Potential prognostic biomarkers identified by DNA methylation profiling analysis for patients with lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29467875", "kind": "science-record", "revision": 5, "content_hash": "sha256:bd6720cd97db2095eca81a14238187c9b8d11aba2b810a1c8906d498c9cca998", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T21:59:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Potential prognostic biomarkers identified by DNA methylation profiling analysis for patients with lung adenocarcinoma.", "doi": "10.3892/ol.2018.7790", "pmid": "29467875", "authors": ["Liankui Han", "Gang Xu", "Chuan Xu", "Bo Liu", "Di Liu"], "journal": "Oncology letters", "year": 2018, "abstract": "Lung adenocarcinoma is frequently occurring type of lung cancer with high metastatic risk. We performed a DNA methylation profiling analysis to identify possible prognostic markers involved in lung adenocarcinoma. DNA methylation profiling data (GSE66386) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially methylated genes were identified using a limma package. GO enrichment analysis was performed to identify vital functions related to differential gene methylation, and pathway analysis was performed to assess the associations between different proteins with regard to regulation of cell function and metabolism. The screening results showed a total of 112,662 differentially methylated genes in lung adenocarcinoma patients compared with those of the normal controls. These CpGs were involved in 16,705 genes. The skeletal system development (P=9.46E-27) and embryonic organ morphogenesis (P=8.67E-24) were found to be involved in lung adenocarcinoma. The cancer (P=3.64E-07), Rap1 signaling (P=9.21E-05) and calcium signaling (P=9.21E-05) pathways constituted the important pathways associated with lung adenocarcinoma. In conclusion, methylated PTPRF, HOXD3, HOXD13 and CACNA1A are potential markers and may be utilized for the diagnosis and therapy of lung adenocarcinoma.", "claims": [{"id": "claim-method", "statement": "Consequently, the P-value was calculated by t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29467875", "locator": "sections[5] \"Identification of genes with methylation differences\" paragraph 2", "quote": "Consequently, the P-value was calculated by t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression dataset (GSE66386) was collected from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. The dataset included 183 samples, of which 164 were lung adenocarcinoma samples, and 19 were matched normal lung tissue samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29467875", "locator": "sections[4] \"Microarray data and preprocessing\" paragraph 2", "quote": "The gene expression dataset (GSE66386) was collected from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. The dataset included 183 samples, of which 164 were lung adenocarcinoma samples, and 19 were matched normal lung tissue samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the GEO microarray dataset GSE66386 and the limma package, the study identified 112,662 differentially methylated CpG regions involving 16,705 genes in lung adenocarcinoma patients compared with normal controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29467875", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "DNA methylation profiling data (GSE66386) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially methylated genes were identified using a limma package."}, {"asset": "source:pmid:29467875", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The screening results showed a total of 112,662 differentially methylated genes in lung adenocarcinoma patients compared with those of the normal controls. 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