Identification of co-expressed central genes and transcription factors in atherosclerosis-related intracranial aneurysm.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36937519", "kind": "science-record", "revision": 4, "content_hash": "sha256:e64cb592b31ca5ad0a56ef1d8d0a94e5a35af27a7cfc57c09f84c1c73c32955d", "created_at": "2026-11-01T19:01:35Z", "updated_at": "2026-11-01T22:51:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of co-expressed central genes and transcription factors in atherosclerosis-related intracranial aneurysm.", "doi": "10.3389/fneur.2023.1055456", "pmid": "36937519", "authors": ["Quan Zhang", "Hengfang Liu", "Min Zhang", "Fang Liu", "Tiantian Liu"], "journal": "Frontiers in neurology", "year": 2023, "abstract": "Background: Numerous clinical studies have shown that atherosclerosis is one of the risk factors for intracranial aneurysms. Calcifications in the intracranial aneurysm walls are frequently correlated with atherosclerosis. However, the pathogenesis of atherosclerosis-related intracranial aneurysms remains unclear. This study aims to investigate this mechanism.\nMethods: The Gene Expression Omnibus (GEO) database was used to download the gene expression profiles for atherosclerosis (GSE100927) and intracranial aneurysms (GSE75436). Following the identification of the common differentially expressed genes (DEGs) of atherosclerosis and intracranial aneurysm, the network creation of protein interactions, functional annotation, the identification of hub genes, and co-expression analysis were conducted. Thereafter, we predicted the transcription factors (TF) of hub genes and verified their expressions.\nResults: A total of 270 common (62 downregulated and 208 upregulated) DEGs were identified for subsequent analysis. Functional analyses highlighted the significant role of phagocytosis, cytotoxicity, and T-cell receptor signaling pathways in this disease progression. Eight hub genes were identified and verified, namely, CCR5, FCGR3A, IL10RA, ITGAX, LCP2, PTPRC, TLR2, and TYROBP. Two TFs were also predicted and verified, which were IKZF1 and SPI1.\nConclusion: Intracranial aneurysms are correlated with atherosclerosis. We identified several hub genes for atherosclerosis-related intracranial aneurysms and explored the underlying pathogenesis. These discoveries may provide new insights for future experiments and clinical practice.", "claims": [{"id": "claim-method", "statement": "We performed differential gene expression analysis on GSE75436 and GSE100927 using the “limma” R package (https:/www.bioconductor.org/packages/3.5/bioc/html/limma.html) (15). Data between groups were compared using the mean t-test, with a p-value of <0.05 as the standard for significant differences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36937519", "locator": "sections[4] \"2.2. Differential expression analysis\" paragraph 2", "quote": "We performed differential gene expression analysis on GSE75436 and GSE100927 using the “limma” R package (https:/www.bioconductor.org/packages/3.5/bioc/html/limma.html) (15)."}, {"asset": "source:pmid:36937519", "locator": "sections[8] \"2.6. Verification and analysis of hub genes\" paragraph 2", "quote": "Data between groups were compared using the mean t-test, with a p-value of <0.05 as the standard for significant differences."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36937519", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Eight hub genes were identified and verified, namely, CCR5, FCGR3A, IL10RA, ITGAX, LCP2, PTPRC, TLR2, and TYROBP.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36937519", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eight hub genes were identified and verified, namely, CCR5, FCGR3A, IL10RA, ITGAX, LCP2, PTPRC, TLR2, and TYROBP."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Eight hub genes were identified and verified, namely, CCR5, FCGR3A, IL10RA, ITGAX, LCP2, PTPRC, TLR2, and TYROBP.", "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:36937519"], "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:GSE100927"], "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:GSE100927"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36937519", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2023.1055456", "sha256": 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