Identification of aberrantly methylated differentially expressed genes in glioblastoma multiforme and their association with patient survival.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31452706", "kind": "science-record", "revision": 7, "content_hash": "sha256:9b4ff0d5c3ffa3afd441954652ccda38cefa059407e6e2ba0cf1cc5b7af9e23a", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:00:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of aberrantly methylated differentially expressed genes in glioblastoma multiforme and their association with patient survival.", "doi": "10.3892/etm.2019.7807", "pmid": "31452706", "authors": ["Miao Zhang", "Xintong Lv", "Yuanjun Jiang", "Guang Li", "Qiao Qiao"], "journal": "Experimental and therapeutic medicine", "year": 2019, "abstract": "Glioblastoma multiforme (GBM) is the most malignant primary tumour type of the central nervous system with limited therapeutic options and poor prognosis, and its pathogenic mechanisms have remained to be fully elucidated. Aberrant DNA methylation is involved in multiple biological processes and may contribute to the occurrence and development of GBM by affecting the expression of certain genes. However, the specific molecular mechanisms remain to be fully elucidated. The present study focused on uncovering differentially expressed genes with altered methylation status in GBM and aimed to discover novel biomarkers for the diagnosis and treatment of GBM. These genes were identified by combined analysis of multiple gene expression and methylation datasets from gene expression omnibus (GSE16011, GSE50161 and GSE 50923) to increase the reliability. In addition, The Cancer Genome Atlas (TCGA) dataset for GBM was used to test the stability of the results. Overall, 251 hypomethylated upregulated genes (Hypo-UGs) and 199 hypermethylated downregulated genes (Hyper-DGs) were identified in the present study. Functional enrichment analysis revealed that the Hypo-UGs are involved in the regulation of immune- and infection-associated signalling, while the Hyper-DGs are involved in the regulation of synaptic transmission. The three hub genes for Hyper-DGs (somatostatin, neuropeptide Y and adenylate cyclase 2) and five hub genes for Hypo-UGs [interleukin-8, matrix metalloproteinase (MMP)9, cyclin-dependent kinase 1, 2'-5'-oligoadenylate synthetase 1, C-X-C motif chemokine ligand 10 and MMP2] were identified by protein-protein interaction network analysis. Among the Hypo-UGs and Hyper-DGs, overexpression of C-type lectin domain containing 5A, epithelial membrane protein 3, solute carrier family 43 member 3, STEAP3 metalloreductase, tumour necrosis factor α-induced protein 6 and apolipoprotein B mRNA editing enzyme catalytic subunit 3G was significantly associated with poor prognosis in the TCGA and GSE16011 datasets (P<0.001). In conclusion, the present study uncovered numerous novel aberrantly methylated genes and pathways associated with GBM. Methylation-based markers, including the hub genes and prognostic genes identified, may potentially serve as markers for the diagnosis of GBM and targets for its treatment.", "claims": [{"id": "claim-method", "statement": "Prognostic assessments for AMDEGs as continuous variables were performed separately for the GSE16011 dataset and the TCGA GBM validation dataset using univariate Cox proportional hazard regression (survival analysis module; Fig. 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31452706", "locator": "sections[7] \"Analysis of the effect of the AMDEGs on overall survival (OS)\" paragraph 2", "quote": "Prognostic assessments for AMDEGs as continuous variables were performed separately for the GSE16011 dataset and the TCGA GBM validation dataset using univariate Cox proportional hazard regression (survival analysis module; Fig. 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during the present study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31452706", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analysed during the present study are included in this published article."}], "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:31452706"], "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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