischemic stroke.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36034287", "kind": "science-record", "revision": 5, "content_hash": "sha256:e3db7720d4b266f2c0b5a2951957bc9cbd87aa9adba48cd53b316311b4160dbb", "created_at": "2026-11-01T18:15:12Z", "updated_at": "2026-11-01T22:49:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis to identify potential biomarkers and therapeutic targets for ST-segment-elevation myocardial infarction-related ischemic stroke.", "doi": "10.3389/fneur.2022.894289", "pmid": "36034287", "authors": ["Shuo Feng", "Rui Li", "Qingqing Zhou", "Fengling Qu", "Wei Hu", "Xinfeng Liu"], "journal": "Frontiers in neurology", "year": 2022, "abstract": "Background: Acute myocardial infarction (AMI) is one of the major causes of mortality and disability worldwide, and ischemic stroke (IS) is a serious complication after AMI. In particular, patients with ST-segment-elevation myocardial infarction (STEMI) are more susceptible to IS. However, the interrelationship between the two disease mechanisms is not clear. Using bioinformatics tools, we investigated genes commonly expressed in patients with STEMI and IS to explore the relationship between these diseases, with the aim of uncovering the underlying biomarkers and therapeutic targets for STEMI-associated IS.\nMethods: Differentially expressed genes (DEGs) related to STEMI and IS were identified through bioinformatics analysis of the Gene Expression Omnibus (GEO) datasets GSE60993 and GSE16561, respectively. Thereafter, we assessed protein-protein interaction networks, gene ontology term annotations, and pathway enrichment for DEGs using various prediction and network analysis methods. The predicted miRNAs targeting the co-expressed STEMI- and IS-related DEGs were also evaluated.\nResults: We identified 210 and 29 DEGs in GSE60993 and GSE16561, respectively. CD8A, TLR2, TLR4, S100A12, and TREM1 were associated with STEMI, while the hubgenes, IL7R, CCR7, FCGR3B, CD79A, and ITK were implicated in IS. In addition, binding of the transcripts of the co-expressed DEGs MMP9, ARG1, CA4, CRISPLD2, S100A12, and GZMK to their corresponding predicted miRNAs, especially miR-654-5p, may be associated with STEMI-related IS.\nConclusions: STEMI and IS are related and MMP9, ARG1, CA4, CRISPLD2, S100A12, and GZMK genes may be underlying biomarkers involved in STEMI-related IS.", "claims": [{"id": "claim-method", "statement": "Before identifying DEGs, we performed boxplot analysis to evaluate the expression level of samples in each dataset and then used the normalize BetweenArrays function in the “limma” package of R to exclude batch effect. The criteria for selecting DEGs were |log2FC|>1.0 and false discovery rate (FDR) <0.05;", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36034287", "locator": "sections[4] \"DEG analysis\" paragraph 2", "quote": "Before identifying DEGs, we performed boxplot analysis to evaluate the expression level of samples in each dataset and then used the normalize BetweenArrays function in the “limma” package of R to exclude batch effect. The criteria for selecting DEGs were |log2FC|>1.0 and false discovery rate (FDR) <0.05;"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo, GSE60993, GSE16561, and GSE60319.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36034287", "locator": "sections[13] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo, GSE60993, GSE16561, and GSE60319."}], "state": "complete"}, {"id": "claim-target-result", "statement": "STEMI and IS are related and MMP9, ARG1, CA4, CRISPLD2, S100A12, and GZMK genes may be underlying biomarkers involved in STEMI-related IS.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36034287", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "STEMI and IS are related and MMP9, ARG1, CA4, CRISPLD2, S100A12, and GZMK genes may be underlying biomarkers involved in STEMI-related IS."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "STEMI and IS are related and MMP9, ARG1, CA4, CRISPLD2, S100A12, and GZMK genes may be underlying biomarkers involved in STEMI-related IS.", "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:36034287"], "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:GSE16561"], "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": {"log2fc_threshold": "ession selection using |log2FC| > 1"}, "inputs": ["data:geo:GSE16561"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36034287", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2022.894289", "sha256": "sha256:0c3b90a5bdb827df00b5a077a933bbe0b3babb14d24fc53c62a4f6f8ebcc2b25", "bytes": 21823, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fneur.2022.894289", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9403764", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16561", "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=GSE16561", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16561", "version": null, "note": "Publicly available datasets were analyzed in this study. 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This data can be found here: National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo, GSE60993, GSE16561, and GSE60319.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. 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