Identification of apoptosis-related key genes and the associated regulation mechanism in thoracic aortic aneurysm.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37770840", "kind": "science-record", "revision": 5, "content_hash": "sha256:3dd1665c3cc0fe51b81ebb7508264b704e5a4e19d9a3e8d68a873b1e766aeef8", "created_at": "2026-11-01T19:02:37Z", "updated_at": "2026-11-01T22:52:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of apoptosis-related key genes and the associated regulation mechanism in thoracic aortic aneurysm.", "doi": "10.1186/s12872-023-03516-0", "pmid": "37770840", "authors": ["Qi Ma", "Long Hu", "Yingwan Luo", "Miao Wang", "Shui Yu", "Aidong Lu", "Leping Zhang", "Huimin Zeng"], "journal": "BMC cardiovascular disorders", "year": 2023, "abstract": "BACKGROUND: This study investigated the role of apoptosis-related genes in thoracic aortic aneurysms (TAA) and provided more insights into TAA's pathogenesis and molecular mechanisms.\nMATERIAL/METHODS: Two gene expression datasets (GSE9106 and GSE26155) were retrieved from the Gene Expression Omnibus (GEO) database. Apoptosis-related genes were obtained from the KEGG apoptosis pathway (hsa04210). Differentially expressed apoptosis-related genes were identified by performing differential expression analysis using limma for TAA blood and tissue samples. GO and KEGG enrichment analysis of the differentially expressed apoptosis genes was performed using the Metascape web tool. The miRNA-mRNA regulatory network was reconstructed using the ENCORI and miRDB databases, and functional enrichment analysis was performed on the related miRNAs using the miEAA tool. The correlation between the expression levels of differentially expressed apoptosis-related genes and genes involved in immune infiltration in TAA was calculated using the CIBERSORT algorithm. The apoptosis modification patterns mediated by differentially expressed apoptosis-related genes were systematically assessed in TAA samples.\nRESULTS: A total of 9 differentially-expressed apoptosis-related genes were identified in TAA samples compared with normal samples. 150 miRNAs and 6 mRNAs regulatory networks were reconstructed using the ENCORI and miRDB databases. Immune infiltration analysis revealed that the GZMB had the strongest positive correlation with activated NK cells and the DFFA presented the strongest positive correlation with T cells follicular helper. 3 distinct apoptosis modification patterns mediated by 9 differentially-expressed apoptosis-related genes were identified. They differ in immune characteristics and drug sensitivity, and their biological functions in these subtypes were further studied.\nCONCLUSIONS: This study identified key apoptosis-related genes related to TAA and evaluated the modification patterns of key apoptosis genes in TAA, providing insights into potential targets and mechanisms of TAA pathogenesis and progression.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed comparing the TAAs group and healthy groups in the GSE9106 dataset. The TAA dataset was screened for DEGs of mRNAs using the limma package [11].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37770840", "locator": "sections[4] \"The landscape of differentially-expressed apoptosis-related genes in TAAs\" paragraph 2", "quote": "Differential expression analysis was performed comparing the TAAs group and healthy groups in the GSE9106 dataset. The TAA dataset was screened for DEGs of mRNAs using the limma package [11]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. The data can be found in GEO, https://www.ncbi.nlm.nih.gov/geo/ (GSE9106).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37770840", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. The data can be found in GEO, https://www.ncbi.nlm.nih.gov/geo/ (GSE9106)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 9 differentially-expressed apoptosis-related genes were identified in TAA samples compared with normal samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37770840", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 9 differentially-expressed apoptosis-related genes were identified in TAA samples compared with normal samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 9 differentially-expressed apoptosis-related genes were identified in TAA samples compared with normal samples.", "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:37770840"], "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:GSE26155"], "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:GSE26155"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37770840", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12872-023-03516-0", "sha256": "sha256:80ae4443d7b3fb72b2562900951ae79a22baea8cd31897455215a79e2f21c35b", "bytes": 41664, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12872-023-03516-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10540322", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE26155", "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=GSE26155", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26155", "version": null, "note": "Publicly available datasets were analyzed in this study. 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