Identification of potential DNA methylation biomarkers related to diagnosis in patients with bladder cancer through integrated bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37563710", "kind": "science-record", "revision": 5, "content_hash": "sha256:41a350b9b445770171b834a127980e2f557e10262007e97f6613ca7fc4333441", "created_at": "2026-11-01T19:02:21Z", "updated_at": "2026-11-01T22:52:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential DNA methylation biomarkers related to diagnosis in patients with bladder cancer through integrated bioinformatic analysis.", "doi": "10.1186/s12894-023-01307-5", "pmid": "37563710", "authors": ["Hongxia Cheng", "Yuhua Liu", "Gang Chen"], "journal": "BMC urology", "year": 2023, "abstract": "BACKGROUND: Bladder cancer (BLCA) is one of the most common malignancies among tumors worldwide. There are no validated biomarkers to facilitate such treatment diagnosis. DNA methylation modification plays important roles in epigenetics. Identifying methylated differentially expressed genes is a common method for the discovery of biomarkers.\nMETHODS: Bladder cancer data were obtained from Gene Expression Omnibus (GEO), including the gene expression microarrays GSE37817( 18 patients and 3 normal ), GSE52519 (9 patients and 3 normal) and the gene methylation microarray GSE37816 (18 patients and 3 normal). Aberrantly expressed genes were obtained by GEO2R. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed using the DAVID database and KOBAS. Protein-protein interactions (PPIs) and hub gene networks were constructed by STRING and Cytoscape software. The validation of the results which was confirmed through four online platforms, including Gene Expression Profiling Interactive Analysis (GEPIA), Gene Set Cancer Analysis (GSCA), cBioProtal and MEXPRESS.\nRESULTS: In total, 253 and 298 upregulated genes and 674 and 454 downregulated genes were identified for GSE37817 and GSE52519, respectively. For the GSE37816 dataset, hypermethylated and hypomethylated genes involving 778 and 3420 genes, respectively, were observed. Seventeen hypermethylated and low expression genes were enriched in biological processes associated with different organ development and morphogenesis. For molecular function, these genes showed enrichment in extracellular matrix structural constituents. Pathway enrichment showed drug metabolic enzymes and several amino acids metabolism, PI3K-Akt, Hedgehog signaling pathway. The top 3 hub genes screened by Cytoscape software were EFEMP1, SPARCL1 and ABCA8. The research results were verified using the GEPIA, GSCA, cBioProtal and EXPRESS databases, and the hub hypermethylated low expression genes were validated.\nCONCLUSION: This study screened possible aberrantly methylated expression hub genes in BLCA by integrated bioinformatics analysis. The results may provide possible methylation-based biomarkers for the precise diagnosis and treatment of BLCA in the future.", "claims": [{"id": "claim-method", "statement": "Limma (Linear Models for Microarray Analysis) was a statistical test to identify differentially expressed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37563710", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "Limma (Linear Models for Microarray Analysis) was a statistical test to identify differentially expressed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during the current study are available in the GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37563710", "locator": "sections[18] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated during the current study are available in the GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using a Venn diagram, 17 hypermethylated, low-expressing genes and 8 hypomethylated, high-expressing genes were identified (Fig. 1A-B).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37563710", "locator": "sections[9] \"Identification of MeDEGs\" paragraph 2", "quote": "Using a Venn diagram, 17 hypermethylated, low-expressing genes and 8 hypomethylated, high-expressing genes were identified (Fig. 1A-B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using a Venn diagram, 17 hypermethylated, low-expressing genes and 8 hypomethylated, high-expressing genes were identified (Fig. 1A-B).", "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:37563710"], "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. 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