Identification of key differential genes in intimal hyperplasia induced by left carotid artery ligation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35586138", "kind": "science-record", "revision": 5, "content_hash": "sha256:06405b8aa44ae0ba5ac11958a5a59a4cc175270c8b6987613ee0ea466afb5076", "created_at": "2026-11-01T18:14:29Z", "updated_at": "2026-11-01T22:49:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key differential genes in intimal hyperplasia induced by left carotid artery ligation.", "doi": "10.7717/peerj.13436", "pmid": "35586138", "authors": ["Lina Zhang", "Jianjun Gu", "Sichuan Wang", "Fuming He", "Kaizheng Gong"], "journal": "PeerJ", "year": 2022, "abstract": "Background: Intimal hyperplasia is a common pathological process of restenosis following angioplasty, atherosclerosis, pulmonary hypertension, vein graft stenosis, and other proliferative diseases. This study aims to screen for potential novel gene targets and mechanisms related to vascular intimal hyperplasia through an integrated microarray analysis of the Gene Expression Omnibus Database (GEO) database.\nMaterial and Methods: The gene expression profile of the GSE56143 dataset was downloaded from the Gene Expression Omnibus database. Functional enrichment analysis, protein-protein interaction (PPI) network analysis, and the transcription factor (TF)-target gene regulatory network were used to reveal the biological functions of differential genes (DEGs). Furthermore, the expression levels of the top 10 key DEGs were verified at the mRNA and protein level in the carotid artery 7 days after ligation.\nResults: A total of 373 DEGs (199 upregulated DEGs and 174 downregulated DEGs) were screened. These DEGs were significantly enriched in biological processes, including immune system process, cell adhesion, and several pathways, which were mainly associated with cell adhesion molecules and the regulation of the actin cytoskeleton. The top 10 key DEGs (Ptprc, Fn1, Tyrobp, Emr1, Itgb2, Itgax, CD44, Ctss, Ly86, and Aif1) acted as key genes in the PPI network. The verification of these key DEGs at the mRNA and protein levels was consistent with the results of the above-mentioned bioinformatics analysis.\nConclusion: The present study identified key genes and pathways involved in intimal hyperplasia induced by carotid artery ligation. These results improved our understanding of the mechanisms underlying the development of intimal hyperplasia and provided candidate targets.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis of LCA vs. RCA was performed on the samples using the classical Bayesian test in the limma package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35586138", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "Differential expression analysis of LCA vs. RCA was performed on the samples using the classical Bayesian test in the limma package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data is available in NCBI GEO: GES56143 and the original measured values are available in the Supplemental File.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35586138", "locator": "sections[23] \"Additional Information and Declarations\" paragraph 5", "quote": "The data is available in NCBI GEO: GES56143 and the original measured values are available in the Supplemental File."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 373 DEGs (199 upregulated DEGs and 174 downregulated DEGs) were screened.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35586138", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 373 DEGs (199 upregulated DEGs and 174 downregulated DEGs) were screened."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 373 DEGs (199 upregulated DEGs and 174 downregulated DEGs) were screened.", "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:35586138"], "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:GSE56143"], "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:GSE56143"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35586138", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.13436", "sha256": "sha256:109d8828f4ddb80c7ef38590229392d371647e750f426b6702e7c6834c2cdf5e", "bytes": 35460, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.13436", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9109685", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE56143", "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=GSE56143", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE56143", "version": null, "note": "The data is available in NCBI GEO: GES56143 and the original measured values are available in the Supplemental File.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data is available in NCBI GEO: GES56143 and the original measured values are available in the Supplemental File.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1356640", "GSM1356641", "GSM1356642", "GSM1356643", "GSM1356644", "GSM1356645", "GSM1356646", "GSM1356647", "GSM1356648", "GSM1356649", "GSM1356650", "GSM1356651"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "6887", "taxon": "Mus musculus", "title": "Identification of mechano- and/or 5Aza-sensitive genes in mouse carotid artery endothelium in vivo exposed to disturbed blood flow for 7 days", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE56143 not downloaded", "asset:data:geo:GSE56143 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": "Differential expression analysis of LCA vs. RCA was performed on the samples using the classical Bayesian test in the limma package."}}, {"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"}}], "targets": [], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE56143"], "resolved_accessions": ["GSE56143"], "statements": ["The data is available in NCBI GEO: GES56143 and the original measured values are available in the Supplemental File."], "basis": "The paper names GSE56143 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35586138", "data:geo:GSE56143"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE56143"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:46:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10006, "completion_tokens": 954, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35586138", "type": "paper", "label": "pmid:35586138"}, {"id": "source:pmid:35586138", "type": "manuscript", "label": "PMID 35586138 full text"}, {"id": "data:geo:GSE56143", "type": "dataset", "label": "GEO GSE56143"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35586138", "type": "paper", "label": "pmid:35586138"}, {"id": "source:pmid:35586138", "type": "manuscript", "label": "PMID 35586138 full text"}, {"id": "data:geo:GSE56143", "type": "dataset", "label": "GEO GSE56143"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35586138", "type": "extraction", "used": ["source:pmid:35586138"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE56143", "type": "accession_resolution", "used": ["data:geo:GSE56143"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35586138", "parent_hash": "sha256:08b6e995acf0041780e5491308c62ac95e2135b18c977b8222f0d79d2c1c1a95", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE56143 licence not read", "asset:data:geo:GSE56143 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ar intimal hyperplasia through an integrated microarray analysis of the Gene Expression Omnibus Data"], "order_basis": "paper_text_order:394", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["f Yangzhou University (Yangzhou, China). The mice were kept at a constant temperature (24 ± 1 °C),", "6:00 am to 6:00 pm), and were fed a standard mouse pellet diet ad libitum. All protocols in thi"], "order_basis": "paper_text_order:2094", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differential expression analysis of LCA vs. RCA was performed on the samples using the classical Bayesian test in the limma package."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}