Bioinformatics Analysis Reveals the Potential Diagnostic Biomarkers for Abdominal Aortic Aneurysm.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34355024", "kind": "science-record", "revision": 8, "content_hash": "sha256:369a698ae78a473885eceea25e56a3fa3d276d61424f0800005a9ab0aeaae145", "created_at": "2026-11-01T15:41:47Z", "updated_at": "2026-11-01T22:47:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis Reveals the Potential Diagnostic Biomarkers for Abdominal Aortic Aneurysm.", "doi": "10.3389/fcvm.2021.656263", "pmid": "34355024", "authors": ["Xinsheng Xie", "En Ci Wang", "Dandan Xu", "Xiaolong Shu", "Yu Fei Zhao", "Daqiao Guo", "Weiguo Fu", "Lixin Wang"], "journal": "Frontiers in cardiovascular medicine", "year": 2021, "abstract": "Objectives: Abdominal aortic aneurysms (AAAs) are associated with high mortality rates. The genes and pathways linked with AAA remain poorly understood. This study aimed to identify key differentially expressed genes (DEGs) linked to the progression of AAA using bioinformatics analysis. Methods: Gene expression profiles of the GSE47472 and GSE57691 datasets were acquired from the Gene Expression Omnibus (GEO) database. These datasets were merged and normalized using the \"sva\" R package, and DEGs were identified using the limma package in R. The functions of these DEGs were assessed using Cytoscape software. We analyzed the DEGs using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Protein-protein interaction networks were assembled using Cytoscape, and crucial genes were identified using the Cytoscape plugin, molecular complex detection. Data from GSE15729 and GSE24342 were also extracted to verify our findings. Results: We found that 120 genes were differentially expressed in AAA. Genes associated with inflammatory responses and nuclear-transcribed mRNA catabolic process were clustered in two gene modules in AAA. The hub genes of the two modules were IL6, RPL21, and RPL7A. The expression levels of IL6 correlated positively with RPL7A and negatively with RPL21. The expression of RPL21 and RPL7A was downregulated, whereas that of IL6 was upregulated in AAA. Conclusions: The expression of RPL21 or RPL7A combined with IL6 has a diagnostic value for AAA. The novel DEGs and pathways identified herein might provide new insights into the underlying molecular mechanisms of AAA.", "claims": [{"id": "claim-method", "statement": "The GSE47472 and GSE57691 datasets were merged and normalized using the “sva” R package. We identified differentially expressed genes (DEGs) using the “limma” package in R. The mRNA expression profiling datasets GSE47472 and GSE57691 both based on GPL10558 (Illumina HumanHT-12 V4.0 expression bead chip) were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34355024", "locator": "sections[3] \"Data Collection and Analysis of Differentially Expressed Genes\" paragraph 2", "quote": "The GSE47472 and GSE57691 datasets were merged and normalized using the “sva” R package."}, {"asset": "source:pmid:34355024", "locator": "sections[3] \"Data Collection and Analysis of Differentially Expressed Genes\" paragraph 2", "quote": "We identified differentially expressed genes (DEGs) using the “limma” package in R."}, {"asset": "source:pmid:34355024", "locator": "sections[3] \"Data Collection and Analysis of Differentially Expressed Genes\" paragraph 2", "quote": "The mRNA expression profiling datasets GSE47472 and GSE57691 both based on GPL10558 (Illumina HumanHT-12 V4.0 expression bead chip) were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34355024", "locator": "sections[13] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34355024"], "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:GSE15729"], "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:GSE15729"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34355024", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2021.656263", "sha256": "sha256:cd70af134ac1b39548cfc91947c38fe14064156b7ad9d5768ad5cb9fa62f836e", "bytes": 41711, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2021.656263", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8329524", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15729", "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=GSE15729", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15729", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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"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": "asset:table:pmid:34355024:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:425322978260eeee6ad12049ab04270b8c3a534917bd2742d6239605ebbb36bf", "bytes": 1540, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "The biological process, cellular component, and molecular functions in enriched analysis of differentially expressed genes between AAA and control (top 3 according to adj.P