Correlation between Complement C1q A Chain (C1QA) and Macrophages in the Progression of Carotid Atherosclerosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39086409", "kind": "science-record", "revision": 3, "content_hash": "sha256:3685cc5b649d876933a38750ea7effe8fa45839c9220f59ea1ab772954b5805e", "created_at": "2026-11-01T20:29:10Z", "updated_at": "2026-11-01T22:12:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Correlation between Complement C1q A Chain (C1QA) and Macrophages in the Progression of Carotid Atherosclerosis.", "doi": "10.18502/ijph.v53i7.16046", "pmid": "39086409", "authors": ["Guanglong Dong", "Xiangwen Yu", "Mingyu Zhao", "Shusen Lin", "Qingyu Meng"], "journal": "Iranian journal of public health", "year": 2024, "abstract": "Background: There is increasing evidence that macrophages are involved in the development of carotid atherosclerosis (CAS), but the specific mechanism is still unclear. We aimed to explore the key genes that play a regulatory role on macrophages in the progression of CAS.\nMethods: From 2021 August to 2023 August, GEO datasets GSE100927 and GSE43292 were downloaded and the key gene modules related to CAS were identified by weighted Gene co-expression network analysis (WGCNA). Kyoto Encyclopedia of Genes and Genes (KEGG) pathway analysis was performed on the genes of the key modules to identify common gene enrichment pathways. Differential expression analysis of pathway-related genes was performed by the \"limma\" package of R software. Case groups were categorized into high and low expression groups based on the expression levels of key genes, and ssGSEA immune infiltration analysis was performed.\nResults: The turquoise module of GSE100924 (threshold=12) and the brown module of GSE43292 (threshold=7) were obtained through WGCNA analysis. The analysis of KEGG showed that the differentially expressed genes in the turquoise and brown modules were co-enriched in the staphylococcus aureus infection signaling pathway. Differential expression analysis identified 18 common differentially expressed genes, all of which were highly expressed in the case group. C1QA is the gene of interest. According to ssGSEA analysis, the high expression group of C1QA showed a significant increase in the number of macrophages (GSE43292, P=0.0011; GSE100927, P=0.025).\nConclusion: This study identified the key gene C1QA involved in regulating macrophage functional activity during the CAS process, providing new ideas for effective control of CAS.", "claims": [{"id": "claim-data-access", "statement": "The gene expression matrix was downloaded for datasets of carotid artery related studies from the GEO database: (https://www.ncbi.nlm.nih.gov/geo/). GSE100927 and GSE43292 are used for screening key genes and signaling pathways, GSE21545 and GSE159677 are used to validate key genes and signaling pathways.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39086409", "locator": "sections[3] \"Data acquisition\" paragraph 2", "quote": "The gene expression matrix was downloaded for datasets of carotid artery related studies from the GEO database: (https://www.ncbi.nlm.nih.gov/geo/). GSE100927 and GSE43292 are used for screening key genes and signaling pathways, GSE21545 and GSE159677 are used to validate key genes and signaling pathways."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study identified the key gene C1QA involved in regulating macrophage functional activity during the CAS process, providing new ideas for effective control of CAS.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39086409", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "This study identified the key gene C1QA involved in regulating macrophage functional activity during the CAS process, providing new ideas for effective control of CAS."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study identified the key gene C1QA involved in regulating macrophage functional activity during the CAS process, providing new ideas for effective control of CAS.", "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:39086409"], "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:39086409", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18502/ijph.v53i7.16046", "sha256": "sha256:020da29236d375bc305f5e3a005de7d26a592095d0baff02c42492f3ff8c8734", "bytes": 27863, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18502/ijph.v53i7.16046", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11287601", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100927", "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=GSE100927", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100927", "version": null, "note": "The gene expression matrix was downloaded for datasets of carotid artery related studies from the GEO database: (https://www.ncbi.nlm.nih.gov/geo/). 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