Identification and cross-validation of autophagy-related genes in cardioembolic stroke.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37305740", "kind": "science-record", "revision": 4, "content_hash": "sha256:b13c7ec19b4b6711cc84ef8f82b8a952104d85c6aa89b4dd43b9d99638bd84ad", "created_at": "2026-11-01T19:02:03Z", "updated_at": "2026-11-01T22:52:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and cross-validation of autophagy-related genes in cardioembolic stroke.", "doi": "10.3389/fneur.2023.1097623", "pmid": "37305740", "authors": ["Yufang Yang", "Min Zhang", "Ziqing Li", "Shen He", "Xueqi Ren", "Linmei Wang", "Zhifei Wang", "Shi Shu"], "journal": "Frontiers in neurology", "year": 2023, "abstract": "Objective: Cardioembolic stroke (CE stroke, also known as cardiogenic cerebral embolism, CCE) has the highest recurrence rate and fatality rate among all subtypes of ischemic stroke, the pathogenesis of which was unclear. Autophagy plays an essential role in the development of CE stroke. We aim to identify the potential autophagy-related molecular markers of CE stroke and uncover the potential therapeutic targets through bioinformatics analysis.\nMethods: The mRNA expression profile dataset GSE58294 was obtained from the GEO database. The potential autophagy-related differentially expressed (DE) genes of CE stroke were screened by R software. Protein-protein interactions (PPIs), correlation analysis, and gene ontology (GO) enrichment analysis were applied to the autophagy-related DE genes. GSE66724, GSE41177, and GSE22255 were introduced for the verification of the autophagy-related DE genes in CE stroke, and the differences in values were re-calculated by Student's t-test.\nResults: A total of 41 autophagy-related DE genes (37 upregulated genes and four downregulated genes) were identified between 23 cardioembolic stroke patients (≤3 h, prior to treatment) and 23 healthy controls. The KEGG and GO enrichment analysis of autophagy-related DE genes indicated several enriched terms related to autophagy, apoptosis, and ER stress. The PPI results demonstrated the interactions between these autophagy-related genes. Moreover, several hub genes, especially for CE stroke, were identified and re-calculated by Student's t-test.\nConclusion: We identified 41 potential autophagy-related genes associated with CE stroke through bioinformatics analysis. SERPINA1, WDFY3, ERN1, RHEB, and BCL2L1 were identified as the most significant DE genes that may affect the development of CE stroke by regulating autophagy. CXCR4 was identified as a hub gene of all types of strokes. ARNT, MAPK1, ATG12, ATG16L2, ATG2B, and BECN1 were identified as particular hub genes for CE stroke. These results may provide insight into the role of autophagy in CE stroke and contribute to the discovery of potential therapeutic targets for CE stroke treatment.", "claims": [{"id": "claim-method", "statement": "The “limma” package of R software was used to identify the autophagy-related DE genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37305740", "locator": "sections[4] \"Analysis of autophagy-related DE genes\" paragraph 2", "quote": "The “limma” package of R software was used to identify the autophagy-related DE genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. The accession numbers are: GSE58294; GSE66724; GSE41177; and GSE22255.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37305740", "locator": "sections[14] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. The accession numbers are: GSE58294; GSE66724; GSE41177; and GSE22255."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 41 autophagy-related differentially expressed genes were identified between 23 cardioembolic stroke patients and 23 healthy controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37305740", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 41 autophagy-related DE genes (37 upregulated genes and four downregulated genes) were identified between 23 cardioembolic stroke patients (≤3 h, prior to treatment) and 23 healthy controls."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 41 autophagy-related differentially expressed genes were identified between 23 cardioembolic stroke patients and 23 healthy controls.", "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:37305740"], "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:GSE22255"], "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:GSE22255"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37305740", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2023.1097623", "sha256": "sha256:56bd73daa43ee81ec29a772cea83a8c1ea33ae51de40f070c9e4f22f229b1f0e", "bytes": 58944, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fneur.2023.1097623", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10248509", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22255", "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=GSE22255", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22255", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. The accession numbers are: GSE58294; GSE66724; GSE41177; and GSE22255.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. 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This data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. The accession numbers are: GSE58294; GSE66724; GSE41177; and GSE22255.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37305740", "data:geo:GSE22255"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22255"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:43:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16931, "completion_tokens": 1459, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37305740", "type": "paper", "label": "pmid:37305740"}, {"id": "source:pmid:37305740", "type": "manuscript", "label": "PMID 37305740 full text"}, {"id": "data:geo:GSE22255", "type": "dataset", "label": "GEO GSE22255"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37305740", "type": "paper", "label": "pmid:37305740"}, {"id": "source:pmid:37305740", "type": "manuscript", "label": "PMID 37305740 full text"}, {"id": "data:geo:GSE22255", "type": "dataset", "label": "GEO GSE22255"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37305740", "type": "extraction", "used": ["source:pmid:37305740"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22255", "type": "accession_resolution", "used": ["data:geo:GSE22255"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37305740", "parent_hash": "sha256:62c8dd11a24bd916442f2e1145380aca421cc95a3aa389efeb5db86ebed9d5b7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE22255 licence not read", "asset:data:geo:GSE22255 not downloaded", "asset:data:geo:GSE41177 licence not read", "asset:data:geo:GSE41177 not downloaded", "asset:data:geo:GSE58294 licence not read", "asset:data:geo:GSE58294 not downloaded", "asset:data:geo:GSE66724 licence not read", "asset:data:geo:GSE66724 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["several enriched terms related to autophagy, apoptosis, and ER stress. 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