Integrated bioinformatics approach reveals methylation-regulated differentially expressed genes in obesity.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37252693", "kind": "science-record", "revision": 3, "content_hash": "sha256:889080524661127f4c7f560078137d5b4fe3b84151909918b3c09bd7e650078d", "created_at": "2026-11-01T19:01:58Z", "updated_at": "2026-11-01T22:09:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics approach reveals methylation-regulated differentially expressed genes in obesity.", "doi": "10.20945/2359-3997000000604", "pmid": "37252693", "authors": ["Guilherme Coutinho Kullmann Duarte", "Felipe Pellenz", "Daisy Crispim", "Tais Silveira Assmann"], "journal": "Archives of endocrinology and metabolism", "year": 2023, "abstract": "Objective: To identify DNA methylation and gene expression profiles involved in obesity by implementing an integrated bioinformatics approach.\nMaterials and methods: Gene expression (GSE94752, GSE55200, and GSE48964) and DNA methylation (GSE67024 and GSE111632) datasets were obtained from the GEO database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in subcutaneous adipose tissue of patients with obesity were identified using GEO2R. Methylation-regulated DEGs (MeDEGs) were identified by overlapping DEGs and DMGs. The protein-protein interaction (PPI) network was constructed with the STRING database and analyzed using Cytoscape. Functional modules and hub-bottleneck genes were identified by using MCODE and CytoHubba plugins. Functional enrichment analyses were performed based on Gene Ontology terms and KEGG pathways. To prioritize and identify candidate genes for obesity, MeDEGs were compared with obesity-related genes available at the DisGeNET database.\nResults: A total of 54 MeDEGs were identified after overlapping the lists of significant 274 DEGs and 11,556 DMGs. Of these, 25 were hypermethylated-low expression genes and 29 were hypomethylated-high expression genes. The PPI network showed three hub-bottleneck genes (PTGS2, TNFAIP3, and FBXL20) and one functional module. The 54 MeDEGs were mainly involved in the regulation of fibroblast growth factor production, the molecular function of arachidonic acid, and ubiquitin-protein transferase activity. Data collected from DisGeNET showed that 11 of the 54 MeDEGs were involved in obesity.\nConclusion: This study identifies new MeDEGs involved in obesity and assessed their related pathways and functions. These results data may provide a deeper understanding of methylation-mediated regulatory mechanisms of obesity.", "claims": [{"id": "claim-method", "statement": "DEGs were defined based on an absolute log2-Fold Change (log FC) > 2.0 and P < 0.05. To identify DMGs, |t|>2 and P < 0.05 were used as cutoff points.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37252693", "locator": "sections[4] \"Data processing\" paragraph 3", "quote": "DEGs were defined based on an absolute log2-Fold Change (log FC) > 2.0 and P < 0.05. To identify DMGs, |t|>2 and P < 0.05 were used as cutoff points."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Ethical approval: this study used anonymized publicly available data, including GSE94752, GSE55200, GSE48964, GSE67024, and GSE111632 (further information on the approval by the Research Ethics Committees is available at: https://www.ncbi.nlm.nih.gov/geo/ ).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37252693", "locator": "sections[16] \"Footnotes\" paragraph 2", "quote": "Ethical approval: this study used anonymized publicly available data, including GSE94752, GSE55200, GSE48964, GSE67024, and GSE111632 (further information on the approval by the Research Ethics Committees is available at: https://www.ncbi.nlm.nih.gov/geo/ )."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 54 methylation-regulated differentially expressed genes in obesity, including 25 hypermethylated-low-expression genes and 29 hypomethylated-high-expression genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37252693", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 54 MeDEGs were identified after overlapping the lists of significant 274 DEGs and 11,556 DMGs. Of these, 25 were hypermethylated-low expression genes and 29 were hypomethylated-high expression genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 54 methylation-regulated differentially expressed genes in obesity, including 25 hypermethylated-low-expression genes and 29 hypomethylated-high-expression 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:37252693"], "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:GSE111632"], "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:GSE111632"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37252693", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.20945/2359-3997000000604", "sha256": 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