ITGAM is a critical gene in ischemic stroke.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38637126", "kind": "science-record", "revision": 4, "content_hash": "sha256:a403243bafceed25cf3019fcd670af54d2056859af75a8784480c07988ce7fd0", "created_at": "2026-11-01T19:20:36Z", "updated_at": "2026-11-01T22:54:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ITGAM is a critical gene in ischemic stroke.", "doi": "10.18632/aging.205729", "pmid": "38637126", "authors": ["Lei Hou", "Zhongchen Li", "Xiaoli Guo", "Jiatao Lv", "Zonglei Chong", "Yilei Xiao", "Liyong Zhang", "Zefu Li"], "journal": "Aging", "year": 2024, "abstract": "BACKGROUND: Globally, ischemic stroke (IS) is ranked as the second most prevailing cause of mortality and is considered lethal to human health. This study aimed to identify genes and pathways involved in the onset and progression of IS.\nMETHODS: GSE16561 and GSE22255 were downloaded from the Gene Expression Omnibus (GEO) database, merged, and subjected to batch effect removal using the ComBat method. The limma package was employed to identify the differentially expressed genes (DEGs), followed by enrichment analysis and protein-protein interaction (PPI) network construction. Afterward, the cytoHubba plugin was utilized to screen the hub genes. Finally, a ROC curve was generated to investigate the diagnostic value of hub genes. Validation analysis through a series of experiments including qPCR, Western blotting, TUNEL, and flow cytometry was performed.\nRESULTS: The analysis incorporated 59 IS samples and 44 control samples, revealing 226 DEGs, of which 152 were up-regulated and 74 were down-regulated. These DEGs were revealed to be linked with the inflammatory and immune responses through enrichment analyses. Overall, the ROC analysis revealed the remarkable diagnostic potential of ITGAM and MMP9 for IS. Quantitative assessment of these genes showed significant overexpression in IS patients. ITGAM modulation influenced the secretion of critical inflammatory cytokines, such as IL-1β, IL-6, and TNF-α, and had a distinct impact on neuronal apoptosis.\nCONCLUSIONS: The inflammation and immune response were identified as potential pathological mechanisms of IS by bioinformatics and experiments. In addition, ITGAM may be considered a potential therapeutic target for IS.", "claims": [{"id": "claim-method", "statement": "This research utilized the R package limma 3.40.6 [31] for the analysis of DEGs in the experimental and control groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38637126", "locator": "sections[15] \"Differential expression analysis\" paragraph 2", "quote": "This research utilized the R package limma 3.40.6 [31] for the analysis of DEGs in the experimental and control groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this work are obtainable from GEO (https://www.ncbi.nlm.nih.gov/geo/). GSE22255: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22255. GSE16561: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16561. GSE58294: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58294.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38637126", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The data that support the findings of this work are obtainable from GEO (https://www.ncbi.nlm.nih.gov/geo/). GSE22255: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22255. GSE16561: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16561. GSE58294: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58294."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The merged analysis identified 226 differentially expressed genes between ischemic stroke and control samples, including 152 up-regulated and 74 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38637126", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The analysis incorporated 59 IS samples and 44 control samples, revealing 226 DEGs, of which 152 were up-regulated and 74 were down-regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The merged analysis identified 226 differentially expressed genes between ischemic stroke and control samples, including 152 up-regulated and 74 down-regulated genes.", "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:38637126"], "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": {}, "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:38637126", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.205729", "sha256": "sha256:d5dcb5060c9f620aee6db4aa46c1e488e4f439de4cac090ecff90e61d1a9b3f2", "bytes": 32019, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.205729", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11087101", "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": "The data that support the findings of this work are obtainable from GEO (https://www.ncbi.nlm.nih.gov/geo/). 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RE"], "order_basis": "paper_text_order:805", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["including qPCR, Western blotting, TUNEL, and flow cytometry was performed. RESULTS: The analysis incorpo"], "order_basis": "paper_text_order:834", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["TNF-α, and had a distinct impact on neuronal apoptosis. CONCLUSIONS: The inflammation and immune re"], "order_basis": "paper_text_order:1460", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["2 incubator. Additional experiments involved transfection with siRNA targeting ITGAM (si-ITGAM) to spe", "off-target effects or alterations due to the transfection process itself. Statistical analysis The sta", "ional experiments involved transfection with siRNA targeting ITGAM (si-ITGAM) to specifically k"], "order_basis": "paper_text_order:3052", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["This research utilized the R package limma 3.40.6 [31] for the analysis of DEGs in the experimental and control groups."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}