Prediction of circRNAs Based on the DNA Methylation-Mediated Feature Sponge Function in Breast Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32039169", "kind": "science-record", "revision": 6, "content_hash": "sha256:0a88ac230dde957a96a50987b8e685a2ebbbc95f05a392f8ab6fc2775e37269f", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T21:22:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prediction of circRNAs Based on the DNA Methylation-Mediated Feature Sponge Function in Breast Cancer.", "doi": "10.3389/fbioe.2019.00365", "pmid": "32039169", "authors": ["Yue Gu", "Ce Ci", "Xingda Zhang", "Mu Su", "Wenhua Lv", "Chuangeng Chen", "Hui Liu", "Dongwei Zhang", "Shumei Zhang", "Yan Zhang"], "journal": "Frontiers in bioengineering and biotechnology", "year": 2019, "abstract": "Several studies have found that DNA methylation is associated with transcriptional regulation and affect sponge regulation of non-coding RNAs in cancer. The integration of circRNA, miRNA, DNA methylation and gene expression data to identify sponge circRNAs is important for revealing the role of DNA methylation-mediated regulation of sponge circRNAs in cancer progression. We established a DNA methylation-mediated circRNA crosstalk network by integrating gene expression, DNA methylation and non-coding RNA data of breast cancer in TCGA. Four modules (26 candidate circRNAs) were mined. Next, 10 DNA methylation-mediated sponge circRNAs (sp_circRNAs) and five sponge driver genes (sp_driver genes) in breast cancer were identified in the CMD network using a computational process. Among the identified genes, ERBB2 was associated with six sponge circRNAs, which illustrates its better sponge regulatory function. Survival analysis showed that DNA methylations of 10 sponge circRNA host genes are potential prognostic biomarkers in the TCGA dataset (p = 0.0239) and GSE78754 dataset (p = 0.0377). In addition, the DNA methylation of two sponge circRNA host genes showed a significant negative correlation with their driver gene expressions. We developed a strategy to predict sponge circRNAs by DNA methylation mediated with playing the role of regulating breast cancer sponge driver genes.", "claims": [{"id": "claim-method", "statement": "Survival analysis was performed using Cox proportional hazards model. The clinical survival data for breast cancer were downloaded from TCGA and GEO (GSE78754).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32039169", "locator": "sections[9] \"Survival Analysis\" paragraph 2", "quote": "Survival analysis was performed using Cox proportional hazards model."}, {"asset": "source:pmid:32039169", "locator": "sections[9] \"Survival Analysis\" paragraph 2", "quote": "The clinical survival data for breast cancer were downloaded from TCGA and GEO (GSE78754)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://gdc.cancer.gov/GSE78754.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32039169", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://gdc.cancer.gov/GSE78754."}], "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:32039169"], "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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