The occurrence and development of abdominal aortic aneurysm may be related to the energy metabolism disorder and local inflammation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38496900", "kind": "science-record", "revision": 4, "content_hash": "sha256:b12413289ea186358cf053108c08bd944d8dbe902709343a2f7a559b6195f942", "created_at": "2026-11-01T19:20:26Z", "updated_at": "2026-11-01T22:53:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The occurrence and development of abdominal aortic aneurysm may be related to the energy metabolism disorder and local inflammation.", "doi": "10.1016/j.heliyon.2024.e27912", "pmid": "38496900", "authors": ["Jun Li", "Yang Liu", "Zhitao Wei", "Jie Cheng", "Yongfa Wu"], "journal": "Heliyon", "year": 2024, "abstract": "Background: The cellular mechanism of the formation of abdominal aortic aneurysm (AAA) is very complicated. A series of sophisticated events eventually led to significant pathological changes in the anatomical structure and function of the arterial wall and they are still not clear nowadays.\nMethods: We pooled publicly available GEO datasets (GSE57691 and GSE47472) to get a comprehensive comparisons between normal tissues and AAA tissues to try to reveal molecular mechanism underlying the disease. Total 63 AAA samples and 18 normal tissue samples were compared and we fond that there were 784 significantly different gene (DEGs, threshold set as adjusted P < 0.05 and Log FC < 1) were identified. At the same time, we validate the possible signaling factor expression of AAA by comparing the normal tissue of the human body with the AAA tissue.\nResults: In the pathway enrichment, we found that FOXP3 related signaling pathways, inflammation-related cytokine signaling pathways, interleukin-8-CXCR1 related signaling pathways and VEGFA and FGFR1 related signal pathway were significantly enrichmented. In Weighted gene co-expression network analysis (WGCNA), we found that the key hub genes were significantly related to lipid catabolic metabolism, which further verified the possibility that AAA might relate to energy metabolism disorders.\nConclusion: Based on the comprehensive analysis of previous high-throughput data and the validation of basic experiments, we found that the occurrence of AAA may be related to energy metabolism disorders and local inflammation.", "claims": [{"id": "claim-method", "statement": "We used the limma (3.44.3) package to calculate and identify differential genes. In the process of determining differential genes, a linear fitting models were used, and the statistical significance is determined by using the T test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38496900", "locator": "sections[3] \"Bioinformatics analysis\" paragraph 3", "quote": "We used the limma (3.44.3) package to calculate and identify differential genes. In the process of determining differential genes, a linear fitting models were used, and the statistical significance is determined by using the T test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data included in article. material/referenced in article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38496900", "locator": "sections[14] \"Data availability statement\" paragraph 2", "quote": "Data included in article. material/referenced in article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "When set threshold adjusted P value as 0.05 and threshold Log FC as 1, total 784 DEGs were identified (Fig. 1A).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38496900", "locator": "sections[10] \"Results\" paragraph 2", "quote": "When set threshold adjusted P value as 0.05 and threshold Log FC as 1, total 784 DEGs were identified (Fig. 1A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "When set threshold adjusted P value as 0.05 and threshold Log FC as 1, total 784 DEGs were identified (Fig. 1A).", "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:38496900"], "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:GSE47472"], "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:GSE47472"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38496900", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e27912", "sha256": "sha256:26d5f9cb91174e389e7f78363bd6a5eceb4b51256a616f49d4655b0dcbfd8c83", "bytes": 39435, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e27912", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10944252", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE47472", "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=GSE47472", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE47472", "version": null, "note": "Data included in article. material/referenced in article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data included in article. material/referenced in article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1150689", "GSM1150690", "GSM1150691", "GSM1150692", "GSM1150693", "GSM1150694", "GSM1150695", "GSM1150696", "GSM1150697", "GSM1150698", "GSM1150699", "GSM1150700", "GSM1150701", "GSM1150702", "GSM1150703", "GSM1150704", "GSM1150705", "GSM1150706", "GSM1150707", "GSM1150708", "GSM1150709", "GSM1150710"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Differential gene expression in the proximal neck of human abdominal aortic aneurysm", "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: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": "Data included in article. material/referenced in article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data included in article. material/referenced in article.", "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}}], "gaps": ["asset:data:geo:GSE47472 not downloaded", "asset:data:geo:GSE47472 licence not read", "asset:data:geo:GSE57691 not downloaded", "asset:data:geo:GSE57691 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used the limma (3.44.3) package to calculate and identify differential genes. 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