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pmid:30226545
Prediction of candidate RNA signatures for recurrent ovarian cancer prognosis by the construction of an integrated competing endogenous RNA network.
Xin Wang · Lei Han · Ling Zhou · Li Wang · Lan-Mei Zhang
Oncology reports · 2018 doi:10.3892/or.2018.6707
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Experiment
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Complete file
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RNA‑sequencing of data from the TCGA database and GSE17260 dataset was carried out. Samples of the data were grouped according to tumor recurrence information. Following data normalization, differentially expressed genes/micro RNAs (miRNAs)/long non‑coding (lncRNAs) (DEGs/DEMs/DELs) were selected between recurrent and non‑recurrent samples. Their correlations with clinical information were analyzed to identify prognostic RNAs. A support vector machine classifier was used to find the optimal gene set with feature genes that could conclusively distinguish different samples. A protein‑protein interaction (PPI) network was established for DEGs using relevant protein databases. An integrated 'lncRNA/miRNA/mRNA' competing endogenous RNA (ceRNA) network was constructed to reveal potential regulatory relationships among different RNAs. We identified 36 feature genes (e.g. TP53 and RBPMS) for the classification of recurrent and non‑recurrent ovarian cancer samples. Prediction with this gene set had a high accuracy (91.8%). Three DELs (WT1‑AS, NBR2 and ZNF883) were highly associated with the prognosis of recurrent ovarian cancer. Predominant DEMs with their targets were hsa‑miR‑375 (target: RBPMS), hsa‑miR‑141 (target: RBPMS), and hsa‑miR‑27b (target: TP53). Highlighted interactions in the ceRNA network were 'WT1‑AS‑hsa‑miR‑375‑RBPMS' and 'WT1‑AS‑-hsa‑miR‑27b‑TP53'. TP53, RBPMS, hsa‑miR‑375, hsa‑miR‑141, hsa‑miR‑27b, and WT1‑AS may be biomarkers for recurrent ovarian cancer. The interactions of 'WT1‑AS‑hsa‑-miR‑375‑RBPMS' and 'WT1‑AS‑hsa‑miR‑27b‑TP53' may be potential regulatory mechanisms during cancer recurrence.", "claims": [{"id": "claim-method", "statement": "Fisher's exact test was used, as indicated in the following formula:", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30226545", "locator": "sections[18] \"Functional and pathway enrichment analysis of genes in the ceRNA network\" paragraph 2", "quote": "Fisher's exact test was used, as indicated in the following formula:"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30226545", "locator": "sections[36] \"Availability of data and materials\" paragraph 2", "quote": "The datasets analyzed during the current study are available from the corresponding author upon reasonable request."}], "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:30226545"], "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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["NOTUM", "mRNA", "−0.080", "0.923", "0.051", "−1.590", "0.006", "Downregulated"], ["CASC1", "mRNA", "0.116", "1.120", "0.075", "1.560", "0.006", "Upregulated"], ["CCDC65", "mRNA", "0.114", "1.120", "0.074", "1.540", "0.006", "Upregulated"], ["ALDH1A2", "mRNA", "−0.063", "0.939", "0.043", "−1.480", "0.007", "Downregulated"], ["REM1", "mRNA", "−0.109", "0.897", "0.075", "−1.450", "0.008", "Downregulated"], ["PHOSPHO1", "mRNA", "0.073", "1.080", "0.055", "1.320", "0.010", "Downregulated"], ["TBX3", "mRNA", "−0.097", "0.908", "0.073", "−1.320", "0.010", "Upregulated"], ["OXGR1", "mRNA", "0.080", "1.080", "0.062", "1.300", "0.010", "Upregulated"], ["C1orf194", "mRNA", "0.050", "1.050", "0.040", "1.230", "0.011", "Upregulated"], ["INHA", "mRNA", "0.098", "1.100", "0.082", "1.190", "0.012", "Upregulated"], ["CLIC6", "mRNA", "−0.079", "0.924", "0.067", "−1.170", "0.012", "Upregulated"], ["BNC2", "mRNA", "0.124", "1.130", "0.107", "1.160", "0.013", "Downregulated"], ["CST6", "mRNA", "−0.080", 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