value).", "structure": {"pmcid": "PMC8329524", "section_index": 9, "section_title": "Functional and Pathway Enrichment Analysis of Differentially Expressed Genes", "row_count": 19, "column_count": 5}, "table": {"label": "Table 1", "caption": "The biological process, cellular component, and molecular functions in enriched analysis of differentially expressed genes between AAA and control (top 3 according to adj.P value).", "rows": [["", "Term", "Name", "Count", "adj.Pval"], ["Upregulated"], ["BP", "GO:0002675", "Positive regulation of acute inflammatory response", "5", "1.03E−06"], ["", "GO:0015671", "Oxygen transport", "4", "2.74E−06"], ["", "GO:0002673", "Regulation of acute inflammatory response", "5", "2.74E−06"], ["CC", "GO:0031838", "Haptoglobin–hemoglobin complex", "4", "3.03E−08"], ["", "GO:0005833", "Hemoglobin complex", "4", "3.03E−08"], ["", "GO:0071682", 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"format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5365b2d61f4a7c40b6144f9e55ee7cb77ec4b67796c0ce34e00c6772bfd061bf", "bytes": 543, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#T2", "version": null, "note": "The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes (DEGs).", "structure": {"pmcid": "PMC8329524", "section_index": 9, "section_title": "Functional and Pathway Enrichment Analysis of Differentially Expressed Genes", "row_count": 4, "column_count": 5}, "table": {"label": "Table 2", "caption": "The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes (DEGs).", "rows": [["", "Term", "Count", "adj.Pval", "Genes"], ["UP", "IL17 signaling pathway", "4", "6.53E−04", "IL6, FOSB, IL1B, PTGS2"], ["", "TNF signaling pathway", "4", "9.78E−04", "IL6, IL1B, PTGS2, SOCS3"], ["Down", "Ribosome", "9", "5.96E−06", "RPL26, RPL21, RPL24, RPL7A, RPL35A, RPL39, RPLP0, RPS17, RPL10A"]], "row_count": 4, "column_count": 5, "numeric_cells": 8, "header_rows": 1, "locator": "section[9]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:GSE15729 not downloaded", "asset:data:geo:GSE15729 licence not read", "asset:data:geo:GSE24342 not downloaded", "asset:data:geo:GSE24342 licence not read", "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": "reordered", "quote": "The GSE47472 and GSE57691 datasets were merged and normalized using the “sva” R package. We identified differentially expressed genes (DEGs) using the “limma” package in R. The mRNA expression profiling datasets GSE47472 and GSE57691 both based on GPL10558 (Illumina HumanHT-12 V4.0 expression bead chip) were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE47472", "GSE57691", "GSE15729", "GSE24342"], "resolved_accessions": ["GSE47472", "GSE57691", "GSE15729", "GSE24342"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE47472, GSE57691, GSE15729, GSE24342 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34355024", "data:geo:GSE15729", "asset:table:pmid:34355024:1", "asset:table:pmid:34355024:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15729"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:21Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 30830, "completion_tokens": 1489, "cached_tokens": 512}}, "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:34355024", "type": "paper", "label": "pmid:34355024"}, {"id": "source:pmid:34355024", "type": "manuscript", "label": "PMID 34355024 full text"}, {"id": "data:geo:GSE15729", "type": "dataset", "label": "GEO GSE15729"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34355024", "type": "paper", "label": "pmid:34355024"}, {"id": "source:pmid:34355024", "type": "manuscript", "label": "PMID 34355024 full text"}, {"id": "data:geo:GSE15729", "type": "dataset", "label": "GEO GSE15729"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34355024", "type": "extraction", "used": ["source:pmid:34355024"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15729", "type": "accession_resolution", "used": ["data:geo:GSE15729"], "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:34355024", "parent_hash": "sha256:d6d7ffcf2c6e8f70974911416ed001b0f928023777d02103821fb5340db85f56", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE15729 licence not read", "asset:data:geo:GSE15729 not downloaded", "asset:data:geo:GSE24342 licence not read", "asset:data:geo:GSE24342 not downloaded", "asset:data:geo:GSE47472 licence not read", "asset:data:geo:GSE47472 not downloaded", "asset:data:geo:GSE57691 licence not read", "asset:data:geo:GSE57691 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["The GSE47472 and GSE57691 datasets were merged and normalized using the “sva” R package. We identified differentially expressed genes (DEGs) using the “limma” package in R. The mRNA expression profiling datasets GSE47472 and GSE57691 both based on GPL10558 (Illumina HumanHT-12 V4.0 expression bead chip) were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/)."], "order_basis": "analysis_only", "id": "assay:1"}]}