Identification and experimental validation of autophagy-related genes in abdominal aortic aneurysm.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37737183", "kind": "science-record", "revision": 4, "content_hash": "sha256:be0c8ff388d6c58674e063264f86c59034a871b7bbff192e5b90644f02c16dbc", "created_at": "2026-11-01T19:02:34Z", "updated_at": "2026-11-01T22:52:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and experimental validation of autophagy-related genes in abdominal aortic aneurysm.", "doi": "10.1186/s40001-023-01354-6", "pmid": "37737183", "authors": ["Xiaoli Yuan", "Yancheng Song", "Hai Xin", "Lu Zhang", "Bingyu Liu", "Jianmin Ma", "Ruicong Sun", "Xiaomei Guan", "Zhirong Jiang"], "journal": "European journal of medical research", "year": 2023, "abstract": "AIM: Autophagy plays essential roles in abdominal aortic aneurysm (AAA) development and progression. The objective of this study was to verify the autophagy-related genes (ARGs) underlying AAA empirically and using bioinformatics analysis.\nMETHODS: Two gene expression profile datasets GSE98278 and GSE57691 were downloaded from the Gene Expression Omnibus (GEO) database, and principal component analysis was performed. Following, the R software (version 4.0.0) was employed to analyze potentially differentially expressed genes related with AAA and autophagy. Subsequently, the candidate genes were screened using protein-protein interaction (PPI), gene ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Finally, quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the RNA expression levels of the top five selected abnormal ARGs in clinical samples obtained from the normal and AAA patients.\nRESULTS: According to the information contained (97 AAA patients and 10 healthy controls) in the two datasets, a total of 44 differentially expressed autophagy-related genes (6 up-regulated genes and 38 down-regulated genes) were screened. GO enrichment analysis of differentially expressed autophagy-related genes (DEARGs) demonstrated that some enrichment items were associated with inflammation, and PPI analysis indicated interaction between these genes. RT-qPCR results presented that the expression levels of IL6, PPARG, SOD1, and MAP1LC3B were in accordance with the bioinformatics prediction results acquired from the mRNA chip.\nCONCLUSION: Bioinformatics analysis identified 44 potential autophagy-related differentially expressed genes in AAA. Further verification by RT- qPCR presented that IL6, PPARG, SOD1, and MAP1LC3B may affect the development of AAA by regulating autophagy. These findings might help explain the pathogenesis of AAA and be helpful in its diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "Subsequently, the LIMMA software package was performed to screen 44 genes (6 up-regulated genes and 38 down-regulated genes) from 796 ARGs using |log FC|> 1.0 and P < 0.05 as criteria (Table 4).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37737183", "locator": "sections[12] \"DEARGs in AAA-Retrospective Analysis of ARGs\" paragraph 2", "quote": "Subsequently, the LIMMA software package was performed to screen 44 genes (6 up-regulated genes and 38 down-regulated genes) from 796 ARGs using |log FC|> 1.0 and P < 0.05 as criteria (Table 4)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Research submitted in the initial contributions includes Supplementary Material in the writing. Additional enquiries can be made to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37737183", "locator": "sections[23] \"notes\" paragraph 1", "quote": "Research submitted in the initial contributions includes Supplementary Material in the writing. Additional enquiries can be made to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 44 differentially expressed autophagy-related genes in AAA, comprising 6 up-regulated and 38 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37737183", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "According to the information contained (97 AAA patients and 10 healthy controls) in the two datasets, a total of 44 differentially expressed autophagy-related genes (6 up-regulated genes and 38 down-regulated genes) were screened."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 44 differentially expressed autophagy-related genes in AAA, comprising 6 up-regulated and 38 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:37737183"], "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:GSE57691"], "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:GSE57691"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37737183", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-023-01354-6", "sha256": "sha256:3ccb3cf99c6a3e5b6f1265f3d00cb1b2bfe8d5ee075c21547a9d3f151833d715", "bytes": 29877, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40001-023-01354-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10515431", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57691", "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=GSE57691", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57691", "version": null, "note": "Research submitted in the initial contributions includes Supplementary Material in the writing. Additional enquiries can be made to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Research submitted in the initial contributions includes Supplementary Material in the writing. Additional enquiries can be made to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1386783", "GSM1386784", "GSM1386785", "GSM1386786", "GSM1386787", "GSM1386788", "GSM1386789", "GSM1386790", "GSM1386791", "GSM1386792", "GSM1386793", "GSM1386794", "GSM1386795", "GSM1386796", "GSM1386797", "GSM1386798", "GSM1386799", "GSM1386800", "GSM1386801", "GSM1386802", "GSM1386803", "GSM1386804", "GSM1386805", "GSM1386806", "GSM1386807", "GSM1386808", "GSM1386809", "GSM1386810", "GSM1386811", "GSM1386812", "GSM1386813", "GSM1386814", "GSM1386815", "GSM1386816", "GSM1386817", "GSM1386818", "GSM1386819", "GSM1386820", "GSM1386821", "GSM1386822", "GSM1386823", "GSM1386824", "GSM1386825", "GSM1386826", "GSM1386827", "GSM1386828", "GSM1386829", "GSM1386830", "GSM1386831", "GSM1386832", "GSM1386833", "GSM1386834", "GSM1386835", "GSM1386836", "GSM1386837", "GSM1386838", "GSM1386839", "GSM1386840", "GSM1386841", "GSM1386842", "GSM1386843", "GSM1386844", "GSM1386845", "GSM1386846", "GSM1386847", "GSM1386848", "GSM1386849", "GSM1386850"], "sample_count": 68, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Differential gene expression in human abdominal aortic aneurysm and atherosclerosis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE98278", "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=GSE98278", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98278", "version": null, "note": "Research submitted in the initial contributions includes Supplementary Material in the writing. Additional enquiries can be made to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Research submitted in the initial contributions includes Supplementary Material in the writing. 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RT-qPCR results presented that the expression levels", "tive real-time polymerase chain reaction (RT-qPCR) was performed to detect the RNA expression", "ndicated interaction between these genes. RT-qPCR results presented that the expression levels"], "order_basis": "paper_text_order:877", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["using RT-qPCR (Table 2). Similar to the mRNA microarray results, IL6 was markedly elevated in AAA (F"], "order_basis": "paper_text_order:9862", "id": "assay:2"}, {"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": ["Subsequently, the LIMMA software package was performed to screen 44 genes (6 up-regulated genes and 38 down-regulated genes) from 796 ARGs using |log FC|> 1.0 and P < 0.05 as criteria (Table 4)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}