Bioinformatics-based identification of lipid- and immune-related biomarkers in abdominal aortic aneurysms.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36879746", "kind": "science-record", "revision": 4, "content_hash": "sha256:484aa0406eebc5c6d6c2c8c7505e6212f82c279717a521bb2dbe33b9c371291e", "created_at": "2026-11-01T19:01:31Z", "updated_at": "2026-11-01T22:51:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics-based identification of lipid- and immune-related biomarkers in abdominal aortic aneurysms.", "doi": "10.1016/j.heliyon.2023.e13622", "pmid": "36879746", "authors": ["Yuejin Li", "Rougang Li", "Shikui Guo", "Yu Li", "Yongzhi Wang", "Xin Wen", "Tian Lan", "Kunmei Gong"], "journal": "Heliyon", "year": 2023, "abstract": "Background: Abdominal aortic aneurysm (AAA) manifest as a natural inflammatory process with permanent dilation and terminal rupture. Nevertheless, the pathogenesis of AAA remains a mystery, and treatment is still controversial. Lipid metabolism and immune system are involved in AAA progression, which has been well documented. However, lipid- and immune-related (LIR) biomarkers need to be further elucidated.\nMethods: The AAA-related datasets were retrieved from the GEO database, and the datasets were analyzed for differential gene expression by NetworkAnalyst. GO and KEGG pathway enrichment analysis of differentially expressed mRNA (DE-mRNA) was performed using Metscape, and LIR DE-mRNA was further screened. AAA rat model was constructed using porcine pancreatic elastase to verify the differential expression of LIR DE-mRNA.\nResults: The GSE47472 and GSE57691 datasets respectively identified 614 (containing 381 down-regulated and 233 up-regulated DE-mRNAs) and 384 (containing 218 down-regulated and 164 up-regulated DE-mRNAs) DE-mRNAs. Intersection and union of DE-mRNAs were 13 and 983, respectively. The main terms involved in the union of DE-mRNAs included \"immune system process\", \"metabolic process\", \"Chemokine signaling pathway\", \"hematopoietic cell lineage\" and \"Cholesterol metabolism\". In vivo experiments revealed that LIR DE-mRNAs of PDIA3, TYROBP, and HSPA1A were significantly low expression in AAA abdominal aortic tissues, and HCK and SERPINE1 were significantly high expression, which is consistent with the bioinformatics analysis.\nConclusions: PDIA3, TYROBP, HSPA1A, HCK and SERPINE1 may serve as LIR biomarkers of AAA, which provides new insights and theoretical guidance for the future treatment, early prevention and progression of AAA.", "claims": [{"id": "claim-method", "statement": "Statistical method is Limma, and screening threshold is adjusted p-value (adj. p-value) < 0.05 and absolute log2 fold change (log2FC) > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36879746", "locator": "sections[4] \"Gene differential expression analysis and functional enrichment analysis\" paragraph 2", "quote": "Statistical method is Limma, and screening threshold is adjusted p-value (adj. p-value) < 0.05 and absolute log2 fold change (log2FC) > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data obtained and materials analyzed in this research are available with the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36879746", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "All the data obtained and materials analyzed in this research are available with the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PDIA3, TYROBP, and HSPA1A were significantly downregulated, whereas HCK and SERPINE1 were significantly upregulated, in AAA abdominal aortic tissues.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36879746", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In vivo experiments revealed that LIR DE-mRNAs of PDIA3, TYROBP, and HSPA1A were significantly low expression in AAA abdominal aortic tissues, and HCK and SERPINE1 were significantly high expression, which is consistent with the bioinformatics analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PDIA3, TYROBP, and HSPA1A were significantly downregulated, whereas HCK and SERPINE1 were significantly upregulated, in AAA abdominal aortic tissues.", "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:36879746"], "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:36879746", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2023.e13622", "sha256": "sha256:be783d77da0b6df1cd19c38ca3542f79d36cead84524b2d0a5687279fac71610", "bytes": 32580, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2023.e13622", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9984436", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "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": "All the data obtained and materials analyzed in this research are available with the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data obtained and materials analyzed in this research are available with the corresponding author upon reasonable request.", "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": "All the data obtained and materials analyzed in this research are available with the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data obtained and materials analyzed in this research are available with the corresponding author upon reasonable request.", "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": "Statistical method is Limma, and screening threshold is adjusted p-value (adj. p-value) < 0.05 and absolute log2 fold change (log2FC) > 1."}}, {"id": "method-2", "family": "group_comparison", 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In vivo experiments revealed that LIR DE-mRNAs of PD", "e, and LIR DE-mRNA was further screened. AAA rat model was constructed using porcine pancreat"], "order_basis": "paper_text_order:783", "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": ["ferential expression analysis of AAA-related microarray data The analysis flow of this study is show"], "order_basis": "paper_text_order:2512", "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": ["Statistical method is Limma, and screening threshold is adjusted p-value (adj. p-value) < 0.05 and absolute log2 fold change (log2FC) > 1."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}