Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37810795", "kind": "science-record", "revision": 5, "content_hash": "sha256:8d3d637f4d6677911e96c7226288c5fe9ef2e0a4a83970f65a8ce79b8439b843", "created_at": "2026-11-01T19:02:40Z", "updated_at": "2026-11-01T22:52:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics.", "doi": "10.7717/peerj.16122", "pmid": "37810795", "authors": ["Da Teng", "Hongping Chen", "Wenjuan Jia", "Qingmiao Ren", "Xiaoning Ding", "Lihui Zhang", "Lei Gong", "Hua Wang", "Lin Zhong", "Jun Yang"], "journal": "PeerJ", "year": 2023, "abstract": "Background: Foam cells play crucial roles in all phases of atherosclerosis. However, until now, the specific mechanisms by which these foam cells contribute to atherosclerosis remain unclear. We aimed to identify novel foam cell biomarkers and interventional targets for atherosclerosis, characterizing their potential mechanisms in the progression of atherosclerosis.\nMethods: Microarray data of atherosclerosis and foam cells were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expression genes (DEGs) were screened using the \"LIMMA\" package in R software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were both carried out. Hub genes were found in Cytoscape after a protein-protein interaction (PPI) enrichment analysis was carried out. Validation of important genes in the GSE41571 dataset, cellular assays, and tissue samples.\nResults: A total of 407 DEGs in atherosclerosis and 219 DEGs in foam cells were identified, and the DEGs in atherosclerosis were mainly involved in cell proliferation and differentiation. CSF1R and PLAUR were identified as common hub genes and validated in GSE41571. In addition, we also found that the expression of CSF1R and PLAUR gradually increased with the accumulation of lipids and disease progression in cell and tissue experiments.\nConclusion: CSF1R and PLAUR are key hub genes of foam cells and may play an important role in the biological process of atherosclerosis. These results advance our understanding of the mechanism behind atherosclerosis and potential therapeutic targets for future development.", "claims": [{"id": "claim-method", "statement": "Differential gene expression (differential expression genes, DEG) was performed with the “LIMMA” package (3.50.0) with —log FC— > 0.5 and adjusted P value < 0.05 (Ritchie et al., 2015).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37810795", "locator": "sections[4] \"Validation of gene expression through DEG analysis\" paragraph 2", "quote": "Differential gene expression (differential expression genes, DEG) was performed with the “LIMMA” package (3.50.0) with —log FC— > 0.5 and adjusted P value < 0.05 (Ritchie et al., 2015)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data are available in the Supplemental File.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37810795", "locator": "sections[30] \"Data Availability\" paragraph 2", "quote": "The raw data are available in the Supplemental File."}], "state": "complete"}, {"id": "claim-target-result", "statement": "LIMMA analysis of GEO microarray datasets identified 407 atherosclerosis-associated DEGs and 219 foam-cell-associated DEGs, and CSF1R and PLAUR emerged as common hub genes whose expression increased with lipid accumulation and disease progression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37810795", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 407 DEGs in atherosclerosis and 219 DEGs in foam cells were identified, and the DEGs in atherosclerosis were mainly involved in cell proliferation and differentiation."}, {"asset": "source:pmid:37810795", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "CSF1R and PLAUR were identified as common hub genes and validated in GSE41571."}, {"asset": "source:pmid:37810795", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In addition, we also found that the expression of CSF1R and PLAUR gradually increased with the accumulation of lipids and disease progression in cell and tissue experiments."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "LIMMA analysis of GEO microarray datasets identified 407 atherosclerosis-associated DEGs and 219 foam-cell-associated DEGs, and CSF1R and PLAUR emerged as common hub genes whose expression increased with lipid accumulation and disease progression.", "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:37810795"], "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. 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