Identifying Obstructive Sleep Apnea Syndrome-Associated Genes and Pathways through Weighted Gene Coexpression Network Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35132330", "kind": "science-record", "revision": 5, "content_hash": "sha256:7c70eb361dfd320af64084a725c4e8539e43c05667c96e782af821787079d940", "created_at": "2026-11-01T17:36:53Z", "updated_at": "2026-11-01T22:05:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying Obstructive Sleep Apnea Syndrome-Associated Genes and Pathways through Weighted Gene Coexpression Network Analysis.", "doi": "10.1155/2022/3993509", "pmid": "35132330", "authors": ["Yan Li", "Li Li", "Hua Zhao", "Xiwen Gao", "Shanqun Li"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "BACKGROUND: Obstructive sleep apnea syndrome (OSAS) is the most common type of sleep apnea disorder. The disease seriously affects the patient's respiratory system. At present, the prognosis of the disease is poor and there is a lack of effective treatments. Therefore, it is urgent to explore its pathogenesis and treatment methods.\nMETHOD: We downloaded a set of expression profile data from GSE75097 related to OSAS based on the Gene Expression Omnibus (GEO) database and selected the representative differentially expressed genes (DEGs) from the sample of the GSE75097 dataset. WGCNA was used to find genes related to OSAS and obtain coexpression modules. The Gene Ontology (GO) function and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to analyze genes from key modules. Finally, Cytoscape software was used to construct a protein-protein interaction (PPI) network and analyze the hub genes.\nRESULT: We obtained a total of 7565 DEGs. Through WGCNA, we got four coexpression modules and the modules most related to OSAS were green-yellow, magenta, purple, and turquoise, and we screened out eight hub genes (DDX46, RNF115, COPA, FBXO4, PA2G4, NHP2L1, CDC20, and PCNA). GO and KEGG analyses indicated that the key modules were mainly enriched in tRNA modification, nucleobase metabolic process, DNA ligation, regulation of cellular component movement, basal transcription factors, Huntington disease, and vitamin digestion and absorption.\nCONCLUSION: These pathways and hub genes can facilitate understanding the molecular mechanism of OSAS and provide a meaningful reference for finding biological targets of OSAS treatment.", "claims": [{"id": "claim-method", "statement": "WGCNA was used to find genes related to OSAS and obtain coexpression modules.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35132330", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "WGCNA was used to find genes related to OSAS and obtain coexpression modules."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data analyzed during this study are obtained from published article or are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35132330", "locator": "sections[15] \"Data Availability\" paragraph 2", "quote": "All data analyzed during this study are obtained from published article or are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "WGCNA identified four OSAS-related coexpression modules and eight hub genes from 7,565 DEGs in the 48-sample GSE75097 dataset.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35132330", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We obtained a total of 7565 DEGs. Through WGCNA, we got four coexpression modules and the modules most related to OSAS were green-yellow, magenta, purple, and turquoise, and we screened out eight hub genes (DDX46, RNF115, COPA, FBXO4, PA2G4, NHP2L1, CDC20, and PCNA)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "WGCNA identified four OSAS-related coexpression modules and eight hub genes from 7,565 DEGs in the 48-sample GSE75097 dataset.", "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:35132330"], "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:GSE75097"], "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:GSE75097"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35132330", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/3993509", "sha256": "sha256:119b74c4f8567c7db8e217aa9ac4f1a43e8fd937f2d52c66f7b521fc06827587", "bytes": 19215, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/3993509", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8817882", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE75097", "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=GSE75097", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75097", "version": null, "note": "All data analyzed during this study are obtained from published article or are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data analyzed during this study are obtained from published article or are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1942590", "GSM1942591", "GSM1942592", "GSM1942593", "GSM1942594", "GSM1942595", "GSM1942596", "GSM1942597", "GSM1942598", "GSM1942599", "GSM1942600", "GSM1942601", "GSM1942602", "GSM1942603", "GSM1942604", "GSM1942605", "GSM1942606", "GSM1942607", "GSM1942608", "GSM1942609", "GSM1942610", "GSM1942611", "GSM1942612", "GSM1942613", "GSM1942614", "GSM1942615", "GSM1942616", "GSM1942617", "GSM1942618", "GSM1942619", "GSM1942620", "GSM1942621", "GSM1942622", "GSM1942623", "GSM1942624", "GSM1942625", "GSM1942626", "GSM1942627", "GSM1942628", "GSM1942629", "GSM1942630", "GSM1942631", "GSM1942632", "GSM1942633", "GSM1942634", "GSM1942635", "GSM1942636", "GSM1942637"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "10904", "taxon": "Homo sapiens", "title": "Microarray gene expression profiles of peripheral blood mononuclear cells (PBMC) in patients with  obstructive sleep apnea and primary snoring", "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:GSE75097 not downloaded", "asset:data:geo:GSE75097 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "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": "GO Enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "weighted gene coexpression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "WGCNA was used to find genes related to OSAS and obtain coexpression modules."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["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. 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