Bioinformatic identification of potential biomarkers and therapeutic targets in carotid atherosclerosis and vascular dementia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36703641", "kind": "science-record", "revision": 3, "content_hash": "sha256:09676e0fc576b0667dd7d1404fc319c8c971ce55820a41857c590809c24aa100", "created_at": "2026-11-01T19:01:15Z", "updated_at": "2026-11-01T22:08:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic identification of potential biomarkers and therapeutic targets in carotid atherosclerosis and vascular dementia.", "doi": "10.3389/fneur.2022.1091453", "pmid": "36703641", "authors": ["Dongshi Li", "Zhixin Huang", "Yingyi Dai", "Linling Guo", "Songbin Lin", "Xintong Liu"], "journal": "Frontiers in neurology", "year": 2022, "abstract": "Background: Vascular disease is the second most common cause of dementia. The prevalence of vascular dementia (VaD) has increased over the past decade. However, there are no licensed treatments for this disease. Carotid atherosclerosis (CAS) is highly prevalent and is the main cause of ischemic stroke and VaD. We studied co-expressed genes to understand the relationships between CAS and VaD and further reveal the potential biomarkers and therapeutic targets of CAS and VaD.\nMethods: CAS and VaD differentially expressed genes (DEGs) were identified through bioinformatic analysis Gene Expression Omnibus (GEO) datasets GSE43292 and GSE122063, respectively. Furthermore, a variety of target prediction methods and network analysis approaches were used to assess the protein-protein interaction (PPI) networks, the Gene Ontology (GO) terms, and the pathway enrichment for DEGs, and the top 7 hub genes, coupled with corresponding predicted miRNAs involved in CAS and VaD, were assessed as well.\nResult: A total of 60 upregulated DEGs and 159 downregulated DEGs were identified, of which the top 7 hub genes with a high degree of connectivity were selected. Overexpression of these hub genes was associated with CAS and VaD. Finally, the top 7 hub genes were coupled with corresponding predicted miRNAs. hsa-miR-567 and hsa-miR-4652-5p may be significantly associated with CAS and VaD.", "claims": [{"id": "claim-method", "statement": "The DEGs were detected using the GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), and the adjusted p-value and |logFC| were calculated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36703641", "locator": "sections[4] \"2.2. Screening for DEGs\" paragraph 2", "quote": "The DEGs were detected using the GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), and the adjusted p-value and |logFC| were calculated."}], "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:36703641", "locator": "sections[16] \"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"}, {"id": "claim-target-result", "statement": "Finally, 219 DEGs were significantly expressed differently in the two groups, with 60 significantly upregulated genes and 159 considerably downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36703641", "locator": "sections[10] \"3.1. Identification of DEGs associated with the progression of CAS and VaD\" paragraph 2", "quote": "Finally, 219 DEGs were significantly expressed differently in the two groups, with 60 significantly upregulated genes and 159 considerably downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Finally, 219 DEGs were significantly expressed differently in the two groups, with 60 significantly upregulated genes and 159 considerably downregulated genes.", "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:36703641"], "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:GSE122063"], "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:GSE122063"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36703641", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2022.1091453", "sha256": "sha256:57ef9bdad17fb3491e5aa26f76dc9bd640ce7949d8f3e3cf6026d45777503f9c", "bytes": 26571, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fneur.2022.1091453", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9872033", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE122063", "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=GSE122063", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE122063", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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