Construction of the coexpression network involved in the pathogenesis of thyroid eye disease via bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36076300", "kind": "science-record", "revision": 4, "content_hash": "sha256:7bd1262eae52c1c7b1c546deec5bb09026e32f1212870d5336b2cfb019873762", "created_at": "2026-11-01T18:15:17Z", "updated_at": "2026-11-01T22:07:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of the coexpression network involved in the pathogenesis of thyroid eye disease via bioinformatics analysis.", "doi": "10.1186/s40246-022-00412-0", "pmid": "36076300", "authors": ["Jinxing Hu", "Shan Zhou", "Weiying Guo"], "journal": "Human genomics", "year": 2022, "abstract": "BACKGROUND: Thyroid eye disease (TED) is the most common orbital pathology that occurs in up to 50% of patients with Graves' disease. Herein, we aimed at discovering the possible hub genes and pathways involved in TED based on bioinformatical approaches.\nRESULTS: The GSE105149 and GSE58331 datasets were downloaded from the Gene Expression Omnibus (GEO) database and merged for identifying TED-associated modules by weighted gene coexpression network analysis (WGCNA) and local maximal quasi-clique merger (lmQCM) analysis. EdgeR was run to screen differentially expressed genes (DEGs). Transcription factor (TF), microRNA (miR) and drug prediction analyses were performed using ToppGene suite. Function enrichment analysis was used to investigate the biological function of genes. Protein-protein interaction (PPI) analysis was performed based on the intersection between the list of genes obtained by WGCNA, lmQCM and DEGs, and hub genes were identified using the MCODE plugin. Based on the overlap of 497 genes retrieved from the different approaches, a robust TED coexpression network was constructed and 11 genes (ATP6V1A, PTGES3, PSMD12, PSMA4, METAP2, DNAJA1, PSMA1, UBQLN1, CCT2, VBP1 and NAA50) were identified as hub genes. Key TFs regulating genes in the TED-associated coexpression network, including NFRKB, ZNF711, ZNF407 and MORC2, and miRs including hsa-miR-144, hsa-miR-3662, hsa-miR-12136 and hsa-miR-3646, were identified. Genes in the coexpression network were enriched in the biological processes including proteasomal protein catabolic process and proteasome-mediated ubiquitin-dependent protein catabolic process and the pathways of endocytosis and ubiquitin-mediated proteolysis. Drugs perturbing genes in the coexpression network were also predicted and included enzyme inhibitors, chlorodiphenyl and finasteride.\nCONCLUSIONS: For the first time, TED-associated coexpression network was constructed and key genes and their functions, as well as TFs, miRs and drugs, were predicted. The results of the present work may be relevant in the treatment and diagnosis of TED and may boost molecular studies regarding TED.", "claims": [{"id": "claim-method", "statement": "The differential expression analysis based on the merged matrix was performed by “limma” package in R with the threshold of |log2FC|> 0.263 and adj. p value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36076300", "locator": "sections[12] \"Identification of DEGs\" paragraph 2", "quote": "The differential expression analysis based on the merged matrix was performed by “limma” package in R with the threshold of |log2FC|> 0.263 and adj. p value < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36076300", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Based on the overlap of 497 genes retrieved from the different approaches, a robust TED coexpression network was constructed and 11 genes (ATP6V1A, PTGES3, PSMD12, PSMA4, METAP2, DNAJA1, PSMA1, UBQLN1, CCT2, VBP1 and NAA50) were identified as hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36076300", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Based on the overlap of 497 genes retrieved from the different approaches, a robust TED coexpression network was constructed and 11 genes (ATP6V1A, PTGES3, PSMD12, PSMA4, METAP2, DNAJA1, PSMA1, UBQLN1, CCT2, VBP1 and NAA50) were identified as hub genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Based on the overlap of 497 genes retrieved from the different approaches, a robust TED coexpression network was constructed and 11 genes (ATP6V1A, PTGES3, PSMD12, PSMA4, METAP2, DNAJA1, PSMA1, UBQLN1, CCT2, VBP1 and NAA50) were identified as hub genes.", "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:36076300"], "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:GSE105149"], "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:GSE105149"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36076300", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40246-022-00412-0", "sha256": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36076300", "data:geo:GSE105149"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE105149"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:04:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15131, "completion_tokens": 1656, "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:36076300", "type": "paper", "label": "pmid:36076300"}, {"id": "source:pmid:36076300", "type": "manuscript", "label": "PMID 36076300 full text"}, {"id": "data:geo:GSE105149", "type": "dataset", "label": "GEO GSE105149"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36076300", "type": "paper", "label": "pmid:36076300"}, {"id": "source:pmid:36076300", "type": "manuscript", "label": "PMID 36076300 full text"}, {"id": "data:geo:GSE105149", "type": "dataset", "label": "GEO GSE105149"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36076300", "type": "extraction", "used": ["source:pmid:36076300"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE105149", "type": "accession_resolution", "used": ["data:geo:GSE105149"], "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:36076300", "parent_hash": "sha256:0c66f0492697cf160b7d73f355005078ceb64a6b336323408e97317ba0264f7c", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE105149 licence not read", "asset:data:geo:GSE105149 not downloaded", "asset:data:geo:GSE58331 licence not read", "asset:data:geo:GSE58331 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.7, "evidence": ["EdgeR"], "order_basis": "analysis_only", "id": "assay:1"}]}