Bioinformatic Analysis Identifies Three Potentially Key Differentially Expressed Genes in Peripheral Blood Mononuclear Cells of Patients with Takayasu's Arteritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29105401", "kind": "science-record", "revision": 8, "content_hash": "sha256:a5f0ff0c11e75567773d9aa51a3d13c305546255ac710bdb4975a1fc1e35b10a", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:59:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic Analysis Identifies Three Potentially Key Differentially Expressed Genes in Peripheral Blood Mononuclear Cells of Patients with Takayasu's Arteritis.", "doi": "10.22074/cellj.2018.4991", "pmid": "29105401", "authors": ["Renping Huang", "Yang He", "Bei Sun", "Bing Liu"], "journal": "Cell journal", "year": 2018, "abstract": "OBJECTIVES: This study aimed to identify several potentially key genes associated with the pathogenesis of Takayasu's arteritis (TA). This identification may lead to a deeper mechanistic understanding of TA etiology and pave the way for potential therapeutic approaches.\nMATERIALS AND METHODS: In this experimental study, the microarray dataset GSE33910, which includes expression data for peripheral blood mononuclear cell (PBMC) samples isolated from TA patients and normal volunteers, was downloaded from the publicly accessible Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified in PBMCs of TA patients compared with normal controls. Gene ontology (GO) enrichment analysis of DEGs and analysis of protein-protein interaction (PPI) network were carried out. Several hub proteins were extracted from the PPI network based on node degrees and random walk algorithm. Additionally, transcription factors (TFs) were predicted and the corresponding regulatory network was constructed.\nRESULTS: A total of 932 DEGs (372 up- and 560 down-regulated genes) were identified in PBMCs from TA patients. Interestingly, up-regulated and down-regulated genes were involved in different GO terms and pathways. A PPI network of proteins encoded by DEGs was constructed and RHOA, FOS, EGR1, and GNB1 were considered to be hub proteins with both higher random walk score and node degree. A total of 13 TFs were predicted to be differentially expressed. A total of 49 DEGs had been reported to be associated with TA in the Comparative Toxicogenomics Database (CTD). The only TA marker gene in the CTD database was NOS2, confirmed by three studies. However, NOS2 was not significantly altered in the analyzed microarray dataset. Nevertheless, NOS3 was a significantly down-regulated gene and was involved in the platelet activation pathway.\nCONCLUSIONS: RHOA, FOS, and EGR1 are potential candidate genes for the diagnosis and therapy of TA.", "claims": [{"id": "claim-method", "statement": "The P values of an unpaired Student’s t test (13) with the matrix of gene expression values as the response variable was used to evaluate significance of differential expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29105401", "locator": "sections[3] \"Data preprocessing and screening of differentially expressed genes\" paragraph 2", "quote": "The P values of an unpaired Student’s t test (13) with the matrix of gene expression values as the response variable was used to evaluate significance of differential expression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this experimental study, the gene expression dataset GSE33910 deposited by Okuzaki et al. (9) was downloaded from the publicly accessible Gene Expression Omnibus (GEO) database (http://www.ncbi. nlm.nih.gov/geo/) (10). Expression data were generated on a GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F. A total of 8 two-color arrays were included and each individual array comprised a target sample (Cy5-labeled) and a control sample (Cy3- labeled). The target samples were derived from PBMCs isolated from eight TA patients who were diagnosed as TA. All RNA samples isolated from the PBMCs of 17 healthy normal volunteers were included as control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29105401", "locator": "sections[2] \"Materials and Methods\" paragraph 2", "quote": "In this experimental study, the gene expression dataset GSE33910 deposited by Okuzaki et al. (9) was downloaded from the publicly accessible Gene Expression Omnibus (GEO) database (http://www.ncbi. nlm.nih.gov/geo/) (10). Expression data were generated on a GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F. A total of 8 two-color arrays were included and each individual array comprised a target sample (Cy5-labeled) and a control sample (Cy3- labeled). The target samples were derived from PBMCs isolated from eight TA patients who were diagnosed as TA. All RNA samples isolated from the PBMCs of 17 healthy normal volunteers were included as control samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:29105401"], "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:GSE33910"], "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:GSE33910"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29105401", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.22074/cellj.2018.4991", "sha256": "sha256:8553e8d0e1afb2f9c512c9870a9eb337d9faf72aab7aaa32ca428ca66846061f", "bytes": 