Identification of the molecular mechanisms associated with acute type A aortic dissection through bioinformatics methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31721906", "kind": "science-record", "revision": 8, "content_hash": "sha256:377a3232bc710ea3b19b85d723745e079ac44565267a22937080d22e92e84849", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:00:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the molecular mechanisms associated with acute type A aortic dissection through bioinformatics methods.", "doi": "10.1590/1414-431X20198950", "pmid": "31721906", "authors": ["Tao Jiang", "Liangyi Si"], "journal": "Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologica", "year": 2019, "abstract": "Aortic dissection is characterized by the redirection of blood flow, which flows through an intimal tear into the aortic media. The purpose of this study was to find potential acute type A aortic dissection (AAAD)-related genes and molecular mechanisms by bioinformatics. The gene expression profiles of GSE52093 were obtained from Gene Expression Omnibus (GEO) database, including 7 AAAD samples and 5 normal samples. The differentially expressed genes (DEGs) were detected between AAAD and normal samples. The functional annotation and pathway enrichment analysis were conducted through the Database for Annotation, Visualization and Integration Discovery (DAVID). A protein-protein interaction network was established by the Search Tool for the Retrieval of Interacting Genes (STRING) software. The microRNAs (miRNAs) of these differentially expressed genes were predicted using <microRNA.org> database. Moreover, DEGs were analyzed in the comparative toxicogenomics (CTD) database to screen out the potential therapeutic small molecules. As a result, there were 172 DEGs identified in patients with AAAD. These DEGs were significantly enriched in 6 pathways, including cell cycle, oocyte meiosis, DNA replication, extracellular matrix-receptor interaction, and mineral absorption pathway. Notably, CDC20, CDK1, CHEK1, KIF20A, MCM10, PBK, PTTG1, RACGAP, and TOP2A were crucial genes with a high degree in the protein-protein interaction network. Furthermore, potential miRNAs (miR-301, miR-302 family, and miR-130 family) were identified. In addition, small molecules like azathioprine and zoledronic acid were identified to be potential drugs for AAAD.", "claims": [{"id": "claim-method", "statement": "After background correction, data normalization, and determination of expression levels, the gene expression between AAAD and normal samples was compared using the linear regression model and empirical Bayes moderated t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31721906", "locator": "sections[4] \"Data preprocessing and identification of DEGs\" paragraph 2", "quote": "After background correction, data normalization, and determination of expression levels, the gene expression between AAAD and normal samples was compared using the linear regression model and empirical Bayes moderated t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiles of GSE52093 (12) were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). This dataset includes five normal ascending aorta samples from normal donors and seven dissected ascending aorta samples from patients with AAAD. The Illumina HumanHT-12 v4.0 expression beadchip (USA) was employed to analyze the samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31721906", "locator": "sections[3] \"Dataset\" paragraph 2", "quote": "The gene expression profiles of GSE52093 (12) were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). This dataset includes five normal ascending aorta samples from normal donors and seven dissected ascending aorta samples from patients with AAAD. The Illumina HumanHT-12 v4.0 expression beadchip (USA) was employed to analyze the samples."}], "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:31721906"], "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:GSE52093"], "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:GSE52093"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31721906", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1590/1414-431X20198950", "sha256": "sha256:caca2cf48a276f0d87ab658218378dd05366c49c70259397e41464328ff4db5d", "bytes": 28355, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1590/1414-431X20198950", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6853077", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE52093", "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=GSE52093", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE52093", "version": null, "note": "The gene expression profiles of GSE52093 (12) were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). 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"row_count": 10, "column_count": 4}, "table": {"label": "Table 2.", "caption": "Protein-protein interaction network degree and gene expression of identified hub genes.", "rows": [["Genes", "Degree", "Log FC", "FDR"], ["CDC20", "20.23", "4.15", "0.0249"], ["CDK1", "28.52", "2.85", "0.0355"], ["CHEK1", "22.54", "3.01", "0.0276"], ["KIF20A", "23.50", "5.31", "0.0344"], ["MCM10", "23.83", "3.22", "0.0370"], ["PBK", "28.91", "5.58", "0.0344"], ["PTTG1", "20.26", "2.77", "0.0334"], ["RACGAP", "24.80", "1.82", "0.0443"], ["TOP2A", "29.14", "4.43", "0.0244"]], "row_count": 10, "column_count": 4, "numeric_cells": 30, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t02"}}, {"id": "asset:table:pmid:31721906:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:13b3a17c472b9f09e7cde6b788e06bdaa20af8abb83182b7420f6a38e920d82d", "bytes": 1675, "access": "open", "state": "verified", "reader": "read_table", "reader_status": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE52093"], "resolved_accessions": ["GSE52093"], "statements": ["The gene expression profiles of GSE52093 (12) were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). This dataset includes five normal ascending aorta samples from normal donors and seven dissected ascending aorta samples from patients with AAAD. The Illumina HumanHT-12 v4.0 expression beadchip (USA) was employed to analyze the samples."], "basis": "The paper names GSE52093 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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These DEGs were significantly enriched"], "order_basis": "paper_text_order:1167", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["ols_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["After background correction, data normalization, and determination of expression levels, the gene expression between AAAD and normal samples was compared using the linear regression model and empirical Bayes moderated t-test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}