An integrative analysis of DNA methylation in osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29234590", "kind": "science-record", "revision": 6, "content_hash": "sha256:6885d71d371fc9ad78534eda7a03b7c200fd83d21ee912b0da2f9e896d2d86a8", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T21:59:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An integrative analysis of DNA methylation in osteosarcoma.", "doi": "10.1016/j.jbo.2017.05.001", "pmid": "29234590", "authors": ["Jie Xu", "Deng Li", "Zhiqing Cai", "Yingbin Zhang", "Yulin Huang", "Baohua Su", "Ruofan Ma"], "journal": "Journal of bone oncology", "year": 2017, "abstract": "BACKGROUND: The study aimed to analyze aberrantly methylated genes, relevant pathways and transcription factors (TFs) in osteosarcoma (OS) development.\nMETHODS: Based on the DNA methylation microarray data GSE36002 that were downloaded from GEO database, the differentially methylated genes in promoter regions were identified between OS and normal samples. Pathway and function enrichment analyses of differentially methylated genes was performed. Subsequently, protein-protein interaction (PPI) network was constructed, followed by identification of cancer-associated differentially methylated genes and significant differentially methylated TFs.\nRESULTS: A total of 1379 hyper-methylation regions and 169 hypo-methylation regions in promoter regions were identified in OS samples compared to normal samples. The differentially hyper-methylated genes were significantly enriched in Neuroactive ligand-receptor interaction pathway, and Peroxisome proliferator activated receptor (PPAR) signaling pathway. The differentially hypo-methylated genes were significantly enriched in Toll-like receptor signaling pathway. In PPI network, signal transducers and activators of transcription (STAT3) had high degree (degree=21). MAX interactor 1, dimerization protein (MXI1), STAT3 and T-cell acute lymphocytic leukemia 1 (TAL1) were significant TFs enriched with target genes in OS samples. They were found to be cancer-associated and hyper-methylated in OS samples.\nCONCLUSION: Neuroactive ligand-receptor interaction, PPAR signaling, Toll-like receptor signaling pathways are implicated in OS. MXI1, STAT3, and TAL1 may be important TFs involved in OS development.", "claims": [{"id": "claim-method", "statement": "FDR method is also called Benjamini and Hochberg (BH) method [15], used to adjust p value.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29234590", "locator": "sections[4] \"Identification of differentially methylated genes\" paragraph 5", "quote": "FDR method is also called Benjamini and Hochberg (BH) method [15], used to adjust p value."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE36002 DNA methylation microarray data [11] were downloaded from GEO database in National Center of Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/gds/)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29234590", "locator": "sections[3] \"DNA methylation microarray data\" paragraph 2", "quote": "The GSE36002 DNA methylation microarray data [11] were downloaded from GEO database in National Center of Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/gds/)"}], "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:29234590"], "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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