26201, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.22074/cellj.2018.4991", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5672105", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33910", "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=GSE33910", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33910", "version": null, "note": "In this experimental study, the gene expression dataset GSE33910 deposited by Okuzaki et al. (9) was downloaded from the publicly accessible Gene Expression Omnibus (GEO) database (http://www.ncbi. nlm.nih.gov/geo/) (10). Expression data were generated on a GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F. A total of 8 two-color arrays were included and each individual array comprised a target sample (Cy5-labeled) and a control sample (Cy3- labeled). The target samples were derived from PBMCs isolated from eight TA patients who were diagnosed as TA. All RNA samples isolated from the PBMCs of 17 healthy normal volunteers were included as control samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In this experimental study, the gene expression dataset GSE33910 deposited by Okuzaki et al. (9) was downloaded from the publicly accessible Gene Expression Omnibus (GEO) database (http://www.ncbi. nlm.nih.gov/geo/) (10). Expression data were generated on a GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F. A total of 8 two-color arrays were included and each individual array comprised a target sample (Cy5-labeled) and a control sample (Cy3- labeled). The target samples were derived from PBMCs isolated from eight TA patients who were diagnosed as TA. 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"numeric_cells": 40, "header_rows": 0, "locator": "section[11]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:29105401:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5bcb1d63c792336934bf33f69248a4609b29bb5636a2b2d847890f53681e4f4c", "bytes": 593, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T4", "version": null, "note": "DEGs associated with TA in the CTD database", "structure": {"pmcid": "PMC5672105", "section_index": 11, "section_title": "Transcriptional regulation network analysis and prediction of Takayasu’s arteritis-associated genes", "row_count": 6, "column_count": 2}, "table": {"label": "Table 4", "caption": "DEGs associated with TA in the CTD database", "rows": [[""], ["Expression change", "TA gene"], [""], ["Up", "DNPH1, ILVBL, CRAT, TNFSF13, ARAP2, PGD, IMPA2, TIMM10B, PSMB9, PSMB8, DCTPP1, PSMB3, SRXN1, OAT, 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"nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE33910"], "resolved_accessions": ["GSE33910"], "statements": ["In this experimental study, the gene expression dataset GSE33910 deposited by Okuzaki et al. (9) was downloaded from the publicly accessible Gene Expression Omnibus (GEO) database (http://www.ncbi. nlm.nih.gov/geo/) (10). Expression data were generated on a GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F. A total of 8 two-color arrays were included and each individual array comprised a target sample (Cy5-labeled) and a control sample (Cy3- labeled). The target samples were derived from PBMCs isolated from eight TA patients who were diagnosed as TA. All RNA samples isolated from the PBMCs of 17 healthy normal volunteers were included as control samples."], "basis": "The paper names GSE33910 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:29105401", "data:geo:GSE33910", "asset:table:pmid:29105401:1", "asset:table:pmid:29105401:2", "asset:table:pmid:29105401:3", "asset:table:pmid:29105401:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE33910"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:10:28Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 21356, "completion_tokens": 1231, "cached_tokens": 784}}, "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:29105401", "type": "paper", "label": "pmid:29105401"}, {"id": "source:pmid:29105401", "type": "manuscript", "label": "PMID 29105401 full text"}, {"id": "data:geo:GSE33910", "type": "dataset", "label": "GEO GSE33910"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29105401", "type": "paper", "label": "pmid:29105401"}, {"id": "source:pmid:29105401", "type": "manuscript", "label": "PMID 29105401 full text"}, {"id": "data:geo:GSE33910", "type": "dataset", "label": "GEO GSE33910"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29105401", "type": "extraction", "used": ["source:pmid:29105401"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE33910", "type": "accession_resolution", "used": ["data:geo:GSE33910"], "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:29105401", "parent_hash": "sha256:0774d52d305b619a8758f3cb75444fc099f9cb8dbdab712aeb797b8fb208df81", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE33910 licence not read", "asset:data:geo:GSE33910 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.99, "evidence": ["AND METHODS: In this experimental study, the microarray dataset GSE33910, which includes expression", "as not significantly altered in the analyzed microarray dataset. 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