Identification of hub genes and pathophysiological mechanism related to acute unilateral vestibulopathy by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36237611", "kind": "science-record", "revision": 5, "content_hash": "sha256:00cd36f014daa9de3ada48b5af67eb9ad454ba818d296ff7dee275ef6111d379", "created_at": "2026-11-01T18:15:36Z", "updated_at": "2026-11-01T22:50:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and pathophysiological mechanism related to acute unilateral vestibulopathy by integrated bioinformatics analysis.", "doi": "10.3389/fneur.2022.987076", "pmid": "36237611", "authors": ["Yajing Cheng", "Jianrong Zheng", "Ying Zhan", "Cong Liu", "Bihua Lu", "Jun Hu"], "journal": "Frontiers in neurology", "year": 2022, "abstract": "Background: Although many pathological mechanisms and etiological hypotheses of acute unilateral vestibulopathy (AUVP) have been reported, but the actual etiology remains to be elucidated.\nObjective: This study was based on comprehensive bioinformatics to identify the critical genes of AUVP and explore its pathological mechanism.\nMethods: Gene expression profiles of AUVP and normal samples were collected from GSE146230 datasets of the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was constructed, and the WGCNA R-package extracted significant modules. The limma R-package was applied to identify differentially expressed genes (DEGs). The common genes of practical modules and DEGs were screened for GO and KEGG pathways analysis. The protein-protein interaction (PPI) layout and hub genes validation was created by Cytoscape software using the link from the STRING database. The functions of hub genes were predicted through the CTD (comparative genetics database).\nResults: A total of 332 common genes were screened from practical modules and DEGs. Functional enrichment analysis revealed that these genes were predominantly associated with inflammation and infection. After construction of PPI, expressions of hub genes, and drawing ROC curves, LILRB2, FPR1, AQP9, and LILRA1 are highly expressed in AUVP (p < 0.05) and have a certain diagnostic efficacy for AUVP (AUC > 0.7), so they were selected as hub genes. The functions of hub genes suggested that the occurrence of AUVP may be related to inflammation, necrosis, hepatomegaly, and other conditions in CTD.\nConclusion: LILRB2, FPR1, AQP9, and LILRA1 may play essential roles in developing AUVP, providing new ideas for diagnosing and treating AUVP.", "claims": [{"id": "claim-method", "statement": "The DEGs between patients with AUVP and control samples were screened by the R language “Limma” package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36237611", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "The DEGs between patients with AUVP and control samples were screened by the R language “Limma” package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36237611", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "LILRB2, FPR1, AQP9, and LILRA1 were identified as hub genes that were highly expressed in AUVP and showed diagnostic efficacy for AUVP.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "LILRB2, FPR1, AQP9, and LILRA1 are highly expressed in AUVP (p < 0.05) and have a certain diagnostic efficacy for AUVP (AUC > 0.7), so they were selected as hub genes."}, "evidence": [{"asset": "source:pmid:36237611", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "LILRB2, FPR1, AQP9, and LILRA1 are highly expressed in AUVP (p < 0.05) and have a certain diagnostic efficacy for AUVP (AUC > 0.7), so they were selected as hub genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "LILRB2, FPR1, AQP9, and LILRA1 were identified as hub genes that were highly expressed in AUVP and showed diagnostic efficacy for AUVP.", "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:36237611"], "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:GSE146230"], "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:GSE146230"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36237611", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2022.987076", "sha256": "sha256:8cfa1ea6fb663adf09afc2a5fe506e2ab74bacf7b4dd2e90a9d91d265ee23f82", "bytes": 33327, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fneur.2022.987076", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9552803", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE146230", "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=GSE146230", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE146230", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4368576", "GSM4368577", "GSM4368578", "GSM4368579", "GSM4368580", "GSM4368581", "GSM4368582", "GSM4368583", "GSM4368584", "GSM4368585", "GSM4368586", "GSM4368587", "GSM4368588", "GSM4368589", "GSM4368590", "GSM4368591", "GSM4368592", "GSM4368593", "GSM4368594", "GSM4368595"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "23159", "taxon": "Homo sapiens", "title": "Neutrophil-mediated immune response as a possible mechanism of acute unilateral vestibulopathy", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE146230 not downloaded", "asset:data:geo:GSE146230 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": "The DEGs between patients with AUVP and control samples were screened by the R language “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"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE146230"], "resolved_accessions": ["GSE146230"], "statements": ["The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE146230 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:36237611", "data:geo:GSE146230"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE146230"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:10:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9441, "completion_tokens": 1020, "cached_tokens": 264}}, "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:36237611", "type": "paper", "label": "pmid:36237611"}, {"id": "source:pmid:36237611", "type": "manuscript", "label": "PMID 36237611 full text"}, {"id": "data:geo:GSE146230", "type": "dataset", "label": "GEO GSE146230"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36237611", "type": "paper", "label": "pmid:36237611"}, {"id": "source:pmid:36237611", "type": "manuscript", "label": "PMID 36237611 full text"}, {"id": "data:geo:GSE146230", "type": "dataset", "label": "GEO GSE146230"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36237611", "type": "extraction", "used": ["source:pmid:36237611"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE146230", "type": "accession_resolution", "used": ["data:geo:GSE146230"], "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:36237611", "parent_hash": "sha256:32c58cc6e5d53c9d7f3e1a42bc12cbe42b1d2bb53e08ca5c7ca65b31c20a9605", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE146230 licence not read", "asset:data:geo:GSE146230 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["The DEGs between patients with AUVP and control samples were screened by the R language “Limma” package."], "order_basis": "analysis_only", "id": "assay:1"}]}