Identification of Susceptibility Modules and Genes for Cardiovascular Disease in Diabetic Patients Using WGCNA Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32455133", "kind": "science-record", "revision": 6, "content_hash": "sha256:90a58cbff9a5fd8de663cf0036b7a2c93ddb90909978589436dfbba5a45a157f", "created_at": "2026-11-01T15:41:02Z", "updated_at": "2026-11-01T21:23:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Susceptibility Modules and Genes for Cardiovascular Disease in Diabetic Patients Using WGCNA Analysis.", "doi": "10.1155/2020/4178639", "pmid": "32455133", "authors": ["Weiwei Liang", "Fangfang Sun", "Yiming Zhao", "Lizhen Shan", "Hanyu Lou"], "journal": "Journal of diabetes research", "year": 2020, "abstract": "OBJECTIVE: To identify susceptibility modules and genes for cardiovascular disease in diabetic patients using weighted gene coexpression network analysis (WGCNA).\nMETHODS: The raw data of GSE13760 were downloaded from the Gene Expression Omnibus (GEO) website. Genes with a false discovery rate < 0.05 and a log2 fold change ≥ 0.5 were included in the analysis. WGCNA was used to build a gene coexpression network, screen important modules, and filter the hub genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for the genes in modules with clinical interest. Genes with a significance over 0.2 and a module membership over 0.8 were used as hub genes. Subsequently, we screened these hub genes in the published genome-wide SNP data of cardiovascular disease. The overlapped genes were defined as key genes.\nRESULTS: Fourteen gene coexpression modules were constructed via WGCNA analysis. Module greenyellow was mostly significantly correlated with diabetes. The GO analysis showed that genes in the module greenyellow were mainly enriched in extracellular matrix organization, extracellular exosome, and calcium ion binding. The KEGG analysis showed that the genes in the module greenyellow were mainly enriched in antigen processing and presentation, phagosome. Fifteen genes were identified as hub genes. Finally, HLA-DRB1, LRP1, and MMP2 were identified as key genes.\nCONCLUSION: This was the first study that used the WGCNA method to construct a coexpression network to explore diabetes-associated susceptibility modules and genes for cardiovascular disease. Our study identified a module and several key genes that acted as essential components in the etiology of diabetes-associated cardiovascular disease, which may enhance our fundamental knowledge of the molecular mechanisms underlying this disease.", "claims": [{"id": "claim-method", "statement": "A classical t-test was performed to compare the differences in the expression of key genes between the two groups using a P value < 0.05 to indicate statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32455133", "locator": "sections[7] \"2.5. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13760"], "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:GSE13760"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32455133", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/4178639", "sha256": "sha256:86ab0f468c9730e2558557b1c748404a392be28ae58b8817ed6701c33ee5ea6f", "bytes": 32572, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/4178639", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7238331", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13760", "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=GSE13760", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13760", "version": null, "note": "The raw data used to support the findings of this study are freely available from GEO datasets GSE13760.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data used to support the findings of this study are freely available from GEO datasets GSE13760.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM346560", "GSM346561", "GSM346563", "GSM346565", "GSM346566", "GSM346568", "GSM346570", "GSM346572", "GSM346573", "GSM346575", "GSM346576", "GSM346578", "GSM346579", "GSM346581", "GSM346582", "GSM346584", "GSM346585", "GSM346586", "GSM346587", "GSM346588", "GSM346589"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Gene expression profiling in arterial tissue from type 2 diabetic patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32455133:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2634c088daf22edb15ca189b9c8d76a6376aa04c7697cfba93efaffe2553b437", "bytes": 693, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab1", "version": null, "note": "Hub genes of the module greenyellow. 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Hub genes were defined as having a gene significance over 0.2 and a module membership over 0.8.", "rows": [["Gene", "Gene significance", "Module membership"], ["SEPT11", "0.39", "0.88"], ["AKR1C1", "0.43", "0.89"], ["CD74", "0.25", "0.89"], ["CST3", "0.37", "0.88"], ["DCN", "0.37", "0.86"], ["FBLN1", "0.51", "0.88"], ["HLA-DRB1", "0.22", "0.83"], ["LRP1", "0.50", "0.82"], ["MMP2", "0.39", "0.92"], ["MRC2", "0.23", "0.82"], ["NPC2", "0.21", "0.85"], ["PCDHGA1", "0.44", "0.80"], ["PRELP", "0.55", "0.84"], ["SPTBN1", "0.42", "0.81"], ["TGFBR2", "0.23", "0.88"]], "row_count": 16, "column_count": 3, "numeric_cells": 32, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tab1"}}], "gaps": ["asset:data:geo:GSE13760 not downloaded", "asset:data:geo:GSE13760 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}, {"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": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "classical t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A classical t-test was performed to compare the differences in the expression of key genes between the two groups using a P value < 0.05 to indicate statistical significance."}}], "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": ["hierarchical_cluster"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: hierarchical."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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