Integrated Bioinformatics-Based Identification of Ferroptosis-Related Genes in Carotid Atherosclerosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36393970", "kind": "science-record", "revision": 4, "content_hash": "sha256:5c756c075b314859b02ceda9c8b82ca06f9fec9014d017e63d22a650e6405976", "created_at": "2026-11-01T19:00:51Z", "updated_at": "2026-11-01T22:50:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics-Based Identification of Ferroptosis-Related Genes in Carotid Atherosclerosis.", "doi": "10.1155/2022/3379883", "pmid": "36393970", "authors": ["Linfeng Wei", "Nan Wang", "Runsheng Li", "Hui Zhao", "Xin Zheng", "Zhihui Deng", "Zhongwei Sun", "Zhuangjie Xing"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Ferroptosis, a type of cell death caused by phospholipid peroxidation, has lately been linked to the onset and development of numerous illnesses. Numerous investigations have demonstrated the close relationship between lipid peroxidation and carotid atherosclerosis. In order to get new knowledge for targeted therapy, bioinformatics analysis was employed in this study to discover the probable ferroptosis-related genes of carotid atherosclerosis.\nMethods: The GSE43292 gene expression dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed ferroptosis-related genes were screened by R software and then analyzed by protein-protein interaction (PPI) network, differential gene correlation analysis, Kyoto Encyclopedia of Gene and Genome (KEGG) pathway, and Gene Ontology (GO) terminology enrichment analysis to explore the functional role.\nResult: In samples of atherosclerosis, we found 33 ferroptosis genes that were differentially expressed, including 21 upregulated genes and 12 downregulated genes. These differentially elevated genes were mainly connected to the ferroptosis and glutathione metabolism pathways, according to GO and KEGG enrichment analysis. We also discovered 10 hub genes and 2 important modules through the analysis of the PPI network and the creation of key modules.\nConclusion: The current findings imply that the carotid atherosclerosis phenomenon involves ferroptosis, and 10 important genes associated to ferroptosis may play a role in the development of carotid atherosclerosis. This study offered a novel approach to future research on the carotid atherosclerosis pathogenic processes and treatment targets.", "claims": [{"id": "claim-method", "statement": "We obtained the differentially expressed ferroptosis-related genes by using the “limma” package in R software, and the threshold was set to adjusted P < 0.05 and log FC > 0.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36393970", "locator": "sections[4] \"2.2. Differential Expression Analysis\" paragraph 2", "quote": "We obtained the differentially expressed ferroptosis-related genes by using the “limma” package in R software, and the threshold was set to adjusted P < 0.05 and log FC > 0.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36393970", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Analysis of GSE43292 using limma identified 21 upregulated and 12 downregulated ferroptosis-related genes in carotid atherosclerotic plaque tissue compared with control tissue.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Then using the threshold of adjusted P value <0.05 and log FC > 0.5, we obtained a total of 21 upregulated and 12 downregulated genes (Table 1)."}, "evidence": [{"asset": "source:pmid:36393970", "locator": "sections[9] \"3.1. Identification of Differentially Expressed Ferroptosis-Related Genes\" paragraph 2", "quote": "Then using the threshold of adjusted P value <0.05 and log FC > 0.5, we obtained a total of 21 upregulated and 12 downregulated genes (Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Analysis of GSE43292 using limma identified 21 upregulated and 12 downregulated ferroptosis-related genes in carotid atherosclerotic plaque tissue compared with control tissue.", "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:36393970"], "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:GSE43292"], "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:GSE43292"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36393970", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/3379883", "sha256": "sha256:029cfbd5f94c2175910722daa89e73cc4a91cc65718ef5f06c068f775c85c4ee", "bytes": 29268, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/3379883", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9663224", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE43292", "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=GSE43292", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43292", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1060117", "GSM1060118", "GSM1060119", "GSM1060120", "GSM1060121", "GSM1060122", "GSM1060123", "GSM1060124", "GSM1060125", "GSM1060126", "GSM1060127", "GSM1060128", "GSM1060129", "GSM1060130", "GSM1060131", "GSM1060132", "GSM1060133", "GSM1060134", "GSM1060135", "GSM1060136", "GSM1060137", "GSM1060138", "GSM1060139", "GSM1060140", "GSM1060141", "GSM1060142", "GSM1060143", "GSM1060144", "GSM1060145", "GSM1060146", "GSM1060147", "GSM1060148", "GSM1060149", "GSM1060150", "GSM1060151", "GSM1060152", "GSM1060153", "GSM1060154", "GSM1060155", "GSM1060156", "GSM1060157", "GSM1060158", "GSM1060159", "GSM1060160", "GSM1060161", "GSM1060162", "GSM1060163", "GSM1060164", "GSM1060165", "GSM1060166", "GSM1060167", "GSM1060168", "GSM1060169", "GSM1060170", "GSM1060171", "GSM1060172", "GSM1060173", "GSM1060174", "GSM1060175", "GSM1060176", "GSM1060177", "GSM1060178", "GSM1060179", "GSM1060180"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Genome-wide expression study of human carotid atheroma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE43292 not downloaded", "asset:data:geo:GSE43292 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We obtained the differentially expressed ferroptosis-related genes by using the “limma” package in R software, and the threshold was set to adjusted P < 0.05 and log FC > 0.5."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "Pathway Enrichment"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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