Construction of miRNA-lncRNA-mRNA co-expression network affecting EMT-mediated cisplatin resistance in ovarian cancer.

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Epithelial-like ovarian cancer cells show decreased sensitivity to cisplatin after cisplatin treatment. Our study prospected the association between epithelial phenotype and response to cisplatin in ovarian cancer. Microarray dataset GSE47856 was acquired from the GEO database. After identifying differentially expressed genes (DEGs) between epithelial-like and mesenchymal-like cells, the module identification analysis was performed using weighted gene co-expression network analysis (WGCNA). The gene ontology (GO) and pathway analyses of the most considerable modules were performed. The protein-protein interaction network was also constructed. The hub genes were specified using Cytoscape plugins MCODE and cytoHubba, followed by the survival analysis and data validation. Finally, the co-expression of miRNA-lncRNA-TF with the hub genes was reconstructed. The co-expression network analysis suggests 20 modules relating to the Epithelial phenotype. The antiquewhite4, brown and darkmagenta modules are the most significant non-preserved modules in the Epithelial phenotype and contain the most differentially expressed genes. GO, and KEGG pathway enrichment analyses on these modules divulge that these genes were primarily enriched in the focal adhesion, DNA replication pathways and stress response processes. ROC curve and overall survival rate analysis show that the co-expression pattern of the brown module's hub genes could be a potential prognostic biomarker for ovarian cancer cisplatin resistance.", "claims": [{"id": "claim-method", "statement": "After identifying differentially expressed genes (DEGs) between epithelial‐like and mesenchymal‐like cells, the module identification analysis was performed using weighted gene co‐expression network analysis (WGCNA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35810383", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "After identifying differentially expressed genes (DEGs) between epithelial‐like and mesenchymal‐like cells, the module identification analysis was performed using weighted gene co‐expression network analysis (WGCNA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are openly available in the NCBI Gene Expression Omnibus (GEO) at (https://www.ncbi.nlm.nih.gov/geo/), reference number (GSE47856, GSE149146).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35810383", "locator": "sections[28] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are openly available in the NCBI Gene Expression Omnibus (GEO) at (https://www.ncbi.nlm.nih.gov/geo/), reference number (GSE47856, GSE149146)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ROC curve and overall survival rate analysis show that the co‐expression pattern of the brown module's hub genes could be a potential prognostic biomarker for ovarian cancer cisplatin resistance.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35810383", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "ROC curve and overall survival rate analysis show that the co‐expression pattern of the brown module's hub genes could be a potential prognostic biomarker for ovarian cancer cisplatin resistance."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ROC curve and overall survival rate analysis show that the co‐expression pattern of the brown module's hub genes could be a potential prognostic biomarker for ovarian cancer cisplatin resistance.", "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:35810383"], "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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