Methylation-related differentially expressed genes as potential prognostic biomarkers for cervical cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39263148", "kind": "science-record", "revision": 3, "content_hash": "sha256:1a21dd3a47ac506422f1dff8a8540d6c85557a7f224c5ae0b9f0932ded765d24", "created_at": "2026-11-01T20:29:25Z", "updated_at": "2026-11-01T22:12:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Methylation-related differentially expressed genes as potential prognostic biomarkers for cervical cancer.", "doi": "10.1016/j.heliyon.2024.e36240", "pmid": "39263148", "authors": ["Yili Chen", "Qiaojian Zou", "Qianrun Chen", "Shuyi Wang", "Qiqiao Du", "Qiuwen Mai", "Xiaojun Wang", "Xiaoying Lin", "Liu Du", "Shuzhong Yao", "Junxiu Liu"], "journal": "Heliyon", "year": 2024, "abstract": "Aim: To discover novel methylation-related differentially expressed genes (MRDEGs) for cervical cancer, with a focus on their potential for early diagnosis and prognostic assessment.\nMaterials & methods: We integrated data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. TCGA-MRDEGs were identified by analyzing differentially methylated genes (DMGs) and their correlation with gene expression. We examined GEO datasets GSE39001, GSE9750, and GSE46306 for GEO-MRDEGs. Overlapping MRDEGs were subjected to overall survival (OS) analysis to identify prognostic markers. The expression and methylation levels of these genes were validated in a total of 30 tissue samples, comprising 20 from cervical cancer patients and 10 from normal cervical tissues, using qRT-PCR and MassARRAY EpiTYPER Assay.\nResults: A total of 314 TCGA-MRDEGs and 40 GEO-MRDEGs were identified. Intersection analysis yielded 10 overlapping MRDEGs. Notably, NOVA1, GSTM5, TRHDE, and CXCL12 were found to have reduced expression and increased methylation in cervical cancer, which correlated with poor prognosis. The methylation status and expression levels of these genes were confirmed in tissue specimens.\nConclusion: We identified four MRDEGs as potential prognostic biomarkers for cervical cancer. Their clinical utility is highlighted, but further validation in larger cohorts is required to establish their clinical significance.", "claims": [{"id": "claim-method", "statement": "The OS analysis of overlapping MRDEGs was conducted using the Kaplan‐Meier (KM) plotter (http://kmplot.com/analysis/index.php) [20], which contained 304 patients with cervical squamous cell carcinoma from the TCGA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39263148", "locator": "sections[6] \"Overall survival (OS) analysis\" paragraph 2", "quote": "The OS analysis of overlapping MRDEGs was conducted using the Kaplan‐Meier (KM) plotter (http://kmplot.com/analysis/index.php) [20], which contained 304 patients with cervical squamous cell carcinoma from the TCGA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data included in article/supp. material/referenced in article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39263148", "locator": "sections[25] \"Data availability\" paragraph 2", "quote": "Data included in article/supp. material/referenced in article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified four MRDEGs as potential prognostic biomarkers for cervical cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39263148", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We identified four MRDEGs as potential prognostic biomarkers for cervical cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified four MRDEGs as potential prognostic biomarkers for cervical cancer.", "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:39263148"], "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:GSE39001"], "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:GSE39001"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39263148", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e36240", "sha256": 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