Identification of candidate aberrantly methylated and differentially expressed genes in Esophageal squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32546690", "kind": "science-record", "revision": 7, "content_hash": "sha256:205da147a60434641aebf33200c12903ee6193f5756ced8f9419848ec65bb089", "created_at": "2026-11-01T15:41:03Z", "updated_at": "2026-11-01T22:01:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of candidate aberrantly methylated and differentially expressed genes in Esophageal squamous cell carcinoma.", "doi": "10.1038/s41598-020-66847-4", "pmid": "32546690", "authors": ["Bao-Ai Han", "Xiu-Ping Yang", "Davood K Hosseini", "Po Zhang", "Ya Zhang", "Jin-Tao Yu", "Shan Chen", "Fan Zhang", "Tao Zhou", "Hai-Ying Sun"], "journal": "Scientific reports", "year": 2020, "abstract": "Aberrant methylated genes (DMGs) play an important role in the etiology and pathogenesis of esophageal squamous cell carcinoma (ESCC). In this study, we aimed to integrate three cohorts profile datasets to ascertain aberrant methylated-differentially expressed genes and pathways associated with ESCC by comprehensive bioinformatics analysis. We downloaded data of gene expression microarrays (GSE20347, GSE38129) and gene methylation microarrays (GSE52826) from the Gene Expression Omnibus (GEO) database. Aberrantly differentially expressed genes (DEGs) were obtained by GEO2R tool. The David database was then used to perform Gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome pathway enrichment analyses on selected genes. STRING and Cytoscape software were used to construct a protein-protein interaction (PPI) network, then the modules in the PPI networks were analyzed with MCODE and the hub genes chose from the PPI networks were verified by Oncomine and TCGA database. In total, 291 hypomethylation-high expression genes and 168 hypermethylation-low expression genes were identified at the screening step, and finally found six mostly changed hub genes including KIF14, CDK1, AURKA, LCN2, TGM1, and DSG1. Pathway analysis indicated that aberrantly methylated DEGs mainly associated with the P13K-AKT signaling, cAMP signaling and cell cycle process. After validation in multiple databases, most hub genes remained significant. Patients with high expression of AURKA were associated with shorter overall survival. To summarize, we have identified six feasible aberrant methylated-differentially expressed genes and pathways in ESCC by bioinformatics analysis, potentially providing valuable information for the molecular mechanisms of ESCC. Our data combined the analysis of gene expression profiling microarrays and gene methylation profiling microarrays, simultaneously, and in this way, it can shed a light for screening and diagnosis of ESCC in future.", "claims": [{"id": "claim-method", "statement": "We used the GEO2R online tool to analyze the raw data of microarrays and identify DMGs and DEGs between the tumor tissues and normal tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32546690", "locator": "sections[12] \"Data acquisition and processing\" paragraph 2", "quote": "We used the GEO2R online tool to analyze the raw data of microarrays and identify DMGs and DEGs between the tumor tissues and normal tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analysed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32546690", "locator": "sections[20] \"Data availability\" paragraph 2", "quote": "The datasets generated and/or analysed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32546690"], "